Diff of the two buildlogs: -- --- b1/build.log 2021-04-07 06:45:15.906701190 +0000 +++ b2/build.log 2021-04-07 06:47:29.597484929 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 6 18:42:29 -12 2021 -I: pbuilder-time-stamp: 1617777749 +I: Current time: Wed May 11 03:08:22 +14 2022 +I: pbuilder-time-stamp: 1652188102 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sun Dec 2 21:35:47 2018 -12 +gpgv: Signature made Mon Dec 3 23:35:47 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying tell_version_properly.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/52717/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/61697/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/61697/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/61697/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3fac25298d1d4b52b9240e7208263769' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='52717' - PS1='# ' - PS2='> ' + INVOCATION_ID=01c70218c0c4438cbe7c0dbc72283a63 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=61697 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/pbuilderrc_lKFJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/b1 --logfile b1/build.log canu_1.8+dfsg-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/pbuilderrc_6eog --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.1c9zZcAaaL/b2 --logfile b2/build.log canu_1.8+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.4-amd64 #1 SMP Debian 5.10.19-1~bpo10+1 (2021-03-13) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Mar 20 20:25 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/52717/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 May 11 03:08 sh -> bash + lrwxrwxrwx 1 root root 4 Apr 24 04:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/61697/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -296,7 +330,7 @@ Get: 90 http://deb.debian.org/debian buster/main amd64 libmeryl-dev amd64 0~20150903+r2013-6 [53.6 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libssw-java amd64 1.1-2 [13.8 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 mhap all 2.1.3+dfsg-2 [160 kB] -Fetched 94.1 MB in 2s (45.2 MB/s) +Fetched 94.1 MB in 1s (65.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -850,7 +884,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/canu-1.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/canu-1.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 1.8+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -860,12 +894,12 @@ fakeroot debian/rules clean dh clean --sourcedirectory=src/ dh_auto_clean -O--sourcedirectory=src/ - cd src && make -j15 clean + cd src && make -j16 clean make[1]: Entering directory '/build/canu-1.8+dfsg/src' WARNING: WARNING: g++ 8 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: -Building for 'Linux' '4.19.0-16-amd64' as 'amd64' into '/build/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. +Building for 'Linux' '5.10.0-0.bpo.4-amd64' as 'amd64' into '/build/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '8'. rm -f /build/canu-1.8+dfsg/Linux-amd64/lib/libcanu.a /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.[doP] /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.[doP] @@ -933,42 +967,35 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-1.8+dfsg' dh_auto_build - cd src && make -j15 "INSTALL=install --strip-program=true" + cd src && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/canu-1.8+dfsg/src' WARNING: WARNING: g++ 8 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: -Building for 'Linux' '4.19.0-16-amd64' as 'amd64' into '/build/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. +Building for 'Linux' '5.10.0-0.bpo.4-amd64' as 'amd64' into '/build/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '8'. g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-compressed.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-buffered.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-compressed.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-memoryMapped.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/strings.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system-stackTrace.C -Building release v1.8 - g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sequence.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-reader.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer.C +Building release v1.8 + g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer-block.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer-stream.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-statistics.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-exact.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/bits.C utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] #warning how to set prefix size for streaming operations? ^~~~~~~ -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] - 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] - write(_fd, _data, _length), close(_fd); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utility/sequence.H:29, from utility/sequence.C:30: @@ -990,23 +1017,14 @@ utility/sequence.C:154:7: note: 'class dnaSeqIndexEntry' declared here class dnaSeqIndexEntry { ^~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/bits.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/hexDump.C -utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': -utility/kmers-writer.C:136:29: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); - ^~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from utility/kmers.H:29, - from utility/kmers-writer.C:26: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/md5.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/mt19937ar.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] + 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] + write(_fd, _data, _length), close(_fd); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': utility/kmers-reader.C:39:29: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); @@ -1031,7 +1049,23 @@ utility/files.C:515:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, FILENAME_MAX, F); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/hexDump.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/md5.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/mt19937ar.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/objectStore.C +utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': +utility/kmers-writer.C:136:29: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); + ^~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from utility/kmers.H:29, + from utility/kmers-writer.C:26: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/speedCounter.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sweatShop.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/computeGlobalScore.C @@ -1043,15 +1077,15 @@ g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreInfo.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreEncode.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStorePartition.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovOverlap.C correction/computeGlobalScore.C: In member function 'uint16 globalScore::compute(uint32, ovOverlap*, uint32, uint32, uint16*)': correction/computeGlobalScore.C:150:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (logFile) ^ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovOverlap.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStore.C stores/ovOverlap.C:184:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStore.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreWriter.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFilter.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, @@ -1104,12 +1138,10 @@ stores/sqRead.H:206:7: note: 'class sqRead' declared here class sqRead { ^~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFile.C stores/ovStoreWriter.C:69:2: warning: #warning not failing if a valid store [-Wcpp] #warning not failing if a valid store ^~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFile.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreHistogram.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgStore.C stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:252:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); @@ -1230,6 +1262,8 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreHistogram.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgStore.C stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_deletePartitions()': stores/sqStoreConstructor.C:399:32: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s/partitions/map", _storePath); @@ -1330,6 +1364,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTig.C In file included from stores/sqStore.H:89, from stores/sqStore.C:38: stores/sqStoreBlobWriter.H: In member function 'void sqStore::sqStore_stashReadData(sqReadData*)': @@ -1345,177 +1380,178 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C: In member function 'void sqStore::sqStore_buildPartitions(uint32*)': -stores/sqStorePartition.C:93:32: warning: '/partitions' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(name, FILENAME_MAX, "%s/partitions", _clonePath); - ^~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C +stores/sqStoreConstructor.C: In constructor 'sqStore::sqStore(const char*, const char*, sqStore_mode, uint32)': +stores/sqStoreConstructor.C:109:33: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(nameI, FILENAME_MAX, "%s/info", _storePath); + ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStorePartition.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + from stores/sqStoreConstructor.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:106:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:106:34: note: using the range [-2147483648, 2147483647] for directive argument +stores/sqStoreConstructor.C:202:33: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(nameI, FILENAME_MAX, "%s/partitions/map", _storePath); + ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStorePartition.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 + from stores/sqStoreConstructor.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4112 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:110:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:110:34: note: using the range [-2147483648, 2147483647] for directive argument +stores/sqStoreConstructor.C:221:33: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(nameL, FILENAME_MAX, "%s/libraries", _storePath); + ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStorePartition.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 + from stores/sqStoreConstructor.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/sqStore.H:88, - from stores/sqStorePartition.C:38: -stores/sqStoreBlobReader.H:66:33: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(N, FILENAME_MAX, "%s/blobs.%04u", storePath, file); - ^~~~~~~~~~~~~~~ +stores/sqStoreConstructor.C:222:33: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(nameR, FILENAME_MAX, "%s/partitions/reads.%04" F_U32P, _storePath, partID); +stores/sqStoreConstructor.C:222:33: note: directive argument in the range [0, 4294967294] In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStorePartition.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + from stores/sqStoreConstructor.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:197:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:197:34: note: using the range [-2147483648, 2147483647] for directive argument +stores/sqStoreConstructor.C:223:33: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(nameB, FILENAME_MAX, "%s/partitions/blobs.%04" F_U32P, _storePath, partID); +stores/sqStoreConstructor.C:223:33: note: directive argument in the range [0, 4294967294] In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStorePartition.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 + from stores/sqStoreConstructor.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:200:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i); - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStorePartition.C:200:34: note: using the range [-2147483648, 2147483647] for directive argument +In file included from stores/sqStore.H:89, + from stores/sqStoreConstructor.C:38: +stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStorePartition.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 + from stores/sqStoreConstructor.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreConstructor.C: In constructor 'sqStore::sqStore(const char*, const char*, sqStore_mode, uint32)': -stores/sqStoreConstructor.C:109:33: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(nameI, FILENAME_MAX, "%s/info", _storePath); - ^~~~~~~~~ +In file included from stores/sqStore.H:89, + from stores/sqStoreConstructor.C:38: +stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreConstructor.C:202:33: warning: '/partitions/map' directive output may be truncated writing 15 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(nameI, FILENAME_MAX, "%s/partitions/map", _storePath); - ^~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc +stores/sqStorePartition.C: In member function 'void sqStore::sqStore_buildPartitions(uint32*)': +stores/sqStorePartition.C:93:32: warning: '/partitions' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(name, FILENAME_MAX, "%s/partitions", _clonePath); + ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4112 bytes into a destination of size 4096 + from stores/sqStorePartition.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreConstructor.C:221:33: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(nameL, FILENAME_MAX, "%s/libraries", _storePath); - ^~~~~~~~~~~~~~ +stores/sqStorePartition.C:106:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/sqStorePartition.C:106:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 + from stores/sqStorePartition.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreConstructor.C:222:33: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(nameR, FILENAME_MAX, "%s/partitions/reads.%04" F_U32P, _storePath, partID); -stores/sqStoreConstructor.C:222:33: note: directive argument in the range [0, 4294967294] +stores/sqStorePartition.C:110:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/sqStorePartition.C:110:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 + from stores/sqStorePartition.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreConstructor.C:223:33: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(nameB, FILENAME_MAX, "%s/partitions/blobs.%04" F_U32P, _storePath, partID); -stores/sqStoreConstructor.C:223:33: note: directive argument in the range [0, 4294967294] +In file included from stores/sqStore.H:88, + from stores/sqStorePartition.C:38: +stores/sqStoreBlobReader.H:66:33: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(N, FILENAME_MAX, "%s/blobs.%04u", storePath, file); + ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 + from stores/sqStorePartition.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/sqStore.H:89, - from stores/sqStoreConstructor.C:38: -stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); +stores/sqStorePartition.C:197:34: warning: '/partitions/blobs.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(name, FILENAME_MAX, "%s/partitions/blobs.%04d", _clonePath, i); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/sqStorePartition.C:197:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + from stores/sqStorePartition.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/sqStore.H:89, - from stores/sqStoreConstructor.C:38: -stores/sqStoreBlobWriter.H:68:39: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , _storePath, _bufferCount); +stores/sqStorePartition.C:200:34: warning: '/partitions/reads.' directive output may be truncated writing 18 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(name, FILENAME_MAX, "%s/partitions/reads.%04d", _clonePath, i); + ^~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/sqStorePartition.C:200:34: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/sqStore.H:37, - from stores/sqStoreConstructor.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + from stores/sqStorePartition.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTig.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C In file included from stores/ovStore.C:55: stores/ovStore.H: In constructor 'ovStore::ovStore(const char*, sqStore*)': stores/ovStore.H:77:36: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -1542,9 +1578,45 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapErrorAdjustment/analyzeAlignment.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C +stores/ovStoreHistogram.C: In member function 'void ovStoreHistogram::mergeScores(ovStoreHistogram*)': +stores/ovStoreHistogram.C:303:80: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class oSH_ovlSco'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + sizeof(oSH_ovlSco) * (other->_scoresLastID - other->_scoresBaseID + 1)); + ^ +In file included from stores/ovStoreHistogram.C:30: +stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here + class oSH_ovlSco { + ^~~~~~~~~~ +stores/tgStore.C: In member function 'void tgStore::insertTig(tgTig*, bool)': +stores/tgStore.C:336:71: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct tgStore::tgStoreEntry'; use assignment or value-initialization instead [-Wclass-memaccess] + memset(nr + _tigLen, 0, sizeof(tgStoreEntry) * (_tigMax - _tigLen)); + ^ +In file included from stores/tgStore.C:44: +stores/tgStore.H:134:10: note: 'struct tgStore::tgStoreEntry' declared here + struct tgStoreEntry { + ^~~~~~~~~~~~ +stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': +stores/tgStore.C:634:42: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct tgStore::tgStoreEntry'; use assignment or value-initialization instead [-Wclass-memaccess] + memset(R, 0, sizeof(tgStoreEntry) * M); + ^ +In file included from stores/tgStore.C:44: +stores/tgStore.H:134:10: note: 'struct tgStore::tgStoreEntry' declared here + struct tgStoreEntry { + ^~~~~~~~~~~~ +In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, + from stores/ovStoreHistogram.H:33, + from stores/ovStoreHistogram.C:30: +utility/arrays.H: In instantiation of 'void allocateArray(TT*&, LL, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint32 = unsigned int]': +stores/ovStoreHistogram.C:282:62: required from here +utility/arrays.H:54:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class oSH_ovlSco'; use assignment or value-initialization instead [-Wclass-memaccess] + memset(array, 0, sizeof(TT) * arrayMax); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/ovStoreHistogram.C:30: +stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here + class oSH_ovlSco { + ^~~~~~~~~~ stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': stores/ovStoreWriter.C:226:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); @@ -1570,6 +1642,21 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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:89:37: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s.oc", prefix); + ^~~~~~~ +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/ovStore.H:37, + from stores/ovStoreFile.C:47: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': stores/ovStoreWriter.C:258:32: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); @@ -1583,7 +1670,29 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C +In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, + from stores/ovStoreHistogram.H:33, + from stores/ovStoreHistogram.C:30: +utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': +utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' +stores/ovStoreHistogram.C:318:112: required from here +utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class oSH_ovlSco'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + memcpy(copy, array, sizeof(TT) * arrayLen); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/ovStoreHistogram.C:30: +stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here + class oSH_ovlSco { + ^~~~~~~~~~ +In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, + from stores/ovStoreHistogram.H:33, + from stores/ovStoreHistogram.C:30: +utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class oSH_ovlSco'; use assignment or value-initialization instead [-Wclass-memaccess] + memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/ovStoreHistogram.C:30: +stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here + class oSH_ovlSco { + ^~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': stores/ovStoreWriter.C:342:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); @@ -1610,15 +1719,57 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C -stores/ovStoreHistogram.C: In member function 'void ovStoreHistogram::mergeScores(ovStoreHistogram*)': -stores/ovStoreHistogram.C:303:80: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class oSH_ovlSco'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - sizeof(oSH_ovlSco) * (other->_scoresLastID - other->_scoresBaseID + 1)); - ^ -In file included from stores/ovStoreHistogram.C:30: -stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here - class oSH_ovlSco { - ^~~~~~~~~~ +stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': +stores/tgStore.C:191:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:192:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:193:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)': +stores/tgStore.C:594:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C In file included from stores/ovStoreWriter.C:54: stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': stores/ovStore.H:79:36: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -1658,77 +1809,81 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': +stores/tgStore.C:626:37: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); + ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:637:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:641:35: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument +In file included from /usr/include/stdio.h:873, + from /build/canu-1.8+dfsg/src/AS_global.H:75, + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, - from stores/ovStoreHistogram.H:33, - from stores/ovStoreHistogram.C:30: -utility/arrays.H: In instantiation of 'void allocateArray(TT*&, LL, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint32 = unsigned int]': -stores/ovStoreHistogram.C:282:62: required from here -utility/arrays.H:54:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class oSH_ovlSco'; use assignment or value-initialization instead [-Wclass-memaccess] - memset(array, 0, sizeof(TT) * arrayMax); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/ovStoreHistogram.C:30: -stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here - class oSH_ovlSco { - ^~~~~~~~~~ -In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, - from stores/ovStoreHistogram.H:33, - from stores/ovStoreHistogram.C:30: -utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': -utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = oSH_ovlSco; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' -stores/ovStoreHistogram.C:318:112: required from here -utility/arrays.H:109:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class oSH_ovlSco'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - memcpy(copy, array, sizeof(TT) * arrayLen); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/ovStoreHistogram.C:30: -stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here - class oSH_ovlSco { - ^~~~~~~~~~ -In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, - from stores/ovStoreHistogram.H:33, - from stores/ovStoreHistogram.C:30: -utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class oSH_ovlSco'; use assignment or value-initialization instead [-Wclass-memaccess] + from stores/tgTig.H:33, + from stores/tgTig.C:34: +utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': +utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' +stores/tgTig.C:455:87: required from here +utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class tgPosition'; use assignment or value-initialization instead [-Wclass-memaccess] memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/ovStoreHistogram.C:30: -stores/ovStoreHistogram.H:50:7: note: 'class oSH_ovlSco' declared here - class oSH_ovlSco { +In file included from stores/tgTig.C:34: +stores/tgTig.H:87:7: note: 'class tgPosition' declared here + class tgPosition { ^~~~~~~~~~ -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:89:37: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s.oc", prefix); - ^~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C +stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': +stores/tgStore.C:695:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); + ^~~~~~~~~~~~~~~~~~~~ +stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/ovStore.H:37, - from stores/ovStoreFile.C:47: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 + from stores/tgStore.C:42: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C: In member function 'void tgStore::insertTig(tgTig*, bool)': -stores/tgStore.C:336:71: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct tgStore::tgStoreEntry'; use assignment or value-initialization instead [-Wclass-memaccess] - memset(nr + _tigLen, 0, sizeof(tgStoreEntry) * (_tigMax - _tigLen)); - ^ -In file included from stores/tgStore.C:44: -stores/tgStore.H:134:10: note: 'struct tgStore::tgStoreEntry' declared here - struct tgStoreEntry { - ^~~~~~~~~~~~ -stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': -stores/tgStore.C:634:42: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct tgStore::tgStoreEntry'; use assignment or value-initialization instead [-Wclass-memaccess] - memset(R, 0, sizeof(tgStoreEntry) * M); - ^ -In file included from stores/tgStore.C:44: -stores/tgStore.H:134:10: note: 'struct tgStore::tgStoreEntry' declared here - struct tgStoreEntry { - ^~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': +stores/tgTig.C:560:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(LINE, LINEmax, F); LINEnum++; + ~~~~~^~~~~~~~~~~~~~~~~~ +stores/tgTig.C:687:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(LINE, LINEmax, F); LINEnum++; + ~~~~~^~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': stores/ovStoreWriter.C:484:34: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C In file included from /usr/include/stdio.h:873, from /build/canu-1.8+dfsg/src/AS_global.H:75, from stores/ovStore.H:37, @@ -1763,6 +1918,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:535:34: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); @@ -1824,128 +1980,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, - from stores/tgTig.H:33, - from stores/tgTig.C:34: -utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': -utility/arrays.H:145:15: required from 'void resizeArray(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]' -stores/tgTig.C:455:87: required from here -utility/arrays.H:115:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class tgPosition'; use assignment or value-initialization instead [-Wclass-memaccess] - memset(array + arrayLen, 0, sizeof(TT) * (arrayMax - arrayLen)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.C:34: -stores/tgTig.H:87:7: note: 'class tgPosition' declared here - class tgPosition { - ^~~~~~~~~~ -stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': -stores/tgStore.C:191:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:192:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:193:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)': -stores/tgStore.C:594:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': -stores/tgStore.C:626:37: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); - ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:637:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:641:35: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C -stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': -stores/tgTig.C:560:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(LINE, LINEmax, F); LINEnum++; - ~~~~~^~~~~~~~~~~~~~~~~~ -stores/tgTig.C:687:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(LINE, LINEmax, F); LINEnum++; - ~~~~~^~~~~~~~~~~~~~~~~~ -stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': -stores/tgStore.C:695:33: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); - ^~~~~~~~~~~~~~~~~~~~ -stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument -In file included from /usr/include/stdio.h:873, - from /build/canu-1.8+dfsg/src/AS_global.H:75, - from stores/tgStore.C:42: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/libedlib/edlib.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C @@ -1962,11 +1996,11 @@ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-mergeRefine.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refine.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refreshMultiAlign.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abColumn.C utgcns/libcns/abAbacus-refine.C:1326:2: warning: #warning SKIPPING ALL REFINEMENTS [-Wcpp] #warning SKIPPING ALL REFINEMENTS ^~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abColumn.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abMultiAlign.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utgcns/libcns/abAbacus.H:60, @@ -1993,7 +2027,6 @@ utgcns/libcns/abBead.H:61:7: note: 'class abBead' declared here class abBead { ^~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/unitigConsensus.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from utgcns/libcns/abAbacus.H:60, from utgcns/libcns/abAbacus-mergeRefine.C:65: @@ -2019,6 +2052,7 @@ utgcns/libcns/abBead.H:61:7: note: 'class abBead' declared here class abBead { ^~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/unitigConsensus.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/gfa.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/bed.C @@ -2034,8 +2068,6 @@ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/sqStoreCreatePartition.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/sqStoreDumpMetaData.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreCompress.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreDump.C stores/sqStoreCreate.C: In function 'uint32 loadFASTA(char*, char*, char*, uint32&, uint8*, compressedFileReader*, FILE*, uint32&)': stores/sqStoreCreate.C:99:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); nLines++; @@ -2066,6 +2098,29 @@ stores/sqStoreCreate.C:483:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, AS_MAX_READLEN+1, F->file()); lineNumber++; ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C: In member function 'void dumpParameters::loadBogartStatus(const char*, uint32)': +stores/ovStoreDump.C:283:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(NN, FILENAME_MAX, E); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:299:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(NN, FILENAME_MAX, E); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(NN, FILENAME_MAX, S); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:321:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(NN, FILENAME_MAX, S); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:327:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(NN, FILENAME_MAX, G); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:343:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(NN, FILENAME_MAX, G); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreCompress.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreDump.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgTigSizeAnalysis.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreLoad.C stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': stores/sqStoreDumpFASTQ.C:498:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (dumpFASTA) // Dear GCC: I'm NOT ambiguous @@ -2073,11 +2128,11 @@ stores/sqStoreDumpFASTQ.C:508:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (dumpFASTQ) // Dear GCC: I'm NOT ambiguous ^ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgTigSizeAnalysis.C stores/tgStoreDump.C:677:2: warning: #warning replace this with genericStatistics [-Wcpp] #warning replace this with genericStatistics ^~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreLoad.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreFilter.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCoverageStat/stores/tgStoreCoverageStat.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreCoverageStat.C stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:88:33: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); @@ -2124,42 +2179,20 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C: In member function 'void dumpParameters::loadBogartStatus(const char*, uint32)': -stores/ovStoreDump.C:283:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(NN, FILENAME_MAX, E); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:299:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(NN, FILENAME_MAX, E); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(NN, FILENAME_MAX, S); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:321:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(NN, FILENAME_MAX, S); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:327:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(NN, FILENAME_MAX, G); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:343:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(NN, FILENAME_MAX, G); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreFilter.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCoverageStat/stores/tgStoreCoverageStat.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgStoreCoverageStat.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/tgTigDisplay.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/loadCorrectedReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility stores/loadErates.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/meryl.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylCountArray.C meryl/meryl.C:265:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] #warning HARD CODED NUMBER OF FILES! ^~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylCountArray.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylInput.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-count.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp.C meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] #warning "need to decide whic direction we're going?" ^~~~~~~ @@ -2180,7 +2213,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Isequence -I/build/canu-1.8+dfsg/src -Iutility sequence/sequence.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp.C meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:415:27: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 1006 [-Wformat-truncation=] snprintf(s, 1024, "Requested memory '%s' (GB) is more than physical memory %.2f GB.", @@ -2209,6 +2242,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Isequence -I/build/canu-1.8+dfsg/src -Iutility sequence/sequence.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C @@ -2217,6 +2251,27 @@ g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+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] + fgets(line, 1024, F); + ~~~~~^~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+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] + #warning do we need to check for contained too? + ^~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C +overlapInCore/overlapImport.C: In function 'int main(int, char**)': +overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(S, 1024, in->file()); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ +overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(S, 1024, in->file()); + ~~~~~^~~~~~~~~~~~~~~~~~~~~ stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': stores/loadErates.C:85:38: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); @@ -2240,35 +2295,16 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - fgets(line, 1024, F); - ~~~~~^~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C -overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp] - #warning do we need to check for contained too? - ^~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C -overlapInCore/overlapImport.C: In function 'int main(int, char**)': -overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(S, 1024, in->file()); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ -overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(S, 1024, in->file()); - ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': overlapInCore/edalign.C:37:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, lineMax, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from wtdbg/wtdbgConvert.C:30: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': @@ -2282,11 +2318,8 @@ stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/readConsensus/correction/readConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/readConsensus.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C In file included from /build/canu-1.8+dfsg/src/AS_global.H:113, from correction/generateCorrectionLayouts.C:34: utility/arrays.H: In instantiation of 'void setArraySize(TT*&, uint64, LL&, uint64, uint32) [with TT = tgPosition; LL = unsigned int; uint64 = long unsigned int; uint32 = unsigned int]': @@ -2300,6 +2333,8 @@ stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': correction/falconsense.C:64:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] for (fgets(L, 1024, R); @@ -2307,15 +2342,14 @@ correction/falconsense.C:66:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(L, 1024, R)) { ~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-quality.C In file included from overlapBasedTrimming/trimReads.C:31: overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': overlapBasedTrimming/trimStat.H:78:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(N); ~~~~~~^~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-quality.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C @@ -2339,16 +2373,15 @@ g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C bogart/AS_BAT_BestOverlapGraph.C:858:2: warning: #warning what is the error rate of the 'best contained' overlap? [-Wcpp] #warning what is the error rate of the 'best contained' overlap? ^~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] #warning deviationGraph hard coded ^~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C bogart/AS_BAT_BestOverlapGraph.C: In member function 'void BestOverlapGraph::findEdges()': bogart/AS_BAT_BestOverlapGraph.C:434:57: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class BestOverlaps'; use assignment or value-initialization instead [-Wclass-memaccess] memset(_bestA, 0, sizeof(BestOverlaps) * (fiLimit + 1)); @@ -2364,8 +2397,10 @@ bogart/AS_BAT_BestOverlapGraph.H:166:7: note: 'class BestScores' declared here class BestScores { ^~~~~~~~~~ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': bogart/AS_BAT_Logging.C:91:34: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); @@ -2380,7 +2415,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C @@ -2398,8 +2432,6 @@ stores/tgTig.H:87:7: note: 'class tgPosition' declared here class tgPosition { ^~~~~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C bogart/AS_BAT_PlaceContains.C: In function 'void placeUnplacedUsingAllOverlaps(TigVector&, const char*)': bogart/AS_BAT_PlaceContains.C:96:66: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class SeqInterval'; use assignment or value-initialization instead [-Wclass-memaccess] memset(placedPos, 0, sizeof(SeqInterval) * (RI->numReads() + 1)); @@ -2411,6 +2443,8 @@ bogart/AS_BAT_PlaceContains.C:108:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (tigs.inUnitig(fid) == 0) // I'm NOT ambiguous! ^ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C bogart/AS_BAT_PlaceReadUsingOverlaps.C: In function 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector&, uint32)': bogart/AS_BAT_PlaceReadUsingOverlaps.C:543:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (logFileFlagSet(LOG_PLACE_READ)) // Nope, not ambiguous. @@ -2474,45 +2508,16 @@ g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqAnalyze/fastq-utilities/fastqAnalyze.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqAnalyze.C g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSample/fastq-utilities/fastqSample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSample.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate/fastq-utilities/fastqSimulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSimulate.C -g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSimulate-sort.C -cp -pf pipelines/canu.pl /build/canu-1.8+dfsg/Linux-amd64/bin/canu -chmod +x /build/canu-1.8+dfsg/Linux-amd64/bin/canu -echo > /build/canu-1.8+dfsg/Linux-amd64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." -chmod -x /build/canu-1.8+dfsg/Linux-amd64/bin/canu.defaults -cp -pf pipelines/canu/Consensus.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/CorrectReads.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Configure.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Defaults.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Execution.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/SequenceStore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_LSF.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_SGE.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Meryl.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Output.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapInCore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMhap.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMMap.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapStore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Report.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ -cp -pf pipelines/canu/Unitig.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ fastq-utilities/fastqAnalyze.C: In function 'void doStats(char*, char*)': fastq-utilities/fastqAnalyze.C:185:25: warning: conversion from 'long unsigned int' to 'uint32' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] uint32 minLen = UINT64_MAX; ^~~~~~~~~~ +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate/fastq-utilities/fastqSimulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSimulate.C gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:151:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(Pfile); ~~~~~~^~~~~~~ -g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap AS_global.C +g++ -o /build/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility fastq-utilities/fastqSimulate-sort.C gfa/alignGFA.C:129:18: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] sprintf(Pname, "plot-%s-%s", Aname, Bname); ^~~~~~~~~~~~ ~~~~~ @@ -2584,6 +2589,27 @@ fastq-utilities/fastqAnalyze.C:410:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(D, MAX_READ_LEN, F); chomp(D); ~~~~~^~~~~~~~~~~~~~~~~~~~ +cp -pf pipelines/canu.pl /build/canu-1.8+dfsg/Linux-amd64/bin/canu +chmod +x /build/canu-1.8+dfsg/Linux-amd64/bin/canu +echo > /build/canu-1.8+dfsg/Linux-amd64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." +chmod -x /build/canu-1.8+dfsg/Linux-amd64/bin/canu.defaults +cp -pf pipelines/canu/Consensus.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/CorrectReads.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Configure.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Defaults.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Execution.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/SequenceStore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_LSF.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_SGE.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Meryl.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Output.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ fastq-utilities/fastqSample.C: In member function 'bool aRead::read(FILE*)': fastq-utilities/fastqSample.C:72:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(a, MAXLEN, F); @@ -2597,10 +2623,31 @@ fastq-utilities/fastqSample.C:75:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(d, MAXLEN, F); ~~~~~^~~~~~~~~~~~~~ +cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapInCore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMhap.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMMap.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapStore.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Report.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +cp -pf pipelines/canu/Unitig.pm /build/canu-1.8+dfsg/Linux-amd64/lib/site_perl/canu/ +g++ -o /build/canu-1.8+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-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/build/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap AS_global.C fastq-utilities/fastqSimulate.C: In function 'int main(int, char**)': fastq-utilities/fastqSimulate.C:1097:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(seq + seqLen, seqMax - seqLen, fastaFile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastq-utilities/fastqSimulate-sort.C: In function 'char* readRead(FILE*, uint32&, uint32&, uint32&)': +fastq-utilities/fastqSimulate-sort.C:98:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(a, hLen, inFile); al = strlen(a); + ~~~~~^~~~~~~~~~~~~~~~~ +fastq-utilities/fastqSimulate-sort.C:99:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(b, sLen, inFile); bl = strlen(b); + ~~~~~^~~~~~~~~~~~~~~~~ +fastq-utilities/fastqSimulate-sort.C:100:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(c, hLen, inFile); cl = strlen(c); + ~~~~~^~~~~~~~~~~~~~~~~ +fastq-utilities/fastqSimulate-sort.C:101:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(d, sLen, inFile); dl = strlen(d); + ~~~~~^~~~~~~~~~~~~~~~~ AS_global.C: In function 'int AS_configure(int, char**)': AS_global.C:161:29: warning: '%lu' directive output may be truncated writing between 1 and 20 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] snprintf(N, FILENAME_MAX, "%s/" F_U64 "_%s_" F_U64 "_%s", @@ -2666,20 +2713,7 @@ a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEdfastq-utilities/fastqSimulate-sort.C: In function 'char* readRead(FILE*, uint32&, uint32&, uint32&)': -fastq-utilities/fastqSimulate-sort.C:98:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(a, hLen, inFile); al = strlen(a); - ~~~~~^~~~~~~~~~~~~~~~~ -fastq-utilities/fastqSimulate-sort.C:99:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(b, sLen, inFile); bl = strlen(b); - ~~~~~^~~~~~~~~~~~~~~~~ -fastq-utilities/fastqSimulate-sort.C:100:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(c, hLen, inFile); cl = strlen(c); - ~~~~~^~~~~~~~~~~~~~~~~ -fastq-utilities/fastqSimulate-sort.C:101:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(d, sLen, inFile); dl = strlen(d); - ~~~~~^~~~~~~~~~~~~~~~~ -itDistance-allocateMoreSpace.o +a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o a - /build/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o @@ -2798,20 +2832,22 @@ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ -dpkg-deb: building package 'canu' in '../canu_1.8+dfsg-2_amd64.deb'. dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_1.8+dfsg-2_amd64.deb'. +dpkg-deb: building package 'canu' in '../canu_1.8+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../canu_1.8+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/61697/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/61697/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/52717 and its subdirectories -I: Current time: Tue Apr 6 18:45:15 -12 2021 -I: pbuilder-time-stamp: 1617777915 +I: removing directory /srv/workspace/pbuilder/61697 and its subdirectories +I: Current time: Wed May 11 03:10:32 +14 2022 +I: pbuilder-time-stamp: 1652188232