Diff of the two buildlogs: -- --- b1/build.log 2021-06-19 12:02:02.794326308 +0000 +++ b2/build.log 2021-06-19 14:10:21.336309114 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 22 06:23:53 -12 2022 -I: pbuilder-time-stamp: 1658514233 +I: Current time: Sun Jun 20 02:02:07 +14 2021 +I: pbuilder-time-stamp: 1624104127 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./canu_2.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.j7JCAfbx/trustedkeys.kbx': General error -gpgv: Signature made Fri Mar 27 11:47:02 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.BBwVtLRp/trustedkeys.kbx': General error +gpgv: Signature made Sat Mar 28 13:47:02 2020 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key @@ -32,137 +32,171 @@ dpkg-source: info: applying canu_version.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/29456/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/24390/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/24390/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/24390/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='29fb0020a23146149b04bc4a37397eec' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='29456' - PS1='# ' - PS2='> ' + INVOCATION_ID=11b512bb7f754781ba3ad8ae7125f6c1 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=24390 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.3q7HEFyJTj/pbuilderrc_OwoD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3q7HEFyJTj/b1 --logfile b1/build.log canu_2.0+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.3q7HEFyJTj/pbuilderrc_slbZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3q7HEFyJTj/b2 --logfile b2/build.log --extrapackages usrmerge canu_2.0+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 21 03:46 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/29456/tmp/hooks/D02_print_environment finished + total 5780 + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 20 02:07 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 18 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/24390/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -283,7 +317,7 @@ Get: 75 http://deb.debian.org/debian bullseye/main i386 libmeryl-dev i386 0~20150903+r2013-8+b1 [68.8 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libssw-java i386 1.1-13 [23.9 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 mhap all 2.1.3+dfsg-3 [160 kB] -Fetched 94.9 MB in 2s (52.0 MB/s) +Fetched 94.9 MB in 21s (4531 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) @@ -613,135 +647,135 @@ Setting up mhap (2.1.3+dfsg-3) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:Izenpe.com.pem +Adding debian:GTS_Root_R4.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Security_Communication_Root_CA.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem -Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem -Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Secure_Global_CA.pem -Adding debian:GTS_Root_R1.pem -Adding debian:NAVER_Global_Root_Certification_Authority.pem -Adding debian:SwissSign_Gold_CA_-_G2.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:Amazon_Root_CA_2.pem -Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:EC-ACC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:GTS_Root_R4.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:XRamp_Global_CA_Root.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:COMODO_ECC_Certification_Authority.pem -Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Certigna.pem -Adding debian:AffirmTrust_Premium.pem -Adding debian:Entrust_Root_Certification_Authority_-_G4.pem -Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:emSign_Root_CA_-_G1.pem -Adding debian:TrustCor_ECA-1.pem -Adding debian:ePKI_Root_Certification_Authority.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:ACCVRAIZ1.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:emSign_ECC_Root_CA_-_G3.pem -Adding debian:DigiCert_Trusted_Root_G4.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:GlobalSign_Root_CA.pem -Adding debian:Security_Communication_RootCA2.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:UCA_Global_G2_Root.pem -Adding debian:AffirmTrust_Premium_ECC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:certSIGN_Root_CA_G2.pem -Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:SecureSign_RootCA11.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:GTS_Root_R3.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:Starfield_Class_2_CA.pem -Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:UCA_Global_G2_Root.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:TrustCor_RootCert_CA-1.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:SecureTrust_CA.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem -Adding debian:XRamp_Global_CA_Root.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:Certigna_Root_CA.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:Actalis_Authentication_Root_CA.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:GTS_Root_R2.pem -Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:USERTrust_ECC_Certification_Authority.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:Amazon_Root_CA_1.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:Izenpe.com.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:Trustwave_Global_Certification_Authority.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:UCA_Extended_Validation_Root.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:AffirmTrust_Commercial.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:Certigna_Root_CA.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem -Adding debian:Hongkong_Post_Root_CA_3.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:DigiCert_Global_Root_G2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem +Adding debian:UCA_Extended_Validation_Root.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:DST_Root_CA_X3.pem -Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:emSign_Root_CA_-_G1.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:emSign_Root_CA_-_C1.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:Go_Daddy_Class_2_CA.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:Hongkong_Post_Root_CA_3.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:Trustwave_Global_Certification_Authority.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:certSIGN_Root_CA_G2.pem +Adding debian:SecureTrust_CA.pem Adding debian:Comodo_AAA_Services_root.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:e-Szigno_Root_CA_2017.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:EC-ACC.pem +Adding debian:Certum_Trusted_Network_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:GlobalSign_Root_CA_-_R2.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:GTS_Root_R1.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem done. Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... @@ -763,9 +797,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 3s (17.9 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38520 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -789,43 +855,31 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-2.0+dfsg' dh_auto_build - cd src && make -j18 "INSTALL=install --strip-program=true" + cd src && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/canu-2.0+dfsg/src' WARNING: WARNING: g++ 10 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: -Building for 'Linux' '4.19.0-16-amd64' as 'amd64' into '/build/canu-2.0+dfsg/Linux-amd64/{bin,obj}'. +Building for 'Linux' '4.19.0-16-686-pae' as 'i686' into '/build/canu-2.0+dfsg/Linux-i686/{bin,obj}'. Using '/usr/bin/g++' version '10'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'. -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C Building release v2.0 -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C In file included from utility/system.C:46: /usr/include/i386-linux-gnu/sys/sysctl.h:21:2: warning: #warning "The header is deprecated and will be removed." [-Wcpp] 21 | #warning "The header is deprecated and will be removed." | ^~~~~~~ -utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] - 58 | #warning how to set prefix size for streaming operations? - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | read(_fd, _data, _length); @@ -834,7 +888,6 @@ utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | write(_fd, _data, _length), close(_fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C utility/files.C: In function 'void writeToFile(void*, const char*, uint64, uint64, FILE*)': utility/files.C:89:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n", @@ -957,51 +1010,6 @@ | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from utility/kmers.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from utility/kmers.H:32, - from utility/kmers-reader.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from utility/kmers.H:32, - from utility/kmers-writer-block.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from utility/kmers.H:32, - from utility/kmers-writer.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from utility/kmers.H:32, - from utility/kmers-writer-stream.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu utility/logging.C: In member function 'void logFileInstance::rotate()': utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); @@ -1054,8 +1062,54 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': +utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 311 | symlink(pathToFile, pathToLink); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': +utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 678 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 684 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=] + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C +utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] + 58 | #warning how to set prefix size for streaming operations? + | ^~~~~~~ +In file included from utility/bits.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from utility/kmers.H:32, - from utility/kmers-exact.C:26: + from utility/kmers-writer.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers.H:32, + from utility/kmers-reader.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -1072,7 +1126,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from utility/bits.C:26: +In file included from utility/kmers.H:32, + from utility/kmers-writer-block.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -1080,27 +1135,58 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=] - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': -utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 311 | symlink(pathToFile, pathToLink); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': -utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 678 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 684 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C -In file included from utility/kmers.C:26: +In file included from utility/kmers.H:32, + from utility/kmers-exact.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers.H:32, + from utility/kmers.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers.H:32, + from utility/kmers-writer-stream.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers-reader.C:26: +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers-writer-block.C:26: +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers-statistics.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1123,6 +1209,17 @@ | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -1134,6 +1231,17 @@ | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -1145,40 +1253,17 @@ | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -In file included from utility/kmers-writer-block.C:26: -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx + | ~~~^ + | | + | long unsigned int + | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -1190,6 +1275,28 @@ | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -1212,7 +1319,18 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers-reader.C:26: +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers-writer.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1268,7 +1386,19 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers-writer.C:26: +In file included from utility/kmers-writer-stream.C:26: +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1291,6 +1421,28 @@ | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -1313,6 +1465,17 @@ | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -1324,7 +1487,18 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers-writer-stream.C:26: +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers-exact.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1380,6 +1554,53 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers-writer.C: In member function 'void kmerCountFileWriter::initialize(uint32, bool)': +utility/kmers-writer.C:78:117: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 78 | fprintf(stderr, "kmerCountFileWriter()-- Creating '%s' for %u-mers, with prefixSize %u suffixSize %u numFiles %lu\n", + | ~~^ + | | + | long unsigned int + | %llu + 79 | _outName, (_prefixSize + _suffixSize) / 2, _prefixSize, _suffixSize, _numFiles); + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-writer.C: In member function 'uint32 kmerCountFileWriter::fileNumber(uint64)': +utility/kmers-writer.C:169:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles); + | ~~^ ~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +utility/kmers-writer.C:169:98: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/kmers-writer.C:170:71: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 170 | fprintf(stderr, "kmerCountFileWriter()-- prefix 0x%016lx\n", prefix); + | ~~~~~^ ~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %016llx +utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': +utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); + | ~~~~~^ ~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %016llx +utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); + | ~~~~~^ ~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %016llx utility/kmers-writer-block.C: In member function 'void kmerCountBlockWriter::mergeBatches(uint32)': utility/kmers-writer-block.C:325:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", @@ -1414,76 +1635,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': -utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); - | ~~~~~^ ~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %016llx -utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); - | ~~~~~^ ~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %016llx -utility/kmers-writer.C: In member function 'void kmerCountFileWriter::initialize(uint32, bool)': -utility/kmers-writer.C:78:117: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 78 | fprintf(stderr, "kmerCountFileWriter()-- Creating '%s' for %u-mers, with prefixSize %u suffixSize %u numFiles %lu\n", - | ~~^ - | | - | long unsigned int - | %llu - 79 | _outName, (_prefixSize + _suffixSize) / 2, _prefixSize, _suffixSize, _numFiles); - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-writer.C: In member function 'uint32 kmerCountFileWriter::fileNumber(uint64)': -utility/kmers-writer.C:169:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles); - | ~~^ ~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/kmers-writer.C:169:98: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/kmers-writer.C:170:71: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 170 | fprintf(stderr, "kmerCountFileWriter()-- prefix 0x%016lx\n", prefix); - | ~~~~~^ ~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %016llx -In file included from utility/kmers-exact.C:26: -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers-reader.C: In function 'void dumpMerylDataFile(char*)': utility/kmers-reader.C:342:29: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", @@ -1495,17 +1646,6 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~^ @@ -1516,17 +1656,6 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~~~^ @@ -1537,17 +1666,6 @@ | ~~ | | | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:68: warning: format '%lx' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~~~^ @@ -1568,62 +1686,6 @@ | ~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers-statistics.C:26: -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers-exact.C: In member function 'bool kmerCountExactLookup::configure()': utility/kmers-exact.C:178:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 178 | fprintf(stderr, " p prefixes bits gigabytes (allowed: %lu GB)\n", _maxMemory >> 33); @@ -1855,8 +1917,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': utility/kmers-writer.C:147:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 147 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); @@ -1870,8 +1930,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); @@ -1885,11 +1943,45 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/sqCache.H:30, + from stores/sqCache.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)': +stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases); + | ~~^ ~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)': +stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n", + | ~~^ + | | + | long unsigned int + | %llu + 357 | nReads, nBases, bgnID, endID); + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)': utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 257 | args[1] = "download"; @@ -1903,11 +1995,12 @@ utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 260 | args[4] = "--output"; | ^~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/falconConsensus.H:75, @@ -1930,6 +2023,14 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C +stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()': +stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] + 82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)': stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 109 | buffer->writeIFFchunk("BLOB"); @@ -1958,61 +2059,6 @@ stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 132 | buffer->closeIFFchunk("BLOB"); | ^~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C -stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] - 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from stores/sqCache.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C -stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)': -stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases); - | ~~^ ~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)': -stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n", - | ~~^ - | | - | long unsigned int - | %llu - 357 | nReads, nBases, bgnID, endID); - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -In file included from stores/sqStoreBlob.C:26: -stores/sqStore.H: In constructor 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)': -stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/sqStore.H:37, - from stores/sqStoreBlob.C:26: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()': -stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] - 82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::readInfo8(char*)': stores/sqStoreInfo.C:229:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 229 | fprintf(stderr, "sqStore_loadInfo()-- Error: Unsupported historical version %lu detected.\n", _sqVersion); @@ -2061,10 +2107,22 @@ stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 348 | B->writeIFFarray("BASE", _bases, sqRead_largest); | ^~~~~~ -stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] - 71 | #warning not failing if a valid store +stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] + 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +In file included from stores/sqStoreBlob.C:26: +stores/sqStore.H: In constructor 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)': +stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/sqStore.H:37, + from stores/sqStoreBlob.C:26: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/sqStoreBlob.C:26: stores/sqStore.H: In member function 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)': stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -2078,7 +2136,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C In file included from stores/sqStoreBlob.C:26: stores/sqStore.H: In member function 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)': stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -2093,7 +2150,41 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +stores/ovStore.C: In member function 'void ovStore::testStore(bool)': +stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n", + | ~~^ + | | + | long unsigned int + | %llu + 183 | nrds, novl, lid); + | ~~~~ + | | + | uint64 {aka long long unsigned int} +stores/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)': +stores/ovStore.C:493:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 493 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii, + | ~~~^ + | | + | long unsigned int + | %9llu +...... + 498 | _index[ii]._overlapID); + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] + 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 75 | dat.ovl.ahg5, dat.ovl.ahg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:204:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 204 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); @@ -2309,19 +2400,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc -stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] - 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 75 | dat.ovl.ahg5, dat.ovl.ahg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] +stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': +stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStore.C:59: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:289:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 289 | snprintf(path, FILENAME_MAX, "%s/info", _storePath); AS_UTL_unlink(path); @@ -2419,32 +2510,188 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C -stores/ovStore.C: In member function 'void ovStore::testStore(bool)': -stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n", - | ~~^ - | | - | long unsigned int - | %llu - 183 | nrds, novl, lid); - | ~~~~ - | | - | uint64 {aka long long unsigned int} -stores/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)': -stores/ovStore.C:493:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 493 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii, - | ~~~^ - | | - | long unsigned int - | %9llu -...... - 498 | _index[ii]._overlapID); - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc +stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] + 71 | #warning not failing if a valid store + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc +stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': +stores/ovStoreWriter.C:228:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); + | ^~~~~~~ +stores/ovStoreWriter.C:228:34: note: directive argument in the range [0, 536870910] + 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4129 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); + | ^~~~~~~ +stores/ovStoreWriter.C:237:34: note: directive argument in the range [0, 536870910] + 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': +stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': +stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': +stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': +stores/ovStoreWriter.C:486:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': +stores/ovStoreWriter.C:505:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 505 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:506:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 506 | snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': +stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:540:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 540 | snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:557:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 557 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:561:39: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 561 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:565:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 565 | snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStore.C:44: @@ -2455,32 +2702,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': -stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'int' [-Wformat=] - 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | int -stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'int' [-Wformat=] -stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] -stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] -stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': -stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStore.C:59: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, - from stores/tgTig.C:34: + from stores/tgTigSizeAnalysis.H:41, + from stores/tgTigSizeAnalysis.C:42: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -2489,8 +2713,7 @@ | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, - from stores/tgTigSizeAnalysis.H:41, - from stores/tgTigSizeAnalysis.C:42: + from stores/tgTig.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -2498,9 +2721,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgTigMultiAlignDisplay.C:42: @@ -2511,6 +2731,33 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': +stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'int' [-Wformat=] + 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | int +stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'int' [-Wformat=] +stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] +stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] +stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': +stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); + | ^~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); + | ^~~~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 143 | printSummary(out, "lenUnassembled", lenUnassembled); + | ^~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 144 | printSummary(out, "lenBubble", lenBubble); + | ^~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 145 | printSummary(out, "lenContig", lenContig); + | ^~~~~~~~~~~ stores/tgTig.C: In member function 'void tgTig::dumpLayout(FILE*, bool)': stores/tgTig.C:547:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 547 | fprintf(stderr, "ERROR: _bases length %ld\n", strlen(_bases)); @@ -2518,6 +2765,14 @@ | | | | long int size_t {aka unsigned int} | %d +stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': +stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': +stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:191:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); @@ -2561,30 +2816,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': -stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); - | ^~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); - | ^~~~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 143 | printSummary(out, "lenUnassembled", lenUnassembled); - | ^~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 144 | printSummary(out, "lenBubble", lenBubble); - | ^~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 145 | printSummary(out, "lenContig", lenContig); - | ^~~~~~~~~~~ -stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': -stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': -stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)': stores/tgStore.C:594:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); @@ -2600,37 +2831,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': -stores/ovStoreWriter.C:228:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); - | ^~~~~~~ -stores/ovStoreWriter.C:228:34: note: directive argument in the range [0, 536870910] - 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4129 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); - | ^~~~~~~ -stores/ovStoreWriter.C:237:34: note: directive argument in the range [0, 536870910] - 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:626:40: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); @@ -2671,33 +2871,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': -stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': -stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': +stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ +stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 690 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': stores/tgStore.C:695:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); @@ -2713,13 +2893,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': -stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 565 | fgets(LINE, LINEmax, F); LINEnum++; - | ~~~~~^~~~~~~~~~~~~~~~~~ -stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 690 | fgets(LINE, LINEmax, F); LINEnum++; - | ~~~~~^~~~~~~~~~~~~~~~~~ In file included from stores/ovStore.H:43, from stores/ovStoreFile.C:47: stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': @@ -2735,21 +2908,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': -stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, @@ -2761,117 +2928,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': -stores/ovStoreWriter.C:486:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': -stores/ovStoreWriter.C:505:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 505 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:506:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 506 | snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': -stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:540:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 540 | snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:557:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 557 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:561:39: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 561 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:565:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 565 | snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -2884,16 +2940,15 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C -gfa/gfa.C: In member function 'void gfaSequence::load(char*)': -gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 123 | findGFAtokenI(_features, "LN:i:", _length); - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C In file included from utgcns/libNDalign/NDalign.C:36: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -2923,8 +2978,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::processHits()': utgcns/libNDalign/NDalign.C:660:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 660 | display("NDalign::processHits()-- ", false); @@ -2941,27 +2994,19 @@ utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 838 | display("NDalign::realignBackward()-- ", displayAlign); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C -stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] - 675 | #warning replace this with genericStatistics - | ^~~~~~~ -stores/ovStoreBucketizer.C: In function 'int main(int, char**)': -stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 139 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreBucketizer.C:142:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 142 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreBucketizer.C:145:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 145 | err.push_back("ERROR: No store configuration (-C) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C +gfa/gfa.C: In member function 'void gfaSequence::load(char*)': +gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 123 | findGFAtokenI(_features, "LN:i:", _length); + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C stores/ovStoreConfig.C: In member function 'void ovStoreConfig::assignReadsToSlices(sqStore*, uint64, uint64)': stores/ovStoreConfig.C:288:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 288 | fprintf(stderr, "ERROR: expected %u slices, generated %u instead. %lu overlaps per slice allowed.\n", @@ -2973,13 +3018,6 @@ | ~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -stores/ovStoreBuild.C: In function 'int main(int, char**)': -stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 125 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 128 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C: In function 'int main(int, char**)': stores/ovStoreConfig.C:372:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 372 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); @@ -2996,10 +3034,30 @@ stores/ovStoreConfig.C:385:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 385 | err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreBuild.C: In function 'int main(int, char**)': +stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 125 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 128 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreBucketizer.C: In function 'int main(int, char**)': +stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 139 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreBucketizer.C:142:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 142 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreBucketizer.C:145:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 145 | err.push_back("ERROR: No store configuration (-C) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreIndexer.C: In function 'int main(int, char**)': stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 80 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreIndexer.C:83:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 83 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3023,6 +3081,23 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +stores/ovStoreDump.C: In function 'int main(int, char**)': +stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C In file included from stores/ovStoreStats.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -3052,35 +3127,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C -stores/ovStoreDump.C: In function 'int main(int, char**)': -stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/tgStoreCompress.C:45: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': -stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 459 | AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName); - | ^~~~~~~ -stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); - | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); @@ -3117,6 +3165,71 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} +stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] + 675 | #warning replace this with genericStatistics + | ^~~~~~~ +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgStoreCompress.C:45: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from stores/tgTig.H:36, + from stores/tgTigSizeAnalysis.H:41, + from stores/tgTigSizeAnalysis.C:42: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgStoreDump.C:55: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': +stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); + | ^~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); + | ^~~~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 143 | printSummary(out, "lenUnassembled", lenUnassembled); + | ^~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 144 | printSummary(out, "lenBubble", lenBubble); + | ^~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 145 | printSummary(out, "lenContig", lenContig); + | ^~~~~~~~~~~ +stores/tgStoreDump.C: In function 'int main(int, char**)': +stores/tgStoreDump.C:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1166 | err.push_back("No sequence store (-S option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1169 | err.push_back("No tig store (-T option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1172 | err.push_back("No tig store version (-T option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1175 | err.push_back("-coverage needs and output prefix (-o option).\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1178 | err.push_back("No DUMP TYPE supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreDumpMetaData.C: In function 'void dumpReads(sqStore*, uint32, uint32, sqRead_which)': stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n", @@ -3136,7 +3249,7 @@ | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from stores/tgStoreDump.C:55: + from stores/tgStoreLoad.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -3144,7 +3257,23 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C +stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': +stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 459 | AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName); + | ^~~~~~~ +stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); + | ^~~~~~~ +stores/tgStoreLoad.C: In function 'int main(int, char**)': +stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 194 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 196 | err.push_back("ERROR: no tig store (-T) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:137:36: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 137 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); @@ -3191,72 +3320,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C -stores/tgStoreDump.C: In function 'int main(int, char**)': -stores/tgStoreDump.C:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1166 | err.push_back("No sequence store (-S option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1169 | err.push_back("No tig store (-T option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1172 | err.push_back("No tig store version (-T option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1175 | err.push_back("-coverage needs and output prefix (-o option).\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1178 | err.push_back("No DUMP TYPE supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C -In file included from stores/tgTig.H:36, - from stores/tgTigSizeAnalysis.H:41, - from stores/tgTigSizeAnalysis.C:42: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/tgStoreLoad.C:33: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C -stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': -stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); - | ^~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); - | ^~~~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 143 | printSummary(out, "lenUnassembled", lenUnassembled); - | ^~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 144 | printSummary(out, "lenBubble", lenBubble); - | ^~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 145 | printSummary(out, "lenContig", lenContig); - | ^~~~~~~~~~~ -stores/tgStoreLoad.C: In function 'int main(int, char**)': -stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 194 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 196 | err.push_back("ERROR: no tig store (-T) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadErates.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadErates.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStoreFilter.C:45: @@ -3267,7 +3337,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgTigDisplay.C:33: @@ -3278,7 +3348,17 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C +stores/loadErates.C: In function 'int main(int, char**)': +stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 214 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 217 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/loadCorrectedReads.C:29: @@ -3289,14 +3369,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C -meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] - 261 | #warning HARD CODED NUMBER OF FILES! - | ^~~~~~~ -stores/loadTrimmedReads.C: In function 'int main(int, char**)': -stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': +stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); + | ^~~~~~~~~~~~~~~~ stores/loadCorrectedReads.C: In function 'int main(int, char**)': stores/loadCorrectedReads.C:76:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 76 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); @@ -3312,32 +3388,32 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C -stores/loadErates.C: In function 'int main(int, char**)': -stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 214 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 217 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/meryl.C:46: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/loadErates.C:43: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/loadErates.C:43: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadTrimmedReads.C: In function 'int main(int, char**)': +stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -3349,15 +3425,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] - 98 | #warning "need to decide whic direction we're going?" - | ^~~~~~~ -meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] - 116 | #warning "rounding issues in word-frequency!" - | ^~~~~~~ In file included from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/meryl.C:46: + from meryl/merylCountArray.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -3413,19 +3483,11 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylInput.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] + 261 | #warning HARD CODED NUMBER OF FILES! + | ^~~~~~~ In file included from meryl/meryl.H:51, - from meryl/meryl.C:46: + from meryl/merylCountArray.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -3442,9 +3504,41 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ +In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, + from meryl/meryl.H:49, + from meryl/merylCountArray.C:26: +meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': +meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]' +meryl/merylCountArray.C:396:16: required from here +utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] + 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' + 41 | _s2 = suffix & uint64MASK(32); + | ^~~~~~~~~~ +meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]': +meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]' +meryl/merylCountArray.C:397:16: required from here +utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] + 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' + 41 | _s2 = suffix & uint64MASK(32); + | ^~~~~~~~~~ +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/meryl.C:46: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: + from meryl/meryl.C:46: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -3501,7 +3595,7 @@ | | | uint64 {aka long long unsigned int} In file included from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: + from meryl/meryl.C:46: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -3518,23 +3612,59 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-count.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +meryl/meryl.C: In function 'int main(int, char**)': +meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from meryl/meryl.H:49, + from meryl/meryl.C:46: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString); + | ^~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from meryl/meryl.H:49, + from meryl/meryl.C:46: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString); + | ^~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from meryl/meryl.H:49, + from meryl/meryl.C:46: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=] + 594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString); + | ^~ ~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from meryl/meryl.H:49, + from meryl/meryl.C:46: +/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp-histogram.C:26: + from meryl/merylInput.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -3600,17 +3730,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-countSimple.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu In file included from meryl/meryl.H:51, from meryl/merylInput.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': @@ -3629,189 +3748,21 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C -In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, - from meryl/meryl.H:49, - from meryl/merylCountArray.C:26: -meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': -meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]' -meryl/merylCountArray.C:396:16: required from here -utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] - 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' - 41 | _s2 = suffix & uint64MASK(32); - | ^~~~~~~~~~ -meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]': -meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]' -meryl/merylCountArray.C:397:16: required from here -utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] - 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' - 41 | _s2 = suffix & uint64MASK(32); - | ^~~~~~~~~~ -In file included from meryl/merylInput.H:30, +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp-count.C:26: -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp-histogram.C:26: -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence.C -In file included from meryl/meryl.H:51, from meryl/merylOp-count.C:26: -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ^ -meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 52 | if (_stream) return("meryl-database"); - | ^ -meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | if (_sequence) return("sequence-file"); - | ^ -meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | if (_store) return("canu-seqStore"); - | ^ -meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 58 | return("invalid-input"); - | ^ -stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': -stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/loadErates.C:43: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/loadErates.C:43: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-countSimple.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -3868,36 +3819,7 @@ | | | uint64 {aka long long unsigned int} In file included from meryl/meryl.H:51, - from meryl/merylOp-histogram.C:26: -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ^ -meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 52 | if (_stream) return("meryl-database"); - | ^ -meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | if (_sequence) return("sequence-file"); - | ^ -meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | if (_store) return("canu-seqStore"); - | ^ -meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 58 | return("invalid-input"); - | ^ -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-nextMer.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from meryl/meryl.H:51, - from meryl/merylOp-countSimple.C:26: + from meryl/merylOp-count.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4041,6 +3963,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C meryl/merylOp-count.C: In member function 'void merylOperation::configureCounting(uint64, bool&, uint32&, uint64&, uint32&, uint64&)': meryl/merylOp-count.C:385:19: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 385 | fprintf(stderr, "Counting %lu (estimated)%s %s%s%s " F_U32 "-mers from " F_SIZE_T " input file%s:\n", @@ -4061,42 +3984,12 @@ | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -meryl/merylOp-countSimple.C: In member function 'void merylOperation::countSimple()': -meryl/merylOp-countSimple.C:107:76: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 107 | fprintf(stderr, "Increasing to %u-bit storage (for kmer 0x%016lx).\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 108 | lowBitsSize + hib + 1, kidx); - | ~~~~ - | | - | uint64 {aka long long unsigned int} -meryl/merylOp-countSimple.C:150:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 150 | fprintf(stderr, " nPrefix %lu\n", nPrefix); - | ~~^ ~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -meryl/merylOp-countSimple.C:151:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 151 | fprintf(stderr, " nSuffix %lu\n", nSuffix); - | ~~^ ~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -meryl/merylOp-countSimple.C:152:38: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 152 | fprintf(stderr, " sMask 0x%016lx\n", sMask); - | ~~~~~^ ~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %016llx +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp.C:26: + from meryl/merylOp-countSimple.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4106,7 +3999,7 @@ | %llu In file included from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp-nextMer.C:26: + from meryl/merylOp-countSimple.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4163,7 +4056,7 @@ | | | uint64 {aka long long unsigned int} In file included from meryl/meryl.H:51, - from meryl/merylOp-nextMer.C:26: + from meryl/merylOp-countSimple.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4180,45 +4073,52 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()': -meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold); - | ~~^ ~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold); - | ~~^ ~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()': -meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", - | ~~^ - | | - | long unsigned int - | %llu - 613 | _kmer.toString(str), _actCount[0], _actCount[1]); - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", - | ~~^ - | | - | long unsigned int - | %llu - 613 | _kmer.toString(str), _actCount[0], _actCount[1]); - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} +meryl/merylOp-countSimple.C: In member function 'void merylOperation::countSimple()': +meryl/merylOp-countSimple.C:107:76: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 107 | fprintf(stderr, "Increasing to %u-bit storage (for kmer 0x%016lx).\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 108 | lowBitsSize + hib + 1, kidx); + | ~~~~ + | | + | uint64 {aka long long unsigned int} +meryl/merylOp-countSimple.C:150:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 150 | fprintf(stderr, " nPrefix %lu\n", nPrefix); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +meryl/merylOp-countSimple.C:151:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 151 | fprintf(stderr, " nSuffix %lu\n", nSuffix); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +meryl/merylOp-countSimple.C:152:38: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 152 | fprintf(stderr, " sMask 0x%016lx\n", sMask); + | ~~~~~^ ~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %016llx +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp-histogram.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp.C:26: + from meryl/merylOp-histogram.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4274,9 +4174,8 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C In file included from meryl/meryl.H:51, - from meryl/merylOp.C:26: + from meryl/merylOp-histogram.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4293,20 +4192,18 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C -In file included from utility/kmers.H:32, - from meryl/meryl-import.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C +meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] + 98 | #warning "need to decide whic direction we're going?" + | ^~~~~~~ +meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] + 116 | #warning "rounding issues in word-frequency!" + | ^~~~~~~ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: + from meryl/merylOp.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4315,7 +4212,9 @@ | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from utility/kmers.H:32, - from meryl/meryl-lookup.C:28: + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp-nextMer.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4323,8 +4222,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C -In file included from meryl/meryl-import.C:26: +In file included from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp-nextMer.C:26: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4347,6 +4247,20 @@ | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +In file included from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp.C:26: +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ @@ -4380,21 +4294,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C -In file included from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ @@ -4439,10 +4338,14 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C In file included from meryl/meryl.H:51, - from meryl/merylCountArray.H:29, - from meryl/meryl-import.C:31: + from meryl/merylOp.C:26: +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ^ +In file included from meryl/meryl.H:51, + from meryl/merylOp-nextMer.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4450,17 +4353,131 @@ meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ^ +meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 52 | if (_stream) return("meryl-database"); + | ^ +meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | if (_sequence) return("sequence-file"); + | ^ meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ^ meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ^ +meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | if (_store) return("canu-seqStore"); + | ^ +meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 58 | return("invalid-input"); + | ^ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ +meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()': +meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold); + | ~~^ ~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold); + | ~~^ ~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()': +meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", + | ~~^ + | | + | long unsigned int + | %llu + 613 | _kmer.toString(str), _actCount[0], _actCount[1]); + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", + | ~~^ + | | + | long unsigned int + | %llu + 613 | _kmer.toString(str), _actCount[0], _actCount[1]); + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers.H:32, + from meryl/meryl-import.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from meryl/meryl-import.C:26: +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} In file included from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: + from meryl/merylCountArray.H:29, + from meryl/meryl-import.C:31: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4477,6 +4494,50 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ +meryl/meryl-import.C: In function 'int main(int, char**)': +meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 92 | err.push_back("No input kmer file (-kmers) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 94 | err.push_back("No output database name (-output) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 96 | err.push_back("No kmer size (-k) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers); + | ~~^ ~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C +sequence/sequence.C: In function 'int main(int, char**)': +sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 418 | err.push_back("ERROR: No input sequence files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 422 | err.push_back("ERROR: No input sequence files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 432 | err.push_back("ERROR: No input sequence files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from utility/kmers.H:32, + from meryl/meryl-lookup.C:28: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from meryl/meryl-lookup.C:28: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -4533,7 +4594,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C meryl/meryl-lookup.C: In function 'void dumpExistence(dnaSeqFile*, compressedFileWriter*, std::vector&, std::vector&)': meryl/meryl-lookup.C:83:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 83 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\n", @@ -4598,10 +4658,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -sequence/sequence.C: In function 'int main(int, char**)': -sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl-lookup.C: In function 'void filter(dnaSeqFile*, dnaSeqFile*, compressedFileWriter*, compressedFileWriter*, std::vector&, bool)': meryl/meryl-lookup.C:204:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads); @@ -4615,34 +4671,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 418 | err.push_back("ERROR: No input sequence files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 422 | err.push_back("ERROR: No input sequence files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 432 | err.push_back("ERROR: No input sequence files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-import.C: In function 'int main(int, char**)': -meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 92 | err.push_back("No input kmer file (-kmers) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 94 | err.push_back("No output database name (-output) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 96 | err.push_back("No kmer size (-k) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers); - | ~~^ ~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu meryl/meryl-lookup.C: In function 'int main(int, char**)': meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 285 | err.push_back("No input sequences (-sequence) supplied.\n"); @@ -4653,6 +4681,95 @@ meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 289 | err.push_back("No report-type (-existence, etc) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylCountArray.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylCountArray.C:26: +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +In file included from meryl/meryl.H:51, + from meryl/merylCountArray.C:26: +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ^ +meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 52 | if (_stream) return("meryl-database"); + | ^ +meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | if (_sequence) return("sequence-file"); + | ^ +meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | if (_store) return("canu-seqStore"); + | ^ +meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 58 | return("invalid-input"); + | ^ In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, from meryl/meryl.H:49, from meryl/merylCountArray.C:26: @@ -4674,65 +4791,26 @@ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C -meryl/meryl.C: In function 'int main(int, char**)': -meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from meryl/meryl.H:49, - from meryl/meryl.C:46: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString); - | ^~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from meryl/meryl.H:49, - from meryl/meryl.C:46: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString); - | ^~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from meryl/meryl.H:49, - from meryl/meryl.C:46: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=] - 594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString); - | ^~ ~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from meryl/meryl.H:49, - from meryl/meryl.C:46: -/usr/include/i386-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)': sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 92 | ">random%08 " F_U64P "\n", nSeqs); | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C sequence/sequence-mutate.C: In function 'void doMutate(std::vector&, mutateParameters&)': sequence/sequence-mutate.C:160:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 160 | AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name()); | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C +In file included from sequence/sequence-shiftregister.C:31: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu sequence/sequence-sample.C: In function 'void doSample_paired(std::vector&, sampleParameters&)': sequence/sequence-sample.C:272:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 272 | AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); @@ -4744,14 +4822,6 @@ sequence/sequence-sample.C:417:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 417 | AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); | ^~~~~~~ -In file included from sequence/sequence-shiftregister.C:31: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu In file included from sequence/sequence-shiftregister-emit-fast.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -4805,7 +4875,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C In file included from sequence/sequence-shiftregister-search-fast.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -4814,6 +4886,14 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +In file included from sequence/sequence-shiftregister-search-slow.C:29: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu sequence/sequence-shiftregister-search-fast.C: In function 'void searchShiftRegisterFast(shiftRegisterParameters&)': sequence/sequence-shiftregister-search-fast.C:47:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 47 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr)); @@ -4853,47 +4933,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo -sequence/sequence-shiftregister-search-fast.C:131:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", - | ~~~~^ - | | - | long unsigned int - | %14llu - 132 | cyclen, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -sequence/sequence-shiftregister-search-fast.C:131:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", - | ~~~~^ - | | - | long unsigned int - | %14llu - 132 | cyclen, - 133 | cycmax, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -sequence/sequence-shiftregister-search-fast.C:131:59: warning: format '%lo' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", - | ~~~~^ - | | - | long unsigned int - | %0*llo -...... - 136 | expandTo3(sv)); - | ~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C -In file included from sequence/sequence-shiftregister-search-slow.C:29: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu sequence/sequence-shiftregister-search-slow.C: In function 'void searchShiftRegisterSlow(shiftRegisterParameters&)': sequence/sequence-shiftregister-search-slow.C:154:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 154 | fprintf(stderr, " cyclen %lu\n", cyclen); @@ -4930,17 +4969,40 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C -sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': -sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 44 | char *path = findSharedFile("share/sequence", distribName); - | ^~~~~~~~~~~~~~~~ +sequence/sequence-shiftregister-search-fast.C:131:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", + | ~~~~^ + | | + | long unsigned int + | %14llu + 132 | cyclen, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +sequence/sequence-shiftregister-search-fast.C:131:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", + | ~~~~^ + | | + | long unsigned int + | %14llu + 132 | cyclen, + 133 | cycmax, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +sequence/sequence-shiftregister-search-fast.C:131:59: warning: format '%lo' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", + | ~~~~^ + | | + | long unsigned int + | %0*llo +...... + 136 | expandTo3(sv)); + | ~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); @@ -4961,7 +5023,6 @@ | | | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! @@ -4978,7 +5039,10 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C +sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': +sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 44 | char *path = findSharedFile("share/sequence", distribName); + | ^~~~~~~~~~~~~~~~ sequence/sequence-simulate.C: In function 'void doSimulate_loadSequences(simulateParameters&, std::vector&, uint64&)': sequence/sequence-simulate.C:89:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 89 | fprintf(stderr, "Loaded %lu sequences.\n", seqs.size()); @@ -5008,12 +5072,13 @@ | ~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore-Build_Hash_Index.C:67: + from overlapInCore/overlapInCore.C:51: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5021,14 +5086,11 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp] - 479 | #warning do we need to check for contained too? - | ^~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore.C:51: + from overlapInCore/overlapInCore-Build_Hash_Index.C:67: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5056,19 +5118,7 @@ from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore-Process_Overlaps.C:71: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: + from overlapInCore/overlapInCore-Output.C:67: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5080,7 +5130,7 @@ from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore-Output.C:67: + from overlapInCore/overlapInCore-Process_Overlaps.C:71: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5107,8 +5157,25 @@ overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 447 | renameToFinal(outputPrefix, "ovlopt"); | ^~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/sqCache.H:30, + from overlapInCore/overlapInCore.H:66, + from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C overlapInCore/overlapImport.C: In function 'int main(int, char**)': overlapInCore/overlapImport.C:158:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 158 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); @@ -5122,6 +5189,54 @@ overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C +overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': +overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | fgets(line, lineMax, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +mhap/mhapConvert.C: In function 'int main(int, char**)': +mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] + 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~ + | | + | int +mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] +mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] +mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] +minimap/mmapConvert.C: In function 'int main(int, char**)': +minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] + 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~ + | | + | int +minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] +minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] +minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from wtdbg/wtdbgConvert.C:33: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C +overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp] + 479 | #warning do we need to check for contained too? + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, @@ -5170,58 +5285,8 @@ overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 587 | aRead, abgn, aend, alen, "Ab3", aID, | ^~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C -overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': -overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | fgets(line, lineMax, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from wtdbg/wtdbgConvert.C:33: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C -mhap/mhapConvert.C: In function 'int main(int, char**)': -mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] - 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~ - | | - | int -mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] -mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] -mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] -minimap/mmapConvert.C: In function 'int main(int, char**)': -minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] - 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~ - | | - | int -minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] -minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] -minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, @@ -5233,17 +5298,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from correction/filterCorrectionLayouts.C:29: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/generateCorrectionLayouts.C:37: @@ -5302,7 +5356,8 @@ | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, @@ -5314,7 +5369,41 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C +overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)': +overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 480 | readsIn .generatePlots(outputPrefix, "inputReads", 250); + | ^~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); + | ^~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250); + | ^~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); + | ^~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); + | ^~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250); + | ^~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250); + | ^~~~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 503 | trim5.generatePlots(outputPrefix, "trim5", 25); + | ^~~~~~~ +overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 504 | trim3.generatePlots(outputPrefix, "trim3", 25); + | ^~~~~~~ +In file included from overlapBasedTrimming/trimReads.C:31: +overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': +overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 74 | system(N); + | ~~~~~~^~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C In file included from utility/kmers.H:32, from haplotyping/splitHaplotype.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -5324,48 +5413,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C -In file included from correction/errorEstimate.C:34: -utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': -utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~~~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); - | ~~^ ~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from correction/falconsense.C:32: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C In file included from haplotyping/splitHaplotype.C:34: utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -5422,39 +5469,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)': -overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 480 | readsIn .generatePlots(outputPrefix, "inputReads", 250); - | ^~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); - | ^~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250); - | ^~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); - | ^~~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); - | ^~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250); - | ^~~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250); - | ^~~~~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 503 | trim5.generatePlots(outputPrefix, "trim5", 25); - | ^~~~~~~ -overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 504 | trim3.generatePlots(outputPrefix, "trim3", 25); - | ^~~~~~~ -In file included from overlapBasedTrimming/trimReads.C:31: -overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': -overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 74 | system(N); - | ~~~~~~^~~ haplotyping/splitHaplotype.C: In member function 'void hapData::initializeKmerTable(uint32)': haplotyping/splitHaplotype.C:443:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 443 | fprintf(stderr, "-- loaded %lu kmers.\n", nKmers); @@ -5495,7 +5509,56 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %12llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from correction/filterCorrectionLayouts.C:29: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from correction/errorEstimate.C:34: +utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': +utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~~~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/sqCache.H:30, + from correction/falconsense.C:32: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu correction/falconsense.C: In function 'void generateFalconConsensus(falconConsensus*, tgTig*, sqCache*, std::map&, bool, uint32)': correction/falconsense.C:207:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 207 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem); @@ -5523,23 +5586,23 @@ correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fgets(L, 1024, R)) { | ~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)': overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 77 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5598,9 +5661,11 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5612,16 +5677,14 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C -overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)': -overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID); - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C overlapErrorAdjustment/findErrors-Dump.C: In function 'int main(int, char**)': overlapErrorAdjustment/findErrors-Dump.C:66:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 66 | char *typeName[13] = { "IDENT", @@ -5659,18 +5722,12 @@ overlapErrorAdjustment/findErrors-Dump.C:77:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 77 | "EXTENSION", | ^~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C -bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] - 486 | #warning deviationGraph hard coded - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C +overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)': +overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID); + | ^~~~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/bogart.C:46: @@ -5702,6 +5759,42 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +bogart/bogart.C: In function 'int main(int, char**)': +bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 736 | writeTigsToStore(contigs, prefix, "ctg", true); + | ^~~~~ +bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 756 | writeTigsToStore(unitigs, prefix, "utg", true); + | ^~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C +In file included from bogart/AS_BAT_Unitig.H:49, + from bogart/AS_BAT_BestOverlapGraph.C:46: +utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': +utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_AssemblyGraph.C:28: @@ -5719,29 +5812,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); - | ~~^ ~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_BestOverlapGraph.C:46: -utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': -utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ @@ -5756,6 +5826,13 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ @@ -5763,31 +5840,21 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -bogart/bogart.C: In function 'int main(int, char**)': -bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 736 | writeTigsToStore(contigs, prefix, "ctg", true); - | ^~~~~ -bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 756 | writeTigsToStore(unitigs, prefix, "utg", true); - | ^~~~~ +utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C +bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] + 486 | #warning deviationGraph hard coded + | ^~~~~~~ In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_CreateUnitigs.C:29: + from bogart/AS_BAT_DetectSpurs.C:31: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5817,7 +5884,8 @@ | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_DetectSpurs.C:31: + from bogart/AS_BAT_AssemblyGraph.H:32, + from bogart/AS_BAT_CreateUnitigs.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5846,6 +5914,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': bogart/AS_BAT_Logging.C:91:37: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); @@ -5862,13 +5932,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_DropDeadEnds.C:29: + from bogart/AS_BAT_Instrumentation.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5897,9 +5962,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_Instrumentation.C:43: + from bogart/AS_BAT_AssemblyGraph.H:32, + from bogart/AS_BAT_MarkRepeatReads.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5928,14 +5993,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C -bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)': -bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false); - | ^~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_MarkRepeatReads.C:29: + from bogart/AS_BAT_DropDeadEnds.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5965,7 +6025,7 @@ | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_OptimizePositions.C:44: + from bogart/AS_BAT_MergeOrphans.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5994,7 +6054,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C +bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)': +bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false); + | ^~~~~ bogart/AS_BAT_MarkRepeatReads.C: In function 'uint32 splitTig(TigVector&, Unitig*, std::vector&, Unitig**, int32*, uint32*, uint32*, bool)': bogart/AS_BAT_MarkRepeatReads.C:170:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 170 | fprintf(stderr, "Failed to place read %u at %d-%d with %lu BPs:\n", frg.ident, frgbgn, frgend, BP.size()); @@ -6002,8 +6065,36 @@ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u +bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': +bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_MergeOrphans.C:35: + from bogart/AS_BAT_OptimizePositions.C:44: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6032,30 +6123,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': -bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int -bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Outputs.C:47: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6086,8 +6153,20 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from bogart/AS_BAT_Outputs.C:51: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_OverlapCache.C:49: + from bogart/AS_BAT_PlaceContains.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6117,7 +6196,7 @@ | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_PlaceContains.C:43: + from bogart/AS_BAT_PlaceReadUsingOverlaps.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6146,19 +6225,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from bogart/AS_BAT_Outputs.C:51: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_PlaceReadUsingOverlaps.C:43: + from bogart/AS_BAT_OverlapCache.C:49: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6187,8 +6255,11 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_PromoteToSingleton.C:40: + from bogart/AS_BAT_PopulateUnitig.C:42: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6218,7 +6289,7 @@ | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_PopulateUnitig.C:42: + from bogart/AS_BAT_PromoteToSingleton.C:40: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6247,11 +6318,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SetParentAndHang.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6282,7 +6348,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SplitDiscontinuous.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6313,9 +6378,13 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_TigGraph.C:28: + from bogart/AS_BAT_TigVector.C:28: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6344,9 +6413,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_TigVector.C:28: + from bogart/AS_BAT_AssemblyGraph.H:32, + from bogart/AS_BAT_TigGraph.C:28: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6375,7 +6444,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C +cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-i686/bin/canu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig.C:39: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6406,8 +6475,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_Unitig_AddRead.C:43: + from bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6437,7 +6507,7 @@ | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C:43: + from bogart/AS_BAT_Unitig_AddRead.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6466,43 +6536,39 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C -cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-amd64/bin/canu -chmod +x /build/canu-2.0+dfsg/Linux-amd64/bin/canu -cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-amd64/bin/canu-time -chmod +x /build/canu-2.0+dfsg/Linux-amd64/bin/canu-time -echo > /build/canu-2.0+dfsg/Linux-amd64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." -chmod -x /build/canu-2.0+dfsg/Linux-amd64/bin/canu.defaults -cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-amd64/share/sequence/ultra-long-nanopore -cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-amd64/share/sequence/pacbio -cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-amd64/share/sequence/pacbio-hifi -cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C +chmod +x /build/canu-2.0+dfsg/Linux-i686/bin/canu +cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-i686/bin/canu-time +chmod +x /build/canu-2.0+dfsg/Linux-i686/bin/canu-time +echo > /build/canu-2.0+dfsg/Linux-i686/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." +chmod -x /build/canu-2.0+dfsg/Linux-i686/bin/canu.defaults +cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-i686/share/sequence/ultra-long-nanopore +cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-i686/share/sequence/pacbio +cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-i686/share/sequence/pacbio-hifi +cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/utgcns.C:46: @@ -6513,6 +6579,17 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from utgcns/stashContains.H:35, + from utgcns/stashContains.C:30: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu utgcns/utgcns.C: In function 'uint32 createPartitions_greedilyPartition(cnsParameters&, tigInfo*, uint32)': utgcns/utgcns.C:294:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n", @@ -6613,17 +6690,6 @@ utgcns/utgcns.C:890:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 890 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from utgcns/stashContains.H:35, - from utgcns/stashContains.C:30: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu bogus/bogusUtil.C: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': bogus/bogusUtil.C:125:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets(inLine, 1024, inFile); // (file paths) @@ -6687,87 +6753,10 @@ gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0"); | ^~~~~~~~~~~~~ -ar rv /build/canu-2.0+dfsg/Linux-amd64/lib/libcanu.a /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -ar: creating /build/canu-2.0+dfsg/Linux-amd64/lib/libcanu.a -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignmentgfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': +gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | system(Pfile); | ~~~~~~^~~~~~~ -.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] 140 | sprintf(Pname, "plot-%s-%s", Aname, Bname); | ^~ ~~~~~ @@ -6801,45 +6790,124 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/meryl-import.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-summarize.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -lcanu +ar rv /build/canu-2.0+dfsg/Linux-i686/lib/libcanu.a /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTig.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/gfa.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/bed.o +ar: creating /build/canu-2.0+dfsg/Linux-i686/lib/libcanu.a +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sequence.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqLibrary.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTig.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/gfa.o +a - /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/bed.o +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgStoreDump.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadErates/stores/loadErates.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/meryl.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylCountArray.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylInput.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-count.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-countSimple.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-histogram.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-nextMer.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/meryl-import.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-extract.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-generate.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-mutate.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-sample.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-simulate.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-summarize.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/edalign/overlapInCore/edalign.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/correction/falconsense.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/utgcns/stashContains.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogusUtil.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/alignGFA/gfa/alignGFA.o -lcanu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/unitigConsensus.H:67, @@ -6851,12 +6919,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu Success! -canu installed in /build/canu-2.0+dfsg/Linux-amd64/bin/canu +canu installed in /build/canu-2.0+dfsg/Linux-i686/bin/canu make[2]: Leaving directory '/build/canu-2.0+dfsg/src' builddir=*-*/; \ find $builddir \ @@ -6896,20 +6962,22 @@ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ -dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-1_i386.deb'. dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-1_i386.deb'. +dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../canu_2.0+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/24390/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/24390/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/29456 and its subdirectories -I: Current time: Fri Jul 22 06:25:00 -12 2022 -I: pbuilder-time-stamp: 1658514300 +I: removing directory /srv/workspace/pbuilder/24390 and its subdirectories +I: Current time: Sun Jun 20 04:10:20 +14 2021 +I: pbuilder-time-stamp: 1624111820