Diff of the two buildlogs: -- --- b1/build.log 2021-07-13 21:31:01.971746390 +0000 +++ b2/build.log 2021-07-13 21:42:30.285814049 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 13 08:55:06 -12 2021 -I: pbuilder-time-stamp: 1626209706 +I: Current time: Wed Jul 14 11:32:27 +14 2021 +I: pbuilder-time-stamp: 1626211947 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ 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.o_5T0UPD/trustedkeys.kbx': General error -gpgv: Signature made Fri Mar 27 11:47:02 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.7c7BkjAS/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 @@ -31,135 +31,169 @@ dpkg-source: info: applying canu_version.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/32385/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/6912/tmp/hooks/D01_modify_environment starting +debug: Running on ff64a. +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/6912/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/6912/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=6' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='f62f974f24cc4faea59c31af06102773' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - 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='32385' - PS1='# ' - PS2='> ' + INVOCATION_ID=da9c7da2ea2c4375b756607e0f04e382 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=6912 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.bdOK5wsnJ5/pbuilderrc_uBtO --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.bdOK5wsnJ5/b1 --logfile b1/build.log canu_2.0+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.bdOK5wsnJ5/pbuilderrc_HWRX --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.bdOK5wsnJ5/b2 --logfile b2/build.log --extrapackages usrmerge canu_2.0+dfsg-1.dsc' + SUDO_GID=114 + SUDO_UID=109 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux cbxi4a 5.10.0-7-armmp #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 9 21:28 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/32385/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 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 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 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 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 14 11:33 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 12 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 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/6912/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -280,7 +314,7 @@ Get: 75 http://deb.debian.org/debian bullseye/main armhf libmeryl-dev armhf 0~20150903+r2013-8+b1 [60.7 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libssw-java armhf 1.1-13 [19.1 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf mhap all 2.1.3+dfsg-3 [160 kB] -Fetched 88.9 MB in 17s (5273 kB/s) +Fetched 88.9 MB in 19s (4602 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 ... 19398 files and directories currently installed.) @@ -609,135 +643,135 @@ 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:TrustCor_RootCert_CA-2.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:emSign_Root_CA_-_G1.pem -Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:e-Szigno_Root_CA_2017.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:Actalis_Authentication_Root_CA.pem +Adding debian:Certigna_Root_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:Trustwave_Global_Certification_Authority.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:GTS_Root_R3.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem +Adding debian:Certigna.pem +Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:DigiCert_Global_Root_G3.pem Adding debian:AffirmTrust_Networking.pem -Adding debian:emSign_ECC_Root_CA_-_G3.pem -Adding debian:Izenpe.com.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem -Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:DigiCert_Assured_ID_Root_G2.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:Trustwave_Global_Certification_Authority.pem +Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Extended_Validation_Root.pem -Adding debian:Hongkong_Post_Root_CA_3.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:QuoVadis_Root_CA.pem -Adding debian:GTS_Root_R1.pem -Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem -Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:certSIGN_Root_CA_G2.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:Security_Communication_RootCA2.pem -Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Izenpe.com.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:TrustCor_ECA-1.pem Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:Secure_Global_CA.pem -Adding debian:AffirmTrust_Premium_ECC.pem -Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:certSIGN_Root_CA_G2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:Certigna.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:GTS_Root_R3.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:GTS_Root_R2.pem +Adding debian:emSign_Root_CA_-_G1.pem Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:AffirmTrust_Premium.pem -Adding debian:DST_Root_CA_X3.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:UCA_Global_G2_Root.pem Adding debian:certSIGN_ROOT_CA.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem +Adding debian:Secure_Global_CA.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:emSign_Root_CA_-_C1.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:DigiCert_Global_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem -Adding debian:Microsec_e-Szigno_Root_CA_2009.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:DigiCert_Global_Root_G2.pem -Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem +Adding debian:Go_Daddy_Class_2_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:SecureSign_RootCA11.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem -Adding debian:emSign_Root_CA_-_C1.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem -Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:E-Tugra_Certification_Authority.pem -Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:USERTrust_ECC_Certification_Authority.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:DigiCert_Trusted_Root_G4.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:GTS_Root_R4.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem +Adding debian:SecureTrust_CA.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:GTS_Root_R2.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:NAVER_Global_Root_Certification_Authority.pem -Adding debian:UCA_Global_G2_Root.pem -Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:Buypass_Class_2_Root_CA.pem -Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem -Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:Starfield_Class_2_CA.pem +Adding debian:DST_Root_CA_X3.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:EC-ACC.pem -Adding debian:Certigna_Root_CA.pem -Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:SecureTrust_CA.pem -Adding debian:TrustCor_ECA-1.pem -Adding debian:Cybertrust_Global_Root.pem +Adding debian:COMODO_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:emSign_ECC_Root_CA_-_C3.pem -Adding debian:Amazon_Root_CA_3.pem Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:DigiCert_Global_Root_G2.pem Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:AffirmTrust_Commercial.pem -Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:Amazon_Root_CA_2.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:Certum_Trusted_Network_CA_2.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:GTS_Root_R1.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Amazon_Root_CA_1.pem +Adding debian:Network_Solutions_Certificate_Authority.pem done. Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... @@ -759,9 +793,42 @@ 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (64.1 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 ... 38239 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../canu_2.0+dfsg-1_source.changes +hostname: Name or service not known +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../canu_2.0+dfsg-1_source.changes dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -785,20 +852,92 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-2.0+dfsg' dh_auto_build - cd src && make -j3 "INSTALL=install --strip-program=true" + cd src && make -j6 "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' '5.10.0-7-armmp' as 'armv7l' into '/build/canu-2.0+dfsg/Linux-armv7l/{bin,obj}'. +Building for 'Linux' '5.10.0-7-arm64' as 'aarch64' into '/build/canu-2.0+dfsg/Linux-aarch64/{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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 Building release v2.0 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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-aarch64/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 +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); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/logging.H:29, + from utility/logging.C:26: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/logging.H:29, + from utility/logging.C:26: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/logging.H:29, + from utility/logging.C:26: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); + | ^ +utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument + 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/logging.H:29, + from utility/logging.C:26: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 8220 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 function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15: +/usr/include/arm-linux-gnueabihf/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-aarch64/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 +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); + | ~~~~^~~~~~~~~~~~~~~~~~~~~ +utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()': +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-aarch64/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 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", @@ -932,86 +1071,14 @@ 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-armv7l/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-armv7l/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-armv7l/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 -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); - | ~~~~^~~~~~~~~~~~~~~~~~~~~ -utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()': -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-armv7l/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 -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); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 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 ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); - | ^ -utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument - 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 8220 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 function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15: -/usr/include/arm-linux-gnueabihf/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-armv7l/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-armv7l/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-aarch64/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 In file included from utility/system.C:46: /usr/include/arm-linux-gnueabihf/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." | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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 In file included from utility/kmers.H:32, from utility/kmers.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -1021,15 +1088,7 @@ | | | | 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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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=] @@ -1086,6 +1145,29 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +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/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-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=] @@ -1208,23 +1290,62 @@ | ~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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? - | ^~~~~~~ -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); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/kmers.H:29, - from utility/kmers-reader.C:26: -/usr/include/arm-linux-gnueabihf/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 ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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} +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 utility/kmers.H:32, from utility/kmers-writer.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -1234,7 +1355,15 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 +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-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=] @@ -1323,30 +1452,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %016llx -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); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/kmers.H:29, - from utility/kmers-writer.C:26: -/usr/include/arm-linux-gnueabihf/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 ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 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=] @@ -1403,6 +1508,19 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +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); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/kmers.H:29, + from utility/kmers-reader.C:26: +/usr/include/arm-linux-gnueabihf/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 ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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", @@ -1437,8 +1555,23 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +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); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/kmers.H:29, + from utility/kmers-writer.C:26: +/usr/include/arm-linux-gnueabihf/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 ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, - from utility/kmers-writer-stream.C:26: + from utility/kmers-statistics.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); @@ -1446,8 +1579,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 In file included from utility/kmers.H:32, - from utility/kmers-statistics.C:26: + 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); @@ -1455,62 +1590,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -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} -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 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=] @@ -1567,27 +1646,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 -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: -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-armv7l/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 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=] @@ -1875,10 +1933,23 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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 +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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 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"; @@ -1892,33 +1963,8 @@ 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-armv7l/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-armv7l/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-armv7l/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 -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from correction/falconConsensus.H:75, - from correction/falconConsensus.C:73: -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/falconConsensus.H:75, - from correction/falconConsensus-alignTag.C:73: -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-armv7l/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-armv7l/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-aarch64/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -1948,9 +1994,30 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from correction/falconConsensus.H:75, + from correction/falconConsensus.C:73: +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/falconConsensus.H:75, + from correction/falconConsensus-alignTag.C:73: +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-aarch64/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-aarch64/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 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"); @@ -1979,49 +2046,13 @@ 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-armv7l/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-armv7l/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/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/arm-linux-gnueabihf/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=] - 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/arm-linux-gnueabihf/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 '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=] - 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); -stores/sqStore.H:126:36: note: directive argument in the range [0, 65535] -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/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4109 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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 +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 + | ^~~~~~~ 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); @@ -2237,6 +2268,32 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/arm-linux-gnueabihf/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=] + 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/arm-linux-gnueabihf/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/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); @@ -2334,10 +2391,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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 - | ^~~~~~~ +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=] + 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +stores/sqStore.H:126:36: note: directive argument in the range [0, 65535] +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/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4109 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", @@ -2390,8 +2457,9 @@ stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 348 | B->writeIFFarray("BASE", _bases, sqRead_largest); | ^~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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", @@ -2404,9 +2472,12 @@ 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=] +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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-aarch64/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-aarch64/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/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", @@ -2456,7 +2527,22 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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/ovStore.H:43, + from stores/ovStoreFile.C:47: +stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': +stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); + | ^~~ +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/ovStoreFile.C:47: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 4 and 4100 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 '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); @@ -2488,6 +2574,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: +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/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); @@ -2527,7 +2623,116 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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 +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/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); + | ^~~~~~~~ +stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument + 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:192:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); + | ^~~~~~~~ +stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument + 192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:193:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); + | ^~~~~~~~ +stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument + 193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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::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); + | ^~~~~~~~ +stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument + 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:637:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + | ^~~~~~~~ +stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument + 637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:641:38: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + | ^~~~~~~~ +stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument + 641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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/ovStoreWriter.C:56: stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': stores/ovStore.H:79:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -2570,6 +2775,31 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~ +stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument + 695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/tgStore.C:42: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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-aarch64/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 +In file included from stores/tgTig.H:36, + 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); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu 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); @@ -2583,6 +2813,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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); @@ -2669,169 +2909,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/tgStore.C:44: -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/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=] -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)': -stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); - | ^~~ -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/ovStoreFile.C:47: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 4 and 4100 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::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); - | ^~~~~~~~ -stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument - 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:192:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); - | ^~~~~~~~ -stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument - 192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:193:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); - | ^~~~~~~~ -stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument - 193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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::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); - | ^~~~~~~~ -stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument - 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:637:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - | ^~~~~~~~ -stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument - 637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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:641:38: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - | ^~~~~~~~ -stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument - 641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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 '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); - | ^~~~~~~~ -stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument - 695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/tgStore.C:42: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 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-armv7l/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-armv7l/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-armv7l/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 -In file included from stores/tgTig.H:36, - 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); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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/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)); @@ -2847,16 +2925,24 @@ 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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/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); + | ^~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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/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++; @@ -2874,27 +2960,10 @@ | | | | 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); - | ^~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 overlapInCore/overlapReadCache.H:37, @@ -2906,12 +2975,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -2924,10 +2991,11 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 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=] @@ -2973,9 +3041,12 @@ 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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 /usr/include/c++/10/set:60, from utility/strings.H:37, from stores/ovOverlap.H:45, @@ -3012,6 +3083,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +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); + | ^~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function 'void NDalign::fastFindMersB(bool)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -3034,16 +3109,28 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 -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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 +stores/ovStoreSorter.C: In function 'int main(int, char**)': +stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 167 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 170 | err.push_back("ERROR: no slice number (-F) 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/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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 86 | err.push_back("ERROR: No config (-C) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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"); @@ -3078,8 +3165,6 @@ 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 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 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"); @@ -3093,26 +3178,8 @@ 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/ovStoreSorter.C: In function 'int main(int, char**)': -stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 167 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 170 | err.push_back("ERROR: no slice number (-F) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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/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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 86 | err.push_back("ERROR: No config (-C) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-aarch64/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/ovStoreDump.C:56: @@ -3162,8 +3229,26 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +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", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 231 | seqs->sqStore_getReadSegm(rid), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] +stores/sqStoreDumpMetaData.C: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)': +stores/sqStoreDumpMetaData.C:277:26: 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=] + 277 | fprintf(stdout, "%lu\n", lengths[ii]); + | ~~^ + | | + | 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); @@ -3171,6 +3256,15 @@ 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); | ^~~~~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from stores/sqStoreDumpMetaData.C:34: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ 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); @@ -3194,6 +3288,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from stores/sqStoreDumpMetaData.C:34: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()': stores/sqStoreDumpFASTQ.C:167:36: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 167 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s); @@ -3217,48 +3321,64 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 -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", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 231 | seqs->sqStore_getReadSegm(rid), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] -stores/sqStoreDumpMetaData.C: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)': -stores/sqStoreDumpMetaData.C:277:26: 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=] - 277 | fprintf(stdout, "%lu\n", lengths[ii]); - | ~~^ - | | - | long unsigned int - | %llu -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, +In file included from /usr/include/c++/10/vector:72, + from utility/files.H:36, + from stores/sqStore.H:38, + from stores/sqStoreDumpMetaData.C:35: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, from /build/canu-2.0+dfsg/src/AS_global.H:105, from stores/sqStoreDumpMetaData.C:34: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +In file included from /usr/include/c++/10/vector:72, + from utility/files.H:36, + from stores/sqStore.H:38, + from stores/sqStoreDumpMetaData.C:35: +/usr/include/c++/10/bits/vector.tcc: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, from /build/canu-2.0+dfsg/src/AS_global.H:105, from stores/sqStoreDumpMetaData.C:34: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +stores/sqStoreDumpMetaData.C:279:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 279 | } + | ^ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +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: + 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); @@ -3302,7 +3422,44 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 +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/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); + | ^~~~~~~~~~~ +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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, @@ -3313,6 +3470,22 @@ /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, @@ -3326,9 +3499,7 @@ | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] - 675 | #warning replace this with genericStatistics - | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3345,26 +3516,16 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from utility/files.H:36, - from stores/sqStore.H:38, - from stores/sqStoreDumpMetaData.C:35: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from stores/sqStoreDumpMetaData.C:34: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgStoreFilter.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 /usr/include/c++/10/vector:72, from utility/strings.H:38, from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, @@ -3388,31 +3549,6 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from utility/files.H:36, - from stores/sqStore.H:38, - from stores/sqStoreDumpMetaData.C:35: -/usr/include/c++/10/bits/vector.tcc: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from stores/sqStoreDumpMetaData.C:34: -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogramSimple(std::vector)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -3443,9 +3579,17 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreDumpMetaData.C:279:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 279 | } - | ^ +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-aarch64/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 /usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -3460,90 +3604,6 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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/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-armv7l/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 -In file included from /usr/include/c++/10/vector:67, - from utility/strings.H:38, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, - from sequence/sequence-summarize.C:30: -/usr/include/c++/10/bits/stl_vector.h: In function 'void doSummarize(std::vector&, summarizeParameters&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from utility/strings.H:38, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, - from sequence/sequence-summarize.C:30: -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 474 | } - | ^ -sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -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 -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); - | ^~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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 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"); @@ -3556,18 +3616,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from stores/tgStoreFilter.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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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/tgStore.H:43, from stores/tgTigDisplay.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=] @@ -3576,8 +3624,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/loadCorrectedReads.C:29: @@ -3603,48 +3649,35 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +In file included from /usr/include/c++/10/vector:67, + from utility/strings.H:38, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, + from sequence/sequence-summarize.C:30: +/usr/include/c++/10/bits/stl_vector.h: In function 'void doSummarize(std::vector&, summarizeParameters&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from utility/strings.H:38, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, + from sequence/sequence-summarize.C:30: +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] + 261 | #warning HARD CODED NUMBER OF FILES! + | ^~~~~~~ +sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 474 | } + | ^ +sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 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 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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] - 261 | #warning HARD CODED NUMBER OF FILES! - | ^~~~~~~ -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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -3656,7 +3689,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 In file included from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/meryl.C:46: @@ -3733,6 +3765,66 @@ 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-aarch64/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 +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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, @@ -3744,6 +3836,30 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/merylCountArray.C:26: @@ -3802,17 +3918,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | 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/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 In file included from meryl/meryl.H:51, from meryl/merylCountArray.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': @@ -3852,6 +3957,19 @@ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylInput.C:26: @@ -3928,56 +4046,6 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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-armv7l/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 utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -4047,6 +4115,7 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 In file included from meryl/meryl.H:51, from meryl/merylOp-count.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': @@ -4212,8 +4281,6 @@ | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -4301,17 +4368,6 @@ 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-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 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", @@ -4344,6 +4400,24 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %016llx +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +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 +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/merylOp-histogram.C:26: @@ -4420,15 +4494,7 @@ 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-armv7l/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 -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!" - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-aarch64/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 utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -4552,6 +4618,8 @@ | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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, @@ -4563,15 +4631,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp.C:26: @@ -4648,6 +4709,42 @@ 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/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 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 +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 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=] @@ -4723,46 +4820,9 @@ 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-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 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 utility/kmers.H:32, - from meryl/merylInput.H:30, +In file included 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/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=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4818,9 +4878,113 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from meryl/merylInput.H:30, - from meryl/meryl.H:51, +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 +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 /usr/include/c++/10/vector:72, + from utility/strings.H:38, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, + from sequence/sequence.C:26: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void extractParameters::finalize()': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from utility/strings.H:38, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, + from sequence/sequence.C:26: +/usr/include/c++/10/bits/stl_vector.h: In function 'void decodeRange(char*, std::vector&, std::vector&) [with T = long long unsigned int]': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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/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=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4963,167 +5127,21 @@ 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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: -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); - | ^~~~~~~~~~ -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 /usr/include/c++/10/vector:72, - from utility/strings.H:38, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, - from sequence/sequence.C:26: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void extractParameters::finalize()': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from utility/strings.H:38, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, - from sequence/sequence.C:26: -/usr/include/c++/10/bits/stl_vector.h: In function 'void decodeRange(char*, std::vector&, std::vector&) [with T = long long unsigned int]': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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-aarch64/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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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-armv7l/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-armv7l/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-armv7l/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-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()); - | ^~~~~~~ -sequence/sequence-sample.C:273:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 273 | AS_UTL_writeFastA(outFile2, seq2.bases(), seq2.length(), 0, ">%s\n", seq2.name()); - | ^~~~~~~ -sequence/sequence-sample.C: In function 'void doSample_single(std::vector&, sampleParameters&)': -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 /usr/include/c++/10/vector:72, - from utility/strings.H:38, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, - from sequence/sequence-sample.C:30: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:30, - from sequence/sequence-sample.C:30: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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=] @@ -5177,97 +5195,27 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1881 | __final_insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:30, - from sequence/sequence-sample.C:30: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = seqEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:30, - from sequence/sequence-sample.C:30: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1662 | __heap_select(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1925 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__heap_select(__first, __middle, __last, __comp); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void doSample_sample(sampleParameters&, uint64, uint64, std::vector&)': -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1977 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1977 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from utility/strings.H:38, - from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, - from sequence/sequence-sample.C:30: -/usr/include/c++/10/bits/stl_vector.h: In function 'void doSample_paired(std::vector&, sampleParameters&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -/usr/include/c++/10/bits/stl_vector.h: In function 'void doSample_single(std::vector&, sampleParameters&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +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()); + | ^~~~~~~ +sequence/sequence-sample.C:273:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 273 | AS_UTL_writeFastA(outFile2, seq2.bases(), seq2.length(), 0, ">%s\n", seq2.name()); + | ^~~~~~~ +sequence/sequence-sample.C: In function 'void doSample_single(std::vector&, sampleParameters&)': +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()); + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +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-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=] @@ -5347,8 +5295,6 @@ | ~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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=] @@ -5393,10 +5339,129 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 /usr/include/c++/10/vector:72, + from utility/strings.H:38, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, + from sequence/sequence-sample.C:30: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:30, + from sequence/sequence-sample.C:30: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1881 | __final_insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:30, + from sequence/sequence-sample.C:30: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = seqEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:30, + from sequence/sequence-sample.C:30: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1662 | __heap_select(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1925 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__heap_select(__first, __middle, __last, __comp); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void doSample_sample(sampleParameters&, uint64, uint64, std::vector&)': +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1977 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1977 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from utility/strings.H:38, + from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, + from sequence/sequence-sample.C:30: +/usr/include/c++/10/bits/stl_vector.h: In function 'void doSample_paired(std::vector&, sampleParameters&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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()); @@ -5426,7 +5491,23 @@ | ~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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 +/usr/include/c++/10/bits/stl_vector.h: In function 'void doSample_single(std::vector&, sampleParameters&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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: +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-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); @@ -5463,7 +5544,24 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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 +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: +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 +overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': +overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 258 | fgets(line, 1024, F); + | ~~~~~^~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, @@ -5476,6 +5574,18 @@ | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +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-Find_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 /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, from /build/canu-2.0+dfsg/src/AS_global.H:105, @@ -5491,18 +5601,6 @@ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -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: -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 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, @@ -5515,6 +5613,7 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 In file included from /usr/include/c++/10/vector:72, from utility/strings.H:38, from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, @@ -5538,6 +5637,18 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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_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 /usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogramSimple(std::vector)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -5549,6 +5660,18 @@ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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-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); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu /usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_dumpLengths(std::vector)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -5568,6 +5691,7 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 /usr/include/c++/10/bits/stl_algo.h: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -5582,11 +5706,14 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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-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); @@ -5594,10 +5721,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': -overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 258 | fgets(line, 1024, F); - | ~~~~~^~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from utility/strings.H:38, from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, @@ -5613,64 +5736,9 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 474 | } - | ^ -sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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-Find_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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from overlapInCore/overlapInCore.H:66, - 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); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 -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_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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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 +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? + | ^~~~~~~ overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)': overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 430 | FILE *BAT = openOutput(outputPrefix, "ovlbat"); @@ -5690,12 +5758,22 @@ 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-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -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-armv7l/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-aarch64/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 +sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 474 | } + | ^ +sequence/sequence-summarize.C:474:1: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from overlapInCore/overlapReadCache.H:37, + from overlapInCore/overlapPair.C:44: +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 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"); @@ -5709,17 +5787,6 @@ 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()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from overlapInCore/overlapReadCache.H:37, - from overlapInCore/overlapPair.C:44: -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 overlapInCore/overlapPair.C: In function 'void* recomputeOverlaps(void*)': overlapInCore/overlapPair.C:429:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | if (extendAlignment(bRead, bbgn, bend, blen, "B", bID, @@ -5757,12 +5824,16 @@ 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-aarch64/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 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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 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", @@ -5775,9 +5846,6 @@ 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=] -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 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", @@ -5790,6 +5858,7 @@ 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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from wtdbg/wtdbgConvert.C:33: @@ -5800,8 +5869,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/generateCorrectionLayouts.C:37: @@ -5860,6 +5928,8 @@ | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, @@ -5871,28 +5941,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from /usr/include/c++/10/set:60, - from utility/strings.H:37, - from stores/ovOverlap.H:45, - from stores/ovStore.H:42, - from wtdbg/wtdbgConvert.C:31: -/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/map:61, - from stores/tgTig.H:38, - from stores/tgStore.H:43, - from wtdbg/wtdbgConvert.C:33: -/usr/include/c++/10/bits/stl_map.h: In function 'void save_tig(sqStore*, tgStore*, tgTig*, std::map >&, std::map >&, std::map >&, std::map&, std::map >&, std::map >&)': -/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 502 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 503 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/filterCorrectionLayouts.C:29: @@ -5903,22 +5951,18 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -/usr/include/c++/10/bits/stl_map.h: In function 'int main(int, char**)': -/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 502 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 503 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 502 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 503 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 +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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 stores/sqCache.H:30, @@ -5930,7 +5974,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 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); @@ -5951,25 +5994,6 @@ correction/falconsense.C:362:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 362 | err.push_back("ERROR: no corStore input (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': -correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 70 | for (fgets(L, 1024, R); - | ~~~~~^~~~~~~~~~~~ -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)) { - | ~~~~~^~~~~~~~~~~~ -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 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=] @@ -5999,9 +6023,37 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-aarch64/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 +correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': +correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 70 | for (fgets(L, 1024, R); + | ~~~~~^~~~~~~~~~~~ +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-aarch64/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 +In file included from /usr/include/c++/10/set:60, + from utility/strings.H:37, + from stores/ovOverlap.H:45, + from stores/ovStore.H:42, + from wtdbg/wtdbgConvert.C:31: +/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 /usr/include/c++/10/map:61, + from stores/tgTig.H:38, + from stores/tgStore.H:43, + from wtdbg/wtdbgConvert.C:33: +/usr/include/c++/10/bits/stl_map.h: In function 'void save_tig(sqStore*, tgStore*, tgTig*, std::map >&, std::map >&, std::map >&, std::map&, std::map >&, std::map >&)': +/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 502 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 503 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, from haplotyping/splitHaplotype.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -6140,19 +6192,37 @@ 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-armv7l/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-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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 +/usr/include/c++/10/bits/stl_map.h: In function 'int main(int, char**)': +/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 502 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 503 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 502 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 503 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 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-aarch64/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-aarch64/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -6164,8 +6234,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-aarch64/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -6213,10 +6283,7 @@ overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 720 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends. | ^~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -6228,6 +6295,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, @@ -6238,8 +6307,9 @@ /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type 'Olap_Info_t' changed in GCC 9.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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 /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = Olap_Info_t*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:355:22: note: parameter passing for argument of type '_ValueType' {aka 'Olap_Info_t'} changed in GCC 9.1 355 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value), @@ -6261,12 +6331,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 | _GLIBCXX_MOVE(__value), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 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", @@ -6304,14 +6373,14 @@ 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-armv7l/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 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-armv7l/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-armv7l/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-armv7l/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-aarch64/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-aarch64/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-aarch64/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-aarch64/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 In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/bogart.C:46: @@ -6365,8 +6434,6 @@ 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-armv7l/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-armv7l/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 In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_AssemblyGraph.C:28: @@ -6398,15 +6465,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -In file included from /usr/include/c++/10/vector:72, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_AssemblyGraph.C:26: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BestPlacement&}; _Tp = BestPlacement; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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()': @@ -6437,6 +6496,20 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] + 486 | #warning deviationGraph hard coded + | ^~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_AssemblyGraph.C:26: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BestPlacement&}; _Tp = BestPlacement; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 In file included from /usr/include/c++/10/vector:67, from utility/files.H:36, from stores/ovStore.H:38, @@ -6446,8 +6519,37 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 +In file included from bogart/AS_BAT_Unitig.H:49, + 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); + | ~~^ ~~ + | | | + | 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 /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from utility/arrays.H:33, @@ -6469,9 +6571,6 @@ | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] - 486 | #warning deviationGraph hard coded - | ^~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, @@ -6492,8 +6591,7 @@ 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -6522,6 +6620,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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-aarch64/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-aarch64/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 In file included from /usr/include/c++/10/vector:72, from utility/files.H:36, from stores/ovStore.H:38, @@ -6533,7 +6635,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 /usr/include/c++/10/bits/vector.tcc: In member function 'void BestOverlapGraph::findErrorRateThreshold()': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -6591,7 +6692,8 @@ 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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_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); @@ -6620,10 +6722,24 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 +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); + | ^~~~ +bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument + 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from bogart/AS_BAT_Logging.H:41, + from bogart/AS_BAT_Logging.C:38: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4115 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 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); @@ -6652,11 +6768,15 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 +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); + | ^~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 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); @@ -6685,30 +6805,15 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -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_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); - | ^~~~ -bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument - 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from bogart/AS_BAT_Logging.H:41, - from bogart/AS_BAT_Logging.C:38: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4115 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-armv7l/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 +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()); + | ~~^ ~~~~~~~~~ + | | | + | long unsigned int std::vector::size_type {aka unsigned int} + | %u 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_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); @@ -6737,13 +6842,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -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()); - | ~~^ ~~~~~~~~~ - | | | - | long unsigned int std::vector::size_type {aka unsigned int} - | %u In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_MergeOrphans.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6797,60 +6895,7 @@ | ~~~~~~~~~~~~~~ | | | int -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -In file included from /usr/include/c++/10/vector:72, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_MergeOrphans.C:30: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_MergeOrphans.C:30: -/usr/include/c++/10/bits/stl_vector.h: In function 'void assignReadsToTargets(Unitig*, std::vector*, std::vector)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from bogart/AS_BAT_Unitig.H:49, - 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); - | ~~^ ~~ - | | | - | 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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -/usr/include/c++/10/bits/stl_vector.h: In function '_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEdd._omp_fn.0': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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()': @@ -6891,7 +6936,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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-aarch64/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 In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_OverlapCache.C:49: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6922,7 +6968,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PlaceContains.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6953,7 +6998,31 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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-aarch64/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 /usr/include/c++/10/vector:72, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_MergeOrphans.C:30: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_MergeOrphans.C:30: +/usr/include/c++/10/bits/stl_vector.h: In function 'void assignReadsToTargets(Unitig*, std::vector*, std::vector)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function '_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEdd._omp_fn.0': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PlaceReadUsingOverlaps.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6984,10 +7053,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-aarch64/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 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); @@ -7016,8 +7084,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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_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); @@ -7046,29 +7116,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -In file included from /usr/include/c++/10/vector:72, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 /usr/include/c++/10/vector:67, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39: -/usr/include/c++/10/bits/stl_vector.h: In function 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector&, uint32)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-aarch64/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-aarch64/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 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()': @@ -7099,7 +7148,16 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 +In file included from /usr/include/c++/10/vector:72, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 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()': @@ -7130,9 +7188,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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); @@ -7162,7 +7220,8 @@ | long unsigned int | %llu 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); @@ -7191,9 +7250,16 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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-armv7l/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 /usr/include/c++/10/vector:67, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_PlaceReadUsingOverlaps.C:39: +/usr/include/c++/10/bits/stl_vector.h: In function 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector&, uint32)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 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()': @@ -7224,6 +7290,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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-aarch64/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 In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig_AddRead.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7284,64 +7354,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 -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) - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:126:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 126 | fgets(inLine, 1024, inFile); // NUCMER - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:127:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 127 | fgets(inLine, 1024, inFile); // (blank) - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:128:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 128 | fgets(inLine, 1024, inFile); // (header) - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:142:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 142 | fgets(inLine, 1024, inFile); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:200:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 200 | fgets(inLine, 1024, inFile); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C: In function 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': -bogus/bogusUtil.C:226:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 226 | fgets(inLine, 1024, inFile); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 274 | fgets(inLine, 1024, inFile); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C: In function 'void loadReferenceSequence(char*, std::vector&, std::map, unsigned int>&)': -bogus/bogusUtil.C:300:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 300 | fgets(refhdr, 1024, F); chomp(refhdr); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:301:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 301 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:326:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fgets(refhdr, 1024, F); chomp(refhdr); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 327 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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 -In file included from /usr/include/c++/10/vector:72, - from utility/files.H:36, - from bogus/bogusUtil.H:44, - from bogus/bogusUtil.C:43: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const genomeAlignment&}; _Tp = genomeAlignment; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from utility/files.H:36, - from bogus/bogusUtil.H:44, - from bogus/bogusUtil.C:43: -/usr/include/c++/10/bits/stl_vector.h: In function 'void addAlignment(std::vector&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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-aarch64/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 stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/utgcns.C:46: @@ -7352,18 +7366,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from /usr/include/c++/10/algorithm:62, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from bogus/bogusUtil.H:42, - from bogus/bogus.C:38: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 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", @@ -7442,10 +7444,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ utgcns/utgcns.C: In function 'std::map* loadPartitionedReads(char*)': utgcns/utgcns.C:582:75: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 582 | fprintf(stderr, "File '%s' isn't a utgcns seqFile: found magic 0x%016lx.\n", seqFile, magc), exit(1); @@ -7468,6 +7466,89 @@ 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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:126:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 126 | fgets(inLine, 1024, inFile); // NUCMER + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:127:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 127 | fgets(inLine, 1024, inFile); // (blank) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:128:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 128 | fgets(inLine, 1024, inFile); // (header) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:142:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 142 | fgets(inLine, 1024, inFile); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:200:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 200 | fgets(inLine, 1024, inFile); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C: In function 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': +bogus/bogusUtil.C:226:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 226 | fgets(inLine, 1024, inFile); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 274 | fgets(inLine, 1024, inFile); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C: In function 'void loadReferenceSequence(char*, std::vector&, std::map, unsigned int>&)': +bogus/bogusUtil.C:300:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 300 | fgets(refhdr, 1024, F); chomp(refhdr); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:301:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 301 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:326:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fgets(refhdr, 1024, F); chomp(refhdr); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 327 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 +In file included from /usr/include/c++/10/vector:72, + from utility/files.H:36, + from bogus/bogusUtil.H:44, + from bogus/bogusUtil.C:43: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const genomeAlignment&}; _Tp = genomeAlignment; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from utility/files.H:36, + from bogus/bogusUtil.H:44, + from bogus/bogusUtil.C:43: +/usr/include/c++/10/bits/stl_vector.h: In function 'void addAlignment(std::vector&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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 /usr/include/c++/10/algorithm:62, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from bogus/bogusUtil.H:42, + from bogus/bogus.C:38: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, @@ -7531,6 +7612,16 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from gfa/alignGFA.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 /usr/include/c++/10/bits/stl_vector.h: In function 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); @@ -7542,79 +7633,6 @@ /usr/include/c++/10/bits/stl_algo.h:4894:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4894 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/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 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 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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-armv7l/bin/canu -chmod +x /build/canu-2.0+dfsg/Linux-armv7l/bin/canu -cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-armv7l/bin/canu-time -chmod +x /build/canu-2.0+dfsg/Linux-armv7l/bin/canu-time -echo > /build/canu-2.0+dfsg/Linux-armv7l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." -chmod -x /build/canu-2.0+dfsg/Linux-armv7l/bin/canu.defaults -cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-armv7l/share/sequence/ultra-long-nanopore -cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-armv7l/share/sequence/pacbio -cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-armv7l/share/sequence/pacbio-hifi -cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/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/unitigConsensus.H:67, - from utgcns/unitigConsensus.C:74: -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 gfa/alignGFA.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 gfa/alignGFA.C: In function 'bool checkRecord(bedRecord*, sequences&, sequences&, sequences&, bool, bool)': gfa/alignGFA.C:507:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 507 | success &= checkRecord_align("ALL", @@ -7633,60 +7651,14 @@ 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); | ~~~~~~^~~~~~~ -ar rv /build/canu-2.0+dfsg/Linux-armv7l/lib/libcanu.a /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o 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/build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -ar: creating /build/canu-2.0+dfsg/Linux-armv7l/lib/libcanu.a -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] +cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-aarch64/bin/canu +chmod +x /build/canu-2.0+dfsg/Linux-aarch64/bin/canu +cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-aarch64/bin/canu-time +chmod +x /build/canu-2.0+dfsg/Linux-aarch64/bin/canu-time +echo > /build/canu-2.0+dfsg/Linux-aarch64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." +chmod -x /build/canu-2.0+dfsg/Linux-aarch64/bin/canu.defaults +cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-aarch64/share/sequence/ultra-long-nanopore +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); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, @@ -7719,75 +7691,170 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreDump 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/build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -lcanu +cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-aarch64/share/sequence/pacbio +cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-aarch64/share/sequence/pacbio-hifi +cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +/usr/include/c++/10/bits/stl_vector.h: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/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/unitigConsensus.H:67, + from utgcns/unitigConsensus.C:74: +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 +ar rv /build/canu-2.0+dfsg/Linux-aarch64/lib/libcanu.a /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgStore.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgTig.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/gfa/gfa.o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/gfa/bed.o +ar: creating /build/canu-2.0+dfsg/Linux-aarch64/lib/libcanu.a +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/AS_global.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/edlib.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-buffered.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-compressed.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-memoryMapped.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/logging.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/strings.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/system.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/system-stackTrace.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/sequence.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers.o +a - /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-reader.o +a - 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-L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/falconsense/correction/falconsense.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/falconsense/utgcns/stashContains.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogus/bogus/bogusUtil.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/alignGFA/gfa/alignGFA.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu Success! -canu installed in /build/canu-2.0+dfsg/Linux-armv7l/bin/canu +canu installed in /build/canu-2.0+dfsg/Linux-aarch64/bin/canu make[2]: Leaving directory '/build/canu-2.0+dfsg/src' builddir=*-*/; \ find $builddir \ @@ -7823,8 +7890,8 @@ dh_strip -O--sourcedirectory=src/ dh_makeshlibs -O--sourcedirectory=src/ dh_shlibdeps -O--sourcedirectory=src/ -dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogart contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapInCore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapPair contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src/ @@ -7840,12 +7907,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/6912/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/6912/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/32385 and its subdirectories -I: Current time: Tue Jul 13 09:30:50 -12 2021 -I: pbuilder-time-stamp: 1626211850 +I: removing directory /srv/workspace/pbuilder/6912 and its subdirectories +I: Current time: Wed Jul 14 11:42:15 +14 2021 +I: pbuilder-time-stamp: 1626212535