Diff of the two buildlogs: -- --- b1/build.log 2023-04-18 15:50:35.079691615 +0000 +++ b2/build.log 2023-04-18 15:55:48.085800091 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 20 10:12:24 -12 2024 -I: pbuilder-time-stamp: 1716243144 +I: Current time: Wed Apr 19 05:50:37 +14 2023 +I: pbuilder-time-stamp: 1681833037 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./canu_2.0+dfsg.orig.tar.xz] I: copying [./canu_2.0+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Oct 28 08:38:47 2021 -12 +gpgv: Signature made Fri Oct 29 10:38:47 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -32,137 +32,169 @@ dpkg-source: info: applying remove-deprecated-sysctl.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/51622/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 19 05:51 /bin/sh -> /bin/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/30765/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='ee2cf9b4e1eb41c8b8ac43bb9c38a5d4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='51622' - PS1='# ' - PS2='> ' + INVOCATION_ID=370855793108475db7725c07eb13bc37 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=30765 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/r-b-build.wupB1E94/pbuilderrc_eWGH --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wupB1E94/b1 --logfile b1/build.log canu_2.0+dfsg-2.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wupB1E94/pbuilderrc_3yG5 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wupB1E94/b2 --logfile b2/build.log --extrapackages usrmerge canu_2.0+dfsg-2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Feb 12 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/51622/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Feb 13 10:21 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:21 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 19 05:51 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -282,7 +314,7 @@ Get: 74 http://deb.debian.org/debian bookworm/main i386 libmeryl-dev i386 0~20150903+r2013-8+b3 [72.6 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libssw-java i386 1.1-13 [23.9 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 mhap all 2.1.3+dfsg-3 [160 kB] -Fetched 105 MB in 3s (39.1 MB/s) +Fetched 105 MB in 4s (27.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:i386. (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 ... 19604 files and directories currently installed.) @@ -761,10 +793,17 @@ Reading package lists... Building dependency tree... Reading state information... +usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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-2_source.changes +I: user script /srv/workspace/pbuilder/30765/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/30765/tmp/hooks/A99_set_merged_usr finished +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-2_source.changes dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -788,36 +827,32 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-2.0+dfsg' dh_auto_build - cd src && make -j16 "INSTALL=install --strip-program=true" + cd src && make -j7 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/canu-2.0+dfsg/src' WARNING: WARNING: g++ 12 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: -Building for 'Linux' '5.10.0-21-amd64' as 'amd64' into '/build/canu-2.0+dfsg/Linux-amd64/{bin,obj}'. +Building for 'Linux' '5.10.0-21-686-pae' as 'i686' into '/build/canu-2.0+dfsg/Linux-i686/{bin,obj}'. Using '/usr/bin/g++' version '12'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'. -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 Building release v2.0 -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 -utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] - 58 | #warning how to set prefix size for streaming operations? - | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ 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", @@ -940,128 +975,7 @@ | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': -utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 311 | symlink(pathToFile, pathToLink); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': -utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 678 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 684 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 -In file included from utility/kmers.H:32, - 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); - | ~~^ ~~~~~~~~ - | | | - | 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.H:32, - from utility/kmers.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from utility/kmers.H:32, - from utility/kmers-writer-block.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from utility/kmers.H:32, - from utility/kmers-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-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 -In file included from utility/kmers.H:32, - from utility/kmers-writer.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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/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); @@ -1121,6 +1035,55 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __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/i386-linux-gnu/bits/stdio2.h:54:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=] + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': +utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 311 | symlink(pathToFile, pathToLink); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': +utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 678 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 684 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] + 58 | #warning how to set prefix size for streaming operations? + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +In file included from utility/kmers.H:32, + from utility/kmers.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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.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 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", @@ -1231,6 +1194,81 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': +utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); + | ~~~~~^ ~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %016llx +utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); + | ~~~~~^ ~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %016llx +utility/kmers-reader.C: In function 'void dumpMerylDataFile(char*)': +utility/kmers-reader.C:342:29: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-reader.C:342:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-reader.C:342:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); + | ~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-reader.C:342:68: warning: format '%lx' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); + | ~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-reader.C:342:77: warning: format '%lx' expects argument of type 'long unsigned int', but argument 11 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); + | ~~ + | | + | uint64 {aka long long unsigned int} +In file included from utility/kmers.H:32, + from utility/kmers-writer-stream.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu utility/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", @@ -1286,6 +1324,34 @@ | ~~~~~~~~~~~~~~~~~~ | | | 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)': +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-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); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers.H:32, + from utility/kmers-writer-block.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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.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", @@ -1341,124 +1407,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=] - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -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", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 326 | oi, ii, prefix, inBlocks[ii].prefix()); - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-writer-block.C:325:96: warning: format '%lx' expects argument of type 'long unsigned int', but argument 6 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", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 326 | oi, ii, prefix, inBlocks[ii].prefix()); - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-writer-block.C:370:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); - | ~~^ ~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/kmers-writer-block.C:370:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': -utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); - | ~~~~~^ ~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %016llx -utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); - | ~~~~~^ ~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %016llx -utility/kmers-reader.C: In function 'void dumpMerylDataFile(char*)': -utility/kmers-reader.C:342:29: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-reader.C:342:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-reader.C:342:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); - | ~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-reader.C:342:68: warning: format '%lx' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); - | ~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-reader.C:342:77: warning: format '%lx' expects argument of type 'long unsigned int', but argument 11 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); - | ~~ - | | - | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C utility/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", @@ -1546,20 +1494,104 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %016llx -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C -utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': -utility/kmers-writer.C:147:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 147 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-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", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 326 | oi, ii, prefix, inBlocks[ii].prefix()); + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-writer-block.C:325:96: warning: format '%lx' expects argument of type 'long unsigned int', but argument 6 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", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 326 | oi, ii, prefix, inBlocks[ii].prefix()); + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-writer-block.C:370:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); + | ~~^ ~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +utility/kmers-writer-block.C:370:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': +utility/kmers-reader.C: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:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from utility/kmers.H:29: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'kmerCountFileWriter::~kmerCountFileWriter()' at utility/kmers-writer.C:147:11: + inlined from 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)' at utility/kmers-reader.C:143:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1567,15 +1599,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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); +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C +utility/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:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from utility/kmers.H:29: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)' at utility/kmers-reader.C:143:11: + inlined from 'kmerCountFileWriter::~kmerCountFileWriter()' at utility/kmers-writer.C:147:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1583,11 +1617,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 utility/kmers.H:32, - from utility/kmers-exact.C:26: +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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); @@ -1595,8 +1626,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C -In file included from utility/bits.C:26: +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C +In file included from utility/kmers.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); @@ -1604,7 +1637,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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", @@ -1897,9 +1929,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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"; @@ -1913,13 +1942,18 @@ utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 260 | args[4] = "--output"; | ^~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 correction/falconConsensus.H:75, - from correction/falconConsensus-alignTag.C:73: + 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); @@ -1927,11 +1961,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/falconConsensus.H:75, - from correction/falconConsensus.C:73: + 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); @@ -1939,11 +1972,38 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C -stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] - 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING - | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/sqCache.H:30, + from stores/sqCache.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)': +stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases); + | ~~^ ~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)': +stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n", + | ~~^ + | | + | long unsigned int + | %llu + 357 | nReads, nBases, bgnID, endID); + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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"); @@ -1972,39 +2032,99 @@ stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 132 | buffer->closeIFFchunk("BLOB"); | ^~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from stores/sqCache.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +In file included from stores/sqStoreBlob.C:26: +In function 'void makeBlobName(char*, uint32, char*)', + inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: +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:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/sqStore.H:37: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, + inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +In function 'void makeBlobName(char*, uint32, char*)', + inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:73:17: +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 function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, + inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:73:17: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +In function 'void makeBlobName(char*, uint32, char*)', + inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:119:17: +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 function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, + inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:119:17: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C +stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] + 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] 71 | #warning not failing if a valid store | ^~~~~~~ -stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)': -stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases); - | ~~^ ~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)': -stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n", - | ~~^ - | | - | long unsigned int - | %llu - 357 | nReads, nBases, bgnID, endID); - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] + 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 75 | dat.ovl.ahg5, dat.ovl.ahg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] + 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 75 | dat.ovl.ahg5, dat.ovl.ahg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 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", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 76 | dat.ovl.bhg5, dat.ovl.bhg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 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", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 76 | dat.ovl.bhg5, dat.ovl.bhg3, + | ~~~~~~~~~~~~ + | | + | int 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", @@ -2057,41 +2177,6 @@ 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-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 -In file included from stores/sqStoreBlob.C:26: -In function 'void makeBlobName(char*, uint32, char*)', - inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: -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:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/sqStore.H:37: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, - inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 function 'void makeBlobName(char*, uint32, char*)', - inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:73:17: -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 function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, - inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:73:17: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ 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); @@ -2328,21 +2413,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In function 'void makeBlobName(char*, uint32, char*)', - inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:119:17: -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 function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, - inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:119:17: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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); @@ -2447,88 +2518,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc -stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] - 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 75 | dat.ovl.ahg5, dat.ovl.ahg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] - 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 75 | dat.ovl.ahg5, dat.ovl.ahg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 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", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 76 | dat.ovl.bhg5, dat.ovl.bhg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 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", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 76 | dat.ovl.bhg5, dat.ovl.bhg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovStore.C: In member function 'void ovStore::testStore(bool)': -stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n", - | ~~^ - | | - | long unsigned int - | %llu - 183 | nrds, novl, lid); - | ~~~~ - | | - | uint64 {aka long long unsigned int} -stores/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)': -stores/ovStore.C:493:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 493 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii, - | ~~~^ - | | - | long unsigned int - | %9llu -...... - 498 | _index[ii]._overlapID); - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C -stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': -stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStore.C:59: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'ovStore::ovStore(const char*, sqStore*)' at stores/ovStore.C:109:11: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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); @@ -2565,37 +2554,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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=] - 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 9 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, - 361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | int -stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 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, - 361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | int 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); @@ -2609,6 +2567,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +stores/ovStore.C: In member function 'void ovStore::testStore(bool)': +stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n", + | ~~^ + | | + | long unsigned int + | %llu + 183 | nrds, novl, lid); + | ~~~~ + | | + | uint64 {aka long long unsigned int} stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); @@ -2622,26 +2591,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __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 -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/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)': +stores/ovStore.C:493:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 493 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii, + | ~~~^ + | | + | long unsigned int + | %9llu +...... + 498 | _index[ii]._overlapID); + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); @@ -2655,46 +2617,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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/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 -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:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'ovFileOCW::ovFileOCW(sqStore*, const char*)' at stores/ovStoreFile.H:89:15, - inlined from 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)' at stores/ovStoreFile.C:221:47: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/tgTigMultiAlignDisplay.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::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); @@ -2708,22 +2630,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': -stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); - | ^~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); - | ^~~~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 143 | printSummary(out, "lenUnassembled", lenUnassembled); - | ^~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 144 | printSummary(out, "lenBubble", lenBubble); - | ^~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 145 | printSummary(out, "lenContig", lenContig); - | ^~~~~~~~~~~ stores/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); @@ -2750,6 +2656,23 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': +stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStore.C:59: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'ovStore::ovStore(const char*, sqStore*)' at stores/ovStore.C:109:11: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); @@ -2815,24 +2738,122 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 -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)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +stores/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=] + 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 9 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, + 361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | int +stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 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, + 361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | int +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +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:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'ovFileOCW::ovFileOCW(sqStore*, const char*)' at stores/ovStoreFile.H:89:15, + inlined from 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)' at stores/ovStoreFile.C:221:47: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __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 +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/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-i686/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +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 +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgTigMultiAlignDisplay.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-i686/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C stores/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/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': -stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/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); | ^~~~~~~~~~~~~~~~~~~~ @@ -2880,10 +2901,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': -stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 stores/tgStore.C: In member function 'void tgStore::dumpMASR(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); @@ -2900,7 +2918,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 +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)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d stores/tgStore.C: In member function 'void tgStore::loadMASR(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); @@ -2949,6 +2974,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': +stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': +stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function '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); @@ -2965,8 +2998,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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++; @@ -2985,13 +3016,13 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -3004,6 +3035,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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=] @@ -3049,22 +3083,13 @@ utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 838 | display("NDalign::realignBackward()-- ", displayAlign); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 -gfa/gfa.C: In member function 'void gfaSequence::load(char*)': -gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 123 | findGFAtokenI(_features, "LN:i:", _length); - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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-i686/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 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"); @@ -3072,6 +3097,16 @@ stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 128 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gfa/gfa.C: In member function 'void gfaSequence::load(char*)': +gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 123 | findGFAtokenI(_features, "LN:i:", _length); + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 stores/ovStoreConfig.C: In member function 'void ovStoreConfig::assignReadsToSlices(sqStore*, uint64, uint64)': stores/ovStoreConfig.C:288:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 288 | fprintf(stderr, "ERROR: expected %u slices, generated %u instead. %lu overlaps per slice allowed.\n", @@ -3099,15 +3134,6 @@ 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-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C -stores/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/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"); @@ -3131,9 +3157,14 @@ 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/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] - 675 | #warning replace this with genericStatistics - | ^~~~~~~ +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-i686/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/ovStoreDump.C:56: @@ -3144,6 +3175,17 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-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 +stores/ovStoreDump.C: In function 'int main(int, char**)': +stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreStats.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -3173,54 +3215,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -stores/ovStoreDump.C: In function 'int main(int, char**)': -stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 -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); - | ~~^ - | | - | long unsigned int - | %llu -sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); - | ~~^ ~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector)': -sequence/sequence-summarize.C:120:24: 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=] - 120 | fprintf(stdout, "%lu\n", lengths[ii]); - | ~~^ - | | - | long unsigned int - | %llu -sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': -sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ - | | - | std::vector::size_type {aka unsigned int} -sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ - | | - | std::vector::size_type {aka unsigned int} -sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ - | | - | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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-i686/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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/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); @@ -3228,52 +3223,6 @@ stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); | ^~~~~~~ -stores/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=] - 226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 232 | seqs->sqStore_getReadByte(rid)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -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 -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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/tgStoreCompress.C:45: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from stores/tgTig.H:36, - from stores/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-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C stores/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); @@ -3329,6 +3278,96 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +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=] + 226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 232 | seqs->sqStore_getReadByte(rid)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +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 +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 +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); + | ~~^ + | | + | long unsigned int + | %llu +sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); + | ~~^ ~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector)': +sequence/sequence-summarize.C:120:24: 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=] + 120 | fprintf(stdout, "%lu\n", lengths[ii]); + | ~~^ + | | + | long unsigned int + | %llu +sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': +sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ + | | + | std::vector::size_type {aka unsigned int} +sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ + | | + | std::vector::size_type {aka unsigned int} +sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ + | | + | std::vector::size_type {aka unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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/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-i686/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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-i686/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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 +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"); @@ -3345,8 +3384,7 @@ stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 1178 | err.push_back("No DUMP TYPE supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C In file included from stores/tgTig.H:36, from stores/tgTigSizeAnalysis.H:41, from stores/tgTigSizeAnalysis.C:42: @@ -3357,7 +3395,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/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/tgStoreLoad.C:33: @@ -3394,8 +3431,6 @@ stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgTigDisplay.C:33: @@ -3416,14 +3451,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] - 261 | #warning HARD CODED NUMBER OF FILES! - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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/loadTrimmedReads.C: In function 'int main(int, char**)': -stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-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 stores/tgTig.H:36, from stores/tgStore.H:43, from stores/loadCorrectedReads.C:29: @@ -3434,18 +3462,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadCorrectedReads.C: In function 'int main(int, char**)': stores/loadCorrectedReads.C:76:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 76 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); @@ -3461,17 +3477,27 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -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 +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadErates.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C +meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] + 261 | #warning HARD CODED NUMBER OF FILES! + | ^~~~~~~ +stores/loadTrimmedReads.C: In function 'int main(int, char**)': +stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C: In 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-i686/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -3554,67 +3580,10 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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/merylInput.C:26: + 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); @@ -3622,23 +3591,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ~^~~~~~~~~~~~~~~~~~ -meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 52 | if (_stream) return("meryl-database"); - | ~^~~~~~~~~~~~~~~~~ -meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | if (_sequence) return("sequence-file"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | if (_store) return("canu-seqStore"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 58 | return("invalid-input"); - | ~^~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 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", @@ -3694,26 +3646,7 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, - from meryl/meryl.H:49: -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); - | ^~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -3730,13 +3663,6 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -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-amd64/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 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); @@ -3769,20 +3695,7 @@ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp-count.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-countSimple.C:26: + from meryl/merylInput.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -3790,7 +3703,26 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 /build/canu-2.0+dfsg/src/AS_global.H:89, + from meryl/meryl.H:49: +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); + | ^~~~~~~~~~ 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", @@ -3846,7 +3778,89 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ~^~~~~~~~~~~~~~~~~~ +meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 52 | if (_stream) return("meryl-database"); + | ~^~~~~~~~~~~~~~~~~ +meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | if (_sequence) return("sequence-file"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | if (_store) return("canu-seqStore"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 58 | return("invalid-input"); + | ~^~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 +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:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from meryl/meryl.H:49: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:331:13: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/meryl.C: In function 'int main(int, char**)': +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 function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:332:13: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/meryl.C: In function 'int main(int, char**)': +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 function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:333:13: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/meryl.C: In function 'int main(int, char**)': +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 function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:594:15: +/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp-count.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu 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", @@ -3918,23 +3932,6 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ~^~~~~~~~~~~~~~~~~~ -meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 52 | if (_stream) return("meryl-database"); - | ~^~~~~~~~~~~~~~~~~ -meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | if (_sequence) return("sequence-file"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | if (_store) return("canu-seqStore"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 58 | return("invalid-input"); - | ~^~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 meryl/merylOp-count.C: In function 'uint64 findMaxInputSizeForMemorySize(uint32, uint64)': meryl/merylOp-count.C:69:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 69 | fprintf(stderr, "For memory size %lu bytes\n", memSize); @@ -4082,6 +4079,89 @@ | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp-countSimple.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 +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} +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ~^~~~~~~~~~~~~~~~~~ +meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 52 | if (_stream) return("meryl-database"); + | ~^~~~~~~~~~~~~~~~~ +meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | if (_sequence) return("sequence-file"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | if (_store) return("canu-seqStore"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 58 | return("invalid-input"); + | ~^~~~~~~~~~~~~~~~ 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", @@ -4114,7 +4194,16 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %016llx -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-i686/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 +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-i686/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-i686/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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, @@ -4137,17 +4226,6 @@ | | | | 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/merylOp.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu 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", @@ -4290,10 +4368,56 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ +meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()': +meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold); + | ~~^ ~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold); + | ~~^ ~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()': +meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", + | ~~^ + | | + | long unsigned int + | %llu + 613 | _kmer.toString(str), _actCount[0], _actCount[1]); + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", + | ~~^ + | | + | long unsigned int + | %llu + 613 | _kmer.toString(str), _actCount[0], _actCount[1]); + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C +In file included from utility/kmers.H:32, + from meryl/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: + from meryl/merylOp.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4356,21 +4480,9 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()': -meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold); - | ~~^ ~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold); - | ~~^ ~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu +In file included from meryl/meryl.H:51, + from meryl/merylCountArray.H:29, + from meryl/meryl-import.C:31: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4387,36 +4499,6 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()': -meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", - | ~~^ - | | - | long unsigned int - | %llu - 613 | _kmer.toString(str), _actCount[0], _actCount[1]); - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", - | ~~^ - | | - | long unsigned int - | %llu - 613 | _kmer.toString(str), _actCount[0], _actCount[1]); - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from meryl/meryl-import.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu 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", @@ -4488,6 +4570,34 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ +meryl/meryl-import.C: In function 'int main(int, char**)': +meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 92 | err.push_back("No input kmer file (-kmers) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 94 | err.push_back("No output database name (-output) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 96 | err.push_back("No kmer size (-k) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers); + | ~~^ ~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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/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 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", @@ -4543,18 +4653,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -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.H:51, - from meryl/merylCountArray.H:29, - from meryl/meryl-import.C:31: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4571,6 +4669,16 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C +In file included from utility/kmers.H:32, + from meryl/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 /build/canu-2.0+dfsg/src/AS_global.H:89, from meryl/meryl.H:49: meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': @@ -4591,39 +4699,6 @@ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ -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 -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 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", @@ -4679,7 +4754,7 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 meryl/meryl-lookup.C: In function 'void dumpExistence(dnaSeqFile*, compressedFileWriter*, std::vector&, std::vector&)': meryl/meryl-lookup.C:83:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 83 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\n", @@ -4767,75 +4842,24 @@ 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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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()); - | ^~~~~~~ -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:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from meryl/meryl.H:49: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:331:13: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -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 function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:332:13: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -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 function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:333:13: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -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 function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:594:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -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-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-amd64/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-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()); @@ -4847,8 +4871,17 @@ 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-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-generate.C: In function 'void doGenerate(generateParameters&)': +sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 92 | ">random%08 " F_U64P "\n", nSeqs); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 +sequence/sequence-mutate.C: In function 'void doMutate(std::vector&, mutateParameters&)': +sequence/sequence-mutate.C:160:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 160 | AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name()); + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 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=] @@ -4857,6 +4890,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C In file included from 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=] @@ -4910,53 +4944,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 sequence/sequence-shiftregister-search-slow.C:29: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -sequence/sequence-shiftregister-search-slow.C: In function 'void searchShiftRegisterSlow(shiftRegisterParameters&)': -sequence/sequence-shiftregister-search-slow.C:154:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 154 | fprintf(stderr, " cyclen %lu\n", cyclen); - | ~~^ ~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -sequence/sequence-shiftregister-search-slow.C:155:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 155 | fprintf(stderr, " cycmax %lu\n", cycmax); - | ~~^ ~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -sequence/sequence-shiftregister-search-slow.C:209:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n", - | ~~~~^ - | | - | long unsigned int - | %14llu - 210 | cyclen, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -sequence/sequence-shiftregister-search-slow.C:209:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n", - | ~~~~^ - | | - | long unsigned int - | %14llu - 210 | cyclen, - 211 | cycmax, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C In file included from sequence/sequence-shiftregister-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=] @@ -5036,39 +5027,51 @@ | ~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': -sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 44 | char *path = findSharedFile("share/sequence", distribName); - | ^~~~~~~~~~~~~~~~ -sequence/sequence-simulate.C: In function 'void doSimulate_loadSequences(simulateParameters&, std::vector&, uint64&)': -sequence/sequence-simulate.C:89:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 89 | fprintf(stderr, "Loaded %lu sequences.\n", seqs.size()); - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector::size_type {aka unsigned int} - | %u -sequence/sequence-simulate.C: In function 'void doSimulate_extract(simulateParameters&, std::vector&, uint64, mtRandom&, uint64, uint64)': -sequence/sequence-simulate.C:194:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n", - | ~~^ - | | - | long unsigned int - | %llu - 195 | nReads+1, - | ~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -sequence/sequence-simulate.C:194:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n", - | ~~^ - | | - | long unsigned int - | %llu -...... - 197 | position, - | ~~~~~~~~ +In file included from sequence/sequence-shiftregister-search-slow.C:29: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +sequence/sequence-shiftregister-search-slow.C: In function 'void searchShiftRegisterSlow(shiftRegisterParameters&)': +sequence/sequence-shiftregister-search-slow.C:154:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 154 | fprintf(stderr, " cyclen %lu\n", cyclen); + | ~~^ ~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +sequence/sequence-shiftregister-search-slow.C:155:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 155 | fprintf(stderr, " cycmax %lu\n", cycmax); + | ~~^ ~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +sequence/sequence-shiftregister-search-slow.C:209:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n", + | ~~~~^ + | | + | long unsigned int + | %14llu + 210 | cyclen, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +sequence/sequence-shiftregister-search-slow.C:209:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n", + | ~~~~^ + | | + | long unsigned int + | %14llu + 210 | cyclen, + 211 | cycmax, + | ~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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: 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); @@ -5089,6 +5092,10 @@ | | | long unsigned int | %llu +sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': +sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 44 | char *path = findSharedFile("share/sequence", distribName); + | ^~~~~~~~~~~~~~~~ sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! @@ -5105,12 +5112,40 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C +sequence/sequence-simulate.C: In 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()); + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector::size_type {aka unsigned int} + | %u +sequence/sequence-simulate.C: In function 'void doSimulate_extract(simulateParameters&, std::vector&, uint64, mtRandom&, uint64, uint64)': +sequence/sequence-simulate.C:194:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n", + | ~~^ + | | + | long unsigned int + | %llu + 195 | nReads+1, + | ~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +sequence/sequence-simulate.C:194:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n", + | ~~^ + | | + | long unsigned int + | %llu +...... + 197 | position, + | ~~~~~~~~ + | | + | uint64 {aka long long unsigned int} In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore.C:51: + from overlapInCore/overlapInCore-Build_Hash_Index.C:67: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5118,11 +5153,12 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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: + 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); @@ -5130,6 +5166,12 @@ | | | | 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-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5142,12 +5184,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -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-i686/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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, @@ -5172,9 +5209,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5187,12 +5221,13 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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"); @@ -5212,9 +5247,8 @@ overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 447 | renameToFinal(outputPrefix, "ovlopt"); | ^~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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"); @@ -5228,6 +5262,11 @@ overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, @@ -5239,8 +5278,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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, @@ -5260,7 +5297,6 @@ overlapInCore/overlapPair.C:507:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 507 | aRead, abgn, aend, alen, "Ab5", aID, | ^~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 overlapInCore/overlapPair.C:532:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 532 | if (extendAlignment(aRead, abgn, aend, alen, "Aa5", aID, | ^~~~~ @@ -5279,10 +5315,9 @@ overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 587 | aRead, abgn, aend, alen, "Ab3", aID, | ^~~~~ -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-i686/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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", @@ -5316,6 +5351,7 @@ | ~~~~~~~~~~~~~~~ | | | int +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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", @@ -5349,11 +5385,11 @@ | ~~~~~~~~~~~~~~~ | | | int -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 wtdbg/wtdbgConvert.C:33: + 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); @@ -5361,11 +5397,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 stores/tgTig.H:36, from stores/tgStore.H:43, - from utgcns/stashContains.H:35, - from utgcns/stashContains.C:30: + from wtdbg/wtdbgConvert.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5383,7 +5417,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 correction/generateCorrectionLayouts.C: In function 'void generateLayout(tgTig*, uint16*, uint32, double, double, ovOverlap*, uint32, FILE*)': correction/generateCorrectionLayouts.C:118:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 118 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - low quality (threshold %.2f)\n", @@ -5432,10 +5465,11 @@ | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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, - from utgcns/stashContains.C:30: + from correction/filterCorrectionLayouts.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5443,10 +5477,12 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from correction/filterCorrectionLayouts.C:29: + from stores/sqCache.H:30, + from correction/falconsense.C:32: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -5454,12 +5490,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from stores/sqCache.H:30, - from correction/falconsense.C:32: + 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); @@ -5467,7 +5501,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 utility/kmers.H:32, from haplotyping/splitHaplotype.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -5477,63 +5511,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)': -overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 480 | readsIn .generatePlots(outputPrefix, "inputReads", 250); - | ^~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); - | ^~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250); - | ^~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); - | ^~~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); - | ^~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250); - | ^~~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250); - | ^~~~~~~~~~~~~~~~~~~~~~ -overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 503 | trim5.generatePlots(outputPrefix, "trim5", 25); - | ^~~~~~~ -overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 504 | trim3.generatePlots(outputPrefix, "trim3", 25); - | ^~~~~~~ -In file included from correction/errorEstimate.C:34: -utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': -utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~~~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); - | ~~^ ~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu 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", @@ -5589,12 +5566,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from overlapBasedTrimming/trimReads.C:31: -overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': -overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 74 | system(N); - | ~~~~~~^~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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); @@ -5608,6 +5579,42 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %10llu +correction/falconsense.C: In function 'int main(int, char**)': +correction/falconsense.C:359:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 359 | err.push_back("ERROR: no seqStore input (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from correction/errorEstimate.C:34: +utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': +utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~~~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu haplotyping/splitHaplotype.C: In member function 'void hapData::initializeKmerTable(uint32)': haplotyping/splitHaplotype.C:443:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 443 | fprintf(stderr, "-- loaded %lu kmers.\n", nKmers); @@ -5616,13 +5623,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -correction/falconsense.C: In function 'int main(int, char**)': -correction/falconsense.C:359:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 359 | err.push_back("ERROR: no seqStore input (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplotyping/splitHaplotype.C: In function 'void outputReadBatch(void*, void*)': haplotyping/splitHaplotype.C:707:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 707 | ">%s\n", s->_names[ii].string()); @@ -5655,7 +5655,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %12llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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); @@ -5663,25 +5662,60 @@ correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fgets(L, 1024, R)) { | ~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)': +overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 480 | readsIn .generatePlots(outputPrefix, "inputReads", 250); + | ^~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); + | ^~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250); + | ^~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); + | ^~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); + | ^~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250); + | ^~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250); + | ^~~~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 503 | trim5.generatePlots(outputPrefix, "trim5", 25); + | ^~~~~~~ +overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 504 | trim3.generatePlots(outputPrefix, "trim3", 25); + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 overlapBasedTrimming/trimReads.C:31: +overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': +overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 74 | system(N); + | ~~~~~~^~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)': overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 77 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, - from overlapAlign/computeOverlapAlignment.C:32: + from overlapAlign/overlapAlign.C:39: 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); @@ -5689,11 +5723,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, - from overlapAlign/overlapAlign.C:39: + from overlapAlign/computeOverlapAlignment.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); @@ -5726,8 +5759,9 @@ 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-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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, @@ -5739,6 +5773,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5750,20 +5785,19 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)': overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID); | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C overlapErrorAdjustment/findErrors-Dump.C: In function 'int main(int, char**)': overlapErrorAdjustment/findErrors-Dump.C:66:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 66 | char *typeName[13] = { "IDENT", @@ -5801,19 +5835,14 @@ 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-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] - 486 | #warning deviationGraph hard coded - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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_AssemblyGraph.H:32, - from bogart/bogart.C:46: + from bogart/AS_BAT_AssemblyGraph.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); @@ -5842,32 +5871,13 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -bogart/bogart.C: In function 'int main(int, char**)': -bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 736 | writeTigsToStore(contigs, prefix, "ctg", true); - | ^~~~~ -bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 756 | writeTigsToStore(unitigs, prefix, "utg", true); - | ^~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_AssemblyGraph.C:28: + from bogart/bogart.C:46: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -5896,6 +5906,22 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +bogart/bogart.C: In function 'int main(int, char**)': +bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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()': @@ -5926,8 +5952,12 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C +bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 736 | writeTigsToStore(contigs, prefix, "ctg", true); + | ^~~~~ +bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 756 | writeTigsToStore(unitigs, prefix, "utg", true); + | ^~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_CreateUnitigs.C:29: @@ -5959,8 +5989,11 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_Instrumentation.C:43: + 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); @@ -5989,8 +6022,12 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_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); @@ -6019,9 +6056,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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_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); @@ -6050,12 +6087,9 @@ | | 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); - | ^~~~~ In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_MergeOrphans.C:35: + 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); @@ -6084,30 +6118,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C -bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': -bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int -bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int +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); @@ -6128,10 +6142,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +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 +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 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); @@ -6160,16 +6181,8 @@ | | 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 -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_OptimizePositions.C:44: + from bogart/AS_BAT_MergeOrphans.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6198,9 +6211,29 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': +bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int 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()': @@ -6271,6 +6304,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PlaceContains.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6301,7 +6337,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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_PlaceReadUsingOverlaps.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6318,8 +6355,22 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_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); @@ -6327,13 +6378,6 @@ | | | | long unsigned int uint64 {aka long 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: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); | ~~^ ~~~~~~~~~~~~~ @@ -6341,13 +6385,6 @@ | | 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 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); | ~~^ ~~~~~~~ @@ -6362,9 +6399,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_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); @@ -6393,7 +6429,11 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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_SetParentAndHang.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6424,10 +6464,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SplitDiscontinuous.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6489,6 +6525,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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_TigVector.C:28: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6519,10 +6556,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-amd64/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig.C:39: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6553,7 +6586,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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-i686/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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()': @@ -6584,40 +6620,18 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-amd64/bin/canu -chmod +x /build/canu-2.0+dfsg/Linux-amd64/bin/canu -cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-amd64/bin/canu-time -chmod +x /build/canu-2.0+dfsg/Linux-amd64/bin/canu-time -echo > /build/canu-2.0+dfsg/Linux-amd64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." -chmod -x /build/canu-2.0+dfsg/Linux-amd64/bin/canu.defaults -cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-amd64/share/sequence/ultra-long-nanopore -cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-amd64/share/sequence/pacbio -cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-amd64/share/sequence/pacbio-hifi -cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -g++ -o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from utgcns/utgcns.C:46: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6648,27 +6662,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from utgcns/stashContains.H:35, - from utgcns/stashContains.C:30: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from utgcns/utgcns.C:46: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu 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", @@ -6762,6 +6755,64 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +utgcns/utgcns.C: In function 'int main(int, char**)': +utgcns/utgcns.C:887:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 887 | err.push_back("ERROR: No sequence data! Need one of seqStore (-S), read file (-R) or package (-p).\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 stores/tgTig.H:36, + from stores/tgStore.H:43, + from utgcns/stashContains.H:35, + from utgcns/stashContains.C:30: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +bogus/bogusUtil.C: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': +bogus/bogusUtil.C:125:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 125 | fgets(inLine, 1024, inFile); // (file paths) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +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 gfa/alignGFA.C:32: @@ -6772,13 +6823,15 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -utgcns/utgcns.C: In function 'int main(int, char**)': -utgcns/utgcns.C:887:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 887 | err.push_back("ERROR: No sequence data! Need one of seqStore (-S), read file (-R) or package (-p).\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-i686/bin/canu +chmod +x /build/canu-2.0+dfsg/Linux-i686/bin/canu +cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-i686/bin/canu-time +chmod +x /build/canu-2.0+dfsg/Linux-i686/bin/canu-time +echo > /build/canu-2.0+dfsg/Linux-i686/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." +chmod -x /build/canu-2.0+dfsg/Linux-i686/bin/canu.defaults +cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-i686/share/sequence/ultra-long-nanopore +cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-i686/share/sequence/pacbio +cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-i686/share/sequence/pacbio-hifi 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", @@ -6789,14 +6842,50 @@ gfa/alignGFA.C:541:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 541 | success &= checkRecord_align("RIGHT", | ^~~~~~~ +cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, double, uint32)': gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0"); | ^~~~~~~~~~~~~ +cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | system(Pfile); | ~~~~~~^~~~~~~ +cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ +g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/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 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); | ^~ ~~~~~ @@ -6838,178 +6927,128 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ar rv /build/canu-2.0+dfsg/Linux-amd64/lib/libcanu.a /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -ar: creating /build/canu-2.0+dfsg/Linux-amd64/lib/libcanu.a -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -a - /build/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -a - 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-Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib 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/build/canu-2.0+dfsg/Linux-amd64/bin/tgStoreFilter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/loadCorrectedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/meryl-import.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-summarize.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu -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 -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-amd64/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-amd64/lib /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu +ar rv /build/canu-2.0+dfsg/Linux-i686/lib/libcanu.a /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTig.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o 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/build/canu-2.0+dfsg/Linux-i686/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/correction/falconsense.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/utgcns/stashContains.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogusUtil.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/alignGFA/gfa/alignGFA.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu Success! -canu installed in /build/canu-2.0+dfsg/Linux-amd64/bin/canu +canu installed in /build/canu-2.0+dfsg/Linux-i686/bin/canu make[2]: Leaving directory '/build/canu-2.0+dfsg/src' builddir=*-*/; \ find $builddir \ @@ -7048,8 +7087,8 @@ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ -dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-2_i386.deb'. dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-2_i386.deb'. +dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../canu_2.0+dfsg-2_i386.buildinfo dpkg-genchanges --build=binary -O../canu_2.0+dfsg-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -7057,12 +7096,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/30765/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30765/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/51622 and its subdirectories -I: Current time: Mon May 20 10:13:34 -12 2024 -I: pbuilder-time-stamp: 1716243214 +I: removing directory /srv/workspace/pbuilder/30765 and its subdirectories +I: Current time: Wed Apr 19 05:55:47 +14 2023 +I: pbuilder-time-stamp: 1681833347