Diff of the two buildlogs: -- --- b1/build.log 2024-07-05 10:37:44.230728944 +0000 +++ b2/build.log 2024-07-05 10:53:24.254762472 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 7 04:59:30 -12 2025 -I: pbuilder-time-stamp: 1754585970 +I: Current time: Sat Jul 6 00:37:47 +14 2024 +I: pbuilder-time-stamp: 1720175867 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./canu_2.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.2OCeFnF6/trustedkeys.kbx': General error -gpgv: Signature made Fri Mar 27 11:47:02 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.YlqNHJiQ/trustedkeys.kbx': General error +gpgv: Signature made Sat Mar 28 13:47:02 2020 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,166 @@ dpkg-source: info: applying canu_version.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2645341/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 6 00:38 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - 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,-fixfilepath parallel=42 ' - DISTRIBUTION='bullseye' - 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + 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,-fixfilepath parallel=20 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9c47466dcf2340ab8a813ed424f9e371' - 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='2645341' - PS1='# ' - PS2='> ' + INVOCATION_ID=61b2771ec57946ae9af50939decc8aea + 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=341593 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0KUWz31F/pbuilderrc_lklY --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0KUWz31F/b1 --logfile b1/build.log canu_2.0+dfsg-1.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://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0KUWz31F/pbuilderrc_aZIt --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0KUWz31F/b2 --logfile b2/build.log canu_2.0+dfsg-1.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://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 2024 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 2024 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 10 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2645341/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 00:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 00:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Jul 6 00:38 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 23:59 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -281,7 +312,7 @@ Get: 75 http://deb.debian.org/debian bullseye/main amd64 libmeryl-dev amd64 0~20150903+r2013-8+b1 [53.9 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libssw-java amd64 1.1-13 [16.7 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 mhap all 2.1.3+dfsg-3 [160 kB] -Fetched 95.7 MB in 2s (61.9 MB/s) +Fetched 95.7 MB in 11s (8503 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19711 files and directories currently installed.) @@ -610,135 +641,135 @@ Setting up mhap (2.1.3+dfsg-3) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:Comodo_AAA_Services_root.pem Adding debian:Amazon_Root_CA_2.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:Buypass_Class_2_Root_CA.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:QuoVadis_Root_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:Izenpe.com.pem -Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:Actalis_Authentication_Root_CA.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:Secure_Global_CA.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:COMODO_Certification_Authority.pem Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:GlobalSign_Root_CA_-_R2.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:DigiCert_Assured_ID_Root_G2.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:e-Szigno_Root_CA_2017.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:TrustCor_ECA-1.pem -Adding debian:Secure_Global_CA.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:emSign_Root_CA_-_G1.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:GTS_Root_R1.pem -Adding debian:DST_Root_CA_X3.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:GTS_Root_R2.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:ePKI_Root_Certification_Authority.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem -Adding debian:AffirmTrust_Commercial.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:UCA_Global_G2_Root.pem -Adding debian:Certigna_Root_CA.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:GTS_Root_R3.pem -Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:Starfield_Class_2_CA.pem -Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:UCA_Extended_Validation_Root.pem -Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:Certum_Trusted_Network_CA_2.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:certSIGN_Root_CA_G2.pem +Adding debian:Certigna_Root_CA.pem +Adding debian:EC-ACC.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:emSign_Root_CA_-_C1.pem Adding debian:Cybertrust_Global_Root.pem -Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:Certigna.pem -Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem -Adding debian:GlobalSign_Root_CA.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:SecureTrust_CA.pem -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:emSign_ECC_Root_CA_-_G3.pem -Adding debian:AffirmTrust_Premium.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:Amazon_Root_CA_1.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:SZAFIR_ROOT_CA2.pem -Adding debian:EC-ACC.pem -Adding debian:emSign_Root_CA_-_C1.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:ISRG_Root_X1.pem Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:Hongkong_Post_Root_CA_3.pem -Adding debian:E-Tugra_Certification_Authority.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem -Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:GTS_Root_R3.pem Adding debian:Security_Communication_RootCA2.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:COMODO_ECC_Certification_Authority.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:e-Szigno_Root_CA_2017.pem -Adding debian:GlobalSign_Root_CA_-_R2.pem +Adding debian:DST_Root_CA_X3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:certSIGN_Root_CA_G2.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:SecureTrust_CA.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem +Adding debian:SecureSign_RootCA11.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:GTS_Root_R4.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:GTS_Root_R1.pem Adding debian:XRamp_Global_CA_Root.pem -Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem -Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:DigiCert_Trusted_Root_G4.pem -Adding debian:GTS_Root_R4.pem -Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:Certigna.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Izenpe.com.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:GTS_Root_R2.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem done. Processing triggers for libc-bin (2.31-13+deb11u10) ... Processing triggers for ca-certificates (20210119) ... @@ -762,7 +793,11 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../canu_2.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../canu_2.0+dfsg-1_source.changes dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -786,18 +821,20 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/canu-2.0+dfsg' dh_auto_build - cd src && make -j42 "INSTALL=install --strip-program=true" + cd src && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/canu-2.0+dfsg/src' WARNING: WARNING: g++ 10 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: -Building for 'Linux' '6.7.12+bpo-amd64' as 'amd64' into '/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/{bin,obj}'. +Building for 'Linux' '6.1.0-22-amd64' as 'amd64' into '/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '10'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'. g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C +Building release v2.0 g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C + g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C @@ -806,8 +843,6 @@ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C -Building release v2.0 - g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C @@ -817,70 +852,37 @@ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C -utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] - 58 | #warning how to set prefix size for streaming operations? - | ^~~~~~~ In file included from utility/system.C:46: /usr/include/x86_64-linux-gnu/sys/sysctl.h:21:2: warning: #warning "The header is deprecated and will be removed." [-Wcpp] 21 | #warning "The header is deprecated and will be removed." | ^~~~~~~ -stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] - 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING - | ^~~~~~~ -stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] - 71 | #warning not failing if a valid store +utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] + 58 | #warning how to set prefix size for streaming operations? | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C -stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)': -stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 109 | buffer->writeIFFchunk("BLOB"); - | ^~~~~~ -stores/sqReadDataWriter.C:110:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 110 | buffer->writeIFFchunk("NAME", _name, _nameLen); - | ^~~~~~ -stores/sqReadDataWriter.C:115:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 115 | buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only) - | ^~~~~~ -stores/sqReadDataWriter.C:117:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 117 | buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN) - | ^~~~~~ -stores/sqReadDataWriter.C:119:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 119 | buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence - | ^~~~~~ -stores/sqReadDataWriter.C:124:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 124 | buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only) - | ^~~~~~ -stores/sqReadDataWriter.C:126:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 126 | buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN) - | ^~~~~~ -stores/sqReadDataWriter.C:128:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 128 | buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence - | ^~~~~~ -stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 132 | buffer->closeIFFchunk("BLOB"); - | ^~~~~~ +utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': +utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] + 76 | read(_fd, _data, _length); + | ~~~~^~~~~~~~~~~~~~~~~~~~~ +utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()': +utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] + 102 | write(_fd, _data, _length), close(_fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C +utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': +utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 311 | symlink(pathToFile, pathToLink); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': +utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 678 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 684 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, from utility/logging.H:29, @@ -892,108 +894,67 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C -utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': -utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 76 | read(_fd, _data, _length); - | ~~~~^~~~~~~~~~~~~~~~~~~~~ -utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()': -utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 102 | write(_fd, _data, _length), close(_fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)': -utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 257 | args[1] = "download"; - | ^~~~~~~~~~ -utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 258 | args[2] = "--overwrite"; - | ^~~~~~~~~~~~~ -utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 259 | args[3] = "--no-progress"; - | ^~~~~~~~~~~~~~~ -utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 260 | args[4] = "--output"; - | ^~~~~~~~~~ -In file included from stores/sqStoreBlob.C:26: -stores/sqStore.H: In constructor 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)': -stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +utility/kmers-exact.C: In member function 'void kmerCountExactLookup::load()': +utility/kmers-exact.C:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'uint64' {aka 'long unsigned int'} [-Wformat=] + 419 | fprintf(stderr, "minValue " F_U32 " maxValue " F_U32 " value " F_U64 " bits " F_U32 "\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 420 | _minValue, _maxValue, value, _valueBits); + | ~~~~~~~~~ + | | + | uint64 {aka long unsigned int} +utility/kmers-exact.C:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'uint64' {aka 'long unsigned int'} [-Wformat=] +utility/logging.C: In member function 'void logFile::setName(const char*)': +utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); + | ^ In file included from /usr/include/stdio.h:867, from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/sqStore.H:37, - from stores/sqStoreBlob.C:26: -/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 utility/logging.H:29, + from utility/logging.C:26: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreInfo.C: In member function 'void sqStoreInfo::writeInfo(char*)': -stores/sqStoreInfo.C:333:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 333 | B->writeIFFobject("MAGC", _sqMagic); - | ^~~~~~ -stores/sqStoreInfo.C:334:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 334 | B->writeIFFobject("VERS", _sqVersion); - | ^~~~~~ -stores/sqStoreInfo.C:336:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 336 | B->writeIFFobject("LSIZ", _sqLibrarySize); - | ^~~~~~ -stores/sqStoreInfo.C:337:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 337 | B->writeIFFobject("RSIZ", _sqReadSize); - | ^~~~~~ -stores/sqStoreInfo.C:338:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 338 | B->writeIFFobject("MLB ", _sqMaxLibrariesBits); - | ^~~~~~ -stores/sqStoreInfo.C:339:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 339 | B->writeIFFobject("LNS ", _sqLibraryNameSize); - | ^~~~~~ -stores/sqStoreInfo.C:340:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 340 | B->writeIFFobject("MRB ", _sqMaxReadBits); - | ^~~~~~ -stores/sqStoreInfo.C:341:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 341 | B->writeIFFobject("MRLB", _sqMaxReadLenBits); - | ^~~~~~ -stores/sqStoreInfo.C:343:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 343 | B->writeIFFobject("NLIB", _numLibraries); - | ^~~~~~ -stores/sqStoreInfo.C:344:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 344 | B->writeIFFobject("NREA", _numReads); - | ^~~~~~ -stores/sqStoreInfo.C:345:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 345 | B->writeIFFobject("NBLO", _numBlobs); - | ^~~~~~ -stores/sqStoreInfo.C:347:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 347 | B->writeIFFarray("READ", _reads, sqRead_largest); - | ^~~~~~ -stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 348 | B->writeIFFarray("BASE", _bases, sqRead_largest); - | ^~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C -In file included from stores/sqStoreBlob.C:26: -stores/sqStore.H: In member function 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)': -stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); + | ^ In file included from /usr/include/stdio.h:867, from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/sqStore.H:37, - from stores/sqStoreBlob.C:26: -/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 utility/logging.H:29, + from utility/logging.C:26: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from utility/logging.H:29, + from utility/logging.C:26: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); + | ^ +utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument + 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from utility/logging.H:29, + from utility/logging.C:26: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 8220 bytes into a destination of size 4096 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': -utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 311 | symlink(pathToFile, pathToLink); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': -utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 678 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 684 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc -utility/logging.C: In member function 'void logFile::setName(const char*)': utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ @@ -1045,6 +1006,39 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C +utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': +utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from utility/kmers.H:29, + from utility/kmers-reader.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 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C +utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': +utility/kmers-writer.C:147:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 147 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + 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 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C +utility/logging.C: In member function 'void logFile::writeLog(const char*, __va_list_tag*)': utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ @@ -1096,6 +1090,90 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C +utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)': +utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 257 | args[1] = "download"; + | ^~~~~~~~~~ +utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 258 | args[2] = "--overwrite"; + | ^~~~~~~~~~~~~ +utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 259 | args[3] = "--no-progress"; + | ^~~~~~~~~~~~~~~ +utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 260 | args[4] = "--output"; + | ^~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C +stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] + 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C +stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)': +stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 109 | buffer->writeIFFchunk("BLOB"); + | ^~~~~~ +stores/sqReadDataWriter.C:110:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 110 | buffer->writeIFFchunk("NAME", _name, _nameLen); + | ^~~~~~ +stores/sqReadDataWriter.C:115:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 115 | buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only) + | ^~~~~~ +stores/sqReadDataWriter.C:117:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 117 | buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN) + | ^~~~~~ +stores/sqReadDataWriter.C:119:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 119 | buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence + | ^~~~~~ +stores/sqReadDataWriter.C:124:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 124 | buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only) + | ^~~~~~ +stores/sqReadDataWriter.C:126:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 126 | buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN) + | ^~~~~~ +stores/sqReadDataWriter.C:128:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 128 | buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence + | ^~~~~~ +stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 132 | buffer->closeIFFchunk("BLOB"); + | ^~~~~~ +stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] + 71 | #warning not failing if a valid store + | ^~~~~~~ +In file included from stores/sqStoreBlob.C:26: +stores/sqStore.H: In constructor 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)': +stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/sqStore.H:37, + from stores/sqStoreBlob.C:26: +/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 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C +In file included from stores/sqStoreBlob.C:26: +stores/sqStore.H: In member function 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)': +stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/sqStore.H:37, + from stores/sqStoreBlob.C:26: +/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 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C In file included from stores/sqStoreBlob.C:26: stores/sqStore.H: In member function 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)': stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -1110,8 +1188,64 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc +stores/sqStoreInfo.C: In member function 'void sqStoreInfo::writeInfo(char*)': +stores/sqStoreInfo.C:333:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 333 | B->writeIFFobject("MAGC", _sqMagic); + | ^~~~~~ +stores/sqStoreInfo.C:334:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 334 | B->writeIFFobject("VERS", _sqVersion); + | ^~~~~~ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc +stores/sqStoreInfo.C:336:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 336 | B->writeIFFobject("LSIZ", _sqLibrarySize); + | ^~~~~~ +stores/sqStoreInfo.C:337:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 337 | B->writeIFFobject("RSIZ", _sqReadSize); + | ^~~~~~ +stores/sqStoreInfo.C:338:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 338 | B->writeIFFobject("MLB ", _sqMaxLibrariesBits); + | ^~~~~~ +stores/sqStoreInfo.C:339:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 339 | B->writeIFFobject("LNS ", _sqLibraryNameSize); + | ^~~~~~ +stores/sqStoreInfo.C:340:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 340 | B->writeIFFobject("MRB ", _sqMaxReadBits); + | ^~~~~~ +stores/sqStoreInfo.C:341:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 341 | B->writeIFFobject("MRLB", _sqMaxReadLenBits); + | ^~~~~~ +stores/sqStoreInfo.C:343:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 343 | B->writeIFFobject("NLIB", _numLibraries); + | ^~~~~~ +stores/sqStoreInfo.C:344:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 344 | B->writeIFFobject("NREA", _numReads); + | ^~~~~~ +stores/sqStoreInfo.C:345:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 345 | B->writeIFFobject("NBLO", _numBlobs); + | ^~~~~~ +stores/sqStoreInfo.C:347:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 347 | B->writeIFFarray("READ", _reads, sqRead_largest); + | ^~~~~~ +stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 348 | B->writeIFFarray("BASE", _bases, sqRead_largest); + | ^~~~~~ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc +stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': +stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] + 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 75 | dat.ovl.ahg5, dat.ovl.ahg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] +stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] +stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': @@ -1329,99 +1463,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C -stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': -stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStore.C:59: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C -utility/kmers-exact.C: In member function 'void kmerCountExactLookup::load()': -utility/kmers-exact.C:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'uint64' {aka 'long unsigned int'} [-Wformat=] - 419 | fprintf(stderr, "minValue " F_U32 " maxValue " F_U32 " value " F_U64 " bits " F_U32 "\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 420 | _minValue, _maxValue, value, _valueBits); - | ~~~~~~~~~ - | | - | uint64 {aka long unsigned int} -utility/kmers-exact.C:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'uint64' {aka 'long unsigned int'} [-Wformat=] -utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': -utility/kmers-writer.C:147:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 147 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - 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 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C -utility/logging.C: In member function 'void logFile::writeLog(const char*, __va_list_tag*)': -utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); - | ^ -utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument - 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from utility/logging.H:29, - from utility/logging.C:26: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 13 and 8220 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:289:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 289 | snprintf(path, FILENAME_MAX, "%s/info", _storePath); AS_UTL_unlink(path); @@ -1519,39 +1560,108 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C -stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': -stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] - 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 75 | dat.ovl.ahg5, dat.ovl.ahg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] -stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] -stores/ovOverlap.C:71:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C -utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': -utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); - | ^~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C +stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': +stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); + | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from utility/kmers.H:29, - from utility/kmers-reader.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 + from stores/ovStore.H:37, + from stores/ovStore.C:59: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C +stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': +stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': +stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': +stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); + | ^~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); + | ^~~~~~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 143 | printSummary(out, "lenUnassembled", lenUnassembled); + | ^~~~~~~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 144 | printSummary(out, "lenBubble", lenBubble); + | ^~~~~~~~~~~ +stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 145 | printSummary(out, "lenContig", lenContig); + | ^~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': +stores/ovStoreWriter.C:228:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/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 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': +stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'int' [-Wformat=] + 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | int +stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'int' [-Wformat=] +stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] +stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': +stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': +stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); + | ^ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37, + from stores/ovStoreWriter.C:56: +/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 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:191:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); @@ -1595,8 +1705,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': +stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ +stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 690 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStore::tgStoreEntry*&, uint32&, uint32)': stores/tgStore.C:594:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); @@ -1612,17 +1729,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': -stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'int' [-Wformat=] - 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | int -stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'int' [-Wformat=] -stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] -stores/ovStoreHistogram.C:359:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': +stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); + | ^ stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStore::tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:626:40: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); @@ -1663,56 +1773,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C -In file included from stores/ovStore.H:43, - from stores/ovStoreFile.C:47: -stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': -stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); - | ^~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - 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 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C -stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': -stores/ovStoreWriter.C:228:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); - | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, from stores/ovStore.H:37, from stores/ovStoreWriter.C:56: -/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 +/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 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': -stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': -stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': stores/tgStore.C:695:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); @@ -1728,76 +1797,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': -stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': -stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/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 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C -stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': -stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); - | ^~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); - | ^~~~~~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 143 | printSummary(out, "lenUnassembled", lenUnassembled); - | ^~~~~~~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 144 | printSummary(out, "lenBubble", lenBubble); - | ^~~~~~~~~~~ -stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 145 | printSummary(out, "lenContig", lenContig); - | ^~~~~~~~~~~ -stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': -stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 565 | fgets(LINE, LINEmax, F); LINEnum++; - | ~~~~~^~~~~~~~~~~~~~~~~~ -stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 690 | fgets(LINE, LINEmax, F); LINEnum++; - | ~~~~~^~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': -stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); - | ^ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37, - from stores/ovStoreWriter.C:56: -/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 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': stores/ovStoreWriter.C:486:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); @@ -1811,6 +1811,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': stores/ovStoreWriter.C:505:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 505 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); @@ -1836,11 +1837,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); | ^ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C In file included from /usr/include/stdio.h:867, from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, from stores/ovStore.H:37, @@ -1898,11 +1899,39 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C +In file included from stores/ovStore.H:43, + from stores/ovStoreFile.C:47: +stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': +stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); + | ^~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + 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 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C +gfa/gfa.C: In member function 'void gfaSequence::load(char*)': +gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 123 | findGFAtokenI(_features, "LN:i:", _length); + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::processHits()': utgcns/libNDalign/NDalign.C:660:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 660 | display("NDalign::processHits()-- ", false); @@ -1919,33 +1948,14 @@ utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 838 | display("NDalign::realignBackward()-- ", displayAlign); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/loadErates.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C -gfa/gfa.C: In member function 'void gfaSequence::load(char*)': -gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 123 | findGFAtokenI(_features, "LN:i:", _length); - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C -stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] - 675 | #warning replace this with genericStatistics - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C -stores/ovStoreSorter.C: In function 'int main(int, char**)': -stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 167 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 170 | err.push_back("ERROR: no slice number (-F) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C stores/ovStoreIndexer.C: In function 'int main(int, char**)': stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 80 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); @@ -1956,16 +1966,6 @@ stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 86 | err.push_back("ERROR: No config (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C -stores/ovStoreBuild.C: In function 'int main(int, char**)': -stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 125 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 128 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C stores/ovStoreBucketizer.C: In function 'int main(int, char**)': stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 139 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); @@ -1973,57 +1973,67 @@ stores/ovStoreBucketizer.C:142:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 142 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': -stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 459 | AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName); - | ^~~~~~~ stores/ovStoreBucketizer.C:145:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 145 | err.push_back("ERROR: No store configuration (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); - | ^~~~~~~ +stores/ovStoreBuild.C: In function 'int main(int, char**)': +stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 125 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C: In function 'int main(int, char**)': -stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); +stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 128 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C +stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] + 675 | #warning replace this with genericStatistics + | ^~~~~~~ stores/ovStoreConfig.C: In function 'int main(int, char**)': stores/ovStoreConfig.C:372:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 372 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C: In function 'int main(int, char**)': +stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:375:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 375 | err.push_back("ERROR: No input overlap files (-L or last on the command line) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:378:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 378 | err.push_back("ERROR: Can't both -create -describe a config.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:381:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 381 | err.push_back("ERROR: Must supply one of -create or -describe.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:385:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 385 | err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C -meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] - 261 | #warning HARD CODED NUMBER OF FILES! - | ^~~~~~~ -meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] - 98 | #warning "need to decide whic direction we're going?" - | ^~~~~~~ -meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] - 116 | #warning "rounding issues in word-frequency!" - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C +stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': +stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 459 | AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName); + | ^~~~~~~ +stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); + | ^~~~~~~ +stores/ovStoreSorter.C: In function 'int main(int, char**)': +stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 167 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 170 | err.push_back("ERROR: no slice number (-F) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:137:36: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 137 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); @@ -2070,10 +2080,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadTrimmedReads.C: In function 'int main(int, char**)': -stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); +stores/tgStoreDump.C: In function 'int main(int, char**)': +stores/tgStoreDump.C:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1166 | err.push_back("No sequence store (-S option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1169 | err.push_back("No tig store (-T option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1172 | err.push_back("No tig store version (-T option) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1175 | err.push_back("-coverage needs and output prefix (-o option).\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 1178 | err.push_back("No DUMP TYPE supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C +stores/tgStoreLoad.C: In function 'int main(int, char**)': +stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 194 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 196 | err.push_back("ERROR: no tig store (-T) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility stores/loadErates.C stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); @@ -2090,22 +2124,18 @@ stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 145 | printSummary(out, "lenContig", lenContig); | ^~~~~~~~~~~ -stores/tgStoreDump.C: In function 'int main(int, char**)': -stores/tgStoreDump.C:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1166 | err.push_back("No sequence store (-S option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1169 | err.push_back("No tig store (-T option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1172 | err.push_back("No tig store version (-T option) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1175 | err.push_back("-coverage needs and output prefix (-o option).\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 1178 | err.push_back("No DUMP TYPE supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C +meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] + 261 | #warning HARD CODED NUMBER OF FILES! + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C +stores/loadTrimmedReads.C: In function 'int main(int, char**)': +stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C stores/loadCorrectedReads.C: In function 'int main(int, char**)': stores/loadCorrectedReads.C:76:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 76 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); @@ -2116,22 +2146,29 @@ stores/loadCorrectedReads.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 80 | err.push_back("ERROR: no input tigs supplied on command line and no -L file supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C -stores/tgStoreLoad.C: In function 'int main(int, char**)': -stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 194 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 196 | err.push_back("ERROR: no tig store (-T) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C +meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] + 98 | #warning "need to decide whic direction we're going?" + | ^~~~~~~ +meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] + 116 | #warning "rounding issues in word-frequency!" + | ^~~~~~~ +stores/loadErates.C: In function 'int main(int, char**)': +stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 214 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 217 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from meryl/meryl.H:51, - from meryl/merylInput.C:26: + from meryl/merylCountArray.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -2149,7 +2186,7 @@ 58 | return("invalid-input"); | ^ In file included from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: + from meryl/meryl.C:46: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -2166,18 +2203,8 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -stores/loadErates.C: In function 'int main(int, char**)': -stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 214 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 217 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from meryl/meryl.H:51, - from meryl/merylOp-count.C:26: + from meryl/merylInput.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -2194,8 +2221,7 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C In file included from meryl/meryl.H:51, from meryl/merylOp-countSimple.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': @@ -2208,36 +2234,18 @@ meryl/merylInput.H:53:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ^ +In file included from meryl/meryl.H:51, + from meryl/merylOp-count.C:26: +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ^ meryl/merylInput.H:55:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ^ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C -meryl/meryl-lookup.C: In function 'int main(int, char**)': -meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 285 | err.push_back("No input sequences (-sequence) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-lookup.C:287:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 287 | err.push_back("No query meryl database (-mers) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 289 | err.push_back("No report-type (-existence, etc) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C -sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)': -sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 92 | ">random%08 " F_U64P "\n", nSeqs); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from meryl/meryl.H:51, - from meryl/merylCountArray.H:29, - from meryl/meryl-import.C:31: -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ^ meryl/merylInput.H:52:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ^ @@ -2250,6 +2258,31 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence.C +stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': +stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/loadErates.C:43: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); + | ^~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from stores/loadErates.C:43: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C In file included from meryl/meryl.H:51, from meryl/merylOp-histogram.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': @@ -2268,8 +2301,10 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C In file included from meryl/meryl.H:51, - from meryl/meryl.C:46: + from meryl/merylOp.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -2286,16 +2321,7 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -meryl/meryl-import.C: In function 'int main(int, char**)': -meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 92 | err.push_back("No input kmer file (-kmers) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 94 | err.push_back("No output database name (-output) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 96 | err.push_back("No kmer size (-k) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C In file included from meryl/meryl.H:51, from meryl/merylOp-nextMer.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': @@ -2314,24 +2340,9 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -sequence/sequence.C: In function 'int main(int, char**)': -sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 418 | err.push_back("ERROR: No input sequence files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 422 | err.push_back("ERROR: No input sequence files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 432 | err.push_back("ERROR: No input sequence files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from meryl/meryl.H:51, - from meryl/merylCountArray.C:26: + from meryl/merylCountArray.H:29, + from meryl/meryl-import.C:31: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -2348,10 +2359,8 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C In file included from meryl/meryl.H:51, - from meryl/merylOp.C:26: + from meryl/merylCountArray.C:26: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -2368,34 +2377,51 @@ meryl/merylInput.H:58:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ^ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C -stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': -stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/loadErates.C:43: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); - | ^~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from stores/loadErates.C:43: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C +meryl/meryl-import.C: In function 'int main(int, char**)': +meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 92 | err.push_back("No input kmer file (-kmers) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 94 | err.push_back("No output database name (-output) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 96 | err.push_back("No kmer size (-k) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C +meryl/meryl-lookup.C: In function 'int main(int, char**)': +meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 285 | err.push_back("No input sequences (-sequence) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-lookup.C:287:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 287 | err.push_back("No query meryl database (-mers) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 289 | err.push_back("No report-type (-existence, etc) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C +sequence/sequence.C: In function 'int main(int, char**)': +sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 418 | err.push_back("ERROR: No input sequence files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 422 | err.push_back("ERROR: No input sequence files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 432 | err.push_back("ERROR: No input sequence files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)': +sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 92 | ">random%08 " F_U64P "\n", nSeqs); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C sequence/sequence-mutate.C: In function 'void doMutate(std::vector&, mutateParameters&)': sequence/sequence-mutate.C:160:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 160 | AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name()); @@ -2411,100 +2437,9 @@ sequence/sequence-sample.C:417:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 417 | AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C -overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp] - 479 | #warning do we need to check for contained too? - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C -sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': -sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 44 | char *path = findSharedFile("share/sequence", distribName); - | ^~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C -overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': -overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 258 | fgets(line, 1024, F); - | ~~~~~^~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C -overlapInCore/overlapImport.C: In function 'int main(int, char**)': -overlapInCore/overlapImport.C:158:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 158 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -overlapInCore/overlapImport.C:161:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 161 | err.push_back("ERROR: no input overlap files supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 274 | 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] - 304 | fgets(S, 1024, in->file()); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': -overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | fgets(line, lineMax, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)': -overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 430 | FILE *BAT = openOutput(outputPrefix, "ovlbat"); - | ^~~~~~~~ -overlapInCore/overlapInCorePartition.C:431:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 431 | FILE *JOB = openOutput(outputPrefix, "ovljob"); - | ^~~~~~~~ -overlapInCore/overlapInCorePartition.C:432:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 432 | FILE *OPT = openOutput(outputPrefix, "ovlopt"); - | ^~~~~~~~ -overlapInCore/overlapInCorePartition.C:445:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 445 | renameToFinal(outputPrefix, "ovlbat"); - | ^~~~~~~~ -overlapInCore/overlapInCorePartition.C:446:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 446 | renameToFinal(outputPrefix, "ovljob"); - | ^~~~~~~~ -overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 447 | renameToFinal(outputPrefix, "ovlopt"); - | ^~~~~~~~ -mhap/mhapConvert.C: In function 'int main(int, char**)': -mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] - 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~ - | | - | int -mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] -mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] -mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 11 has type 'int' [-Wformat=] -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C -minimap/mmapConvert.C: In function 'int main(int, char**)': -minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] - 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~ - | | - | int -minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] -minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] -minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString); @@ -2554,6 +2489,72 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C +sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': +sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 44 | char *path = findSharedFile("share/sequence", distribName); + | ^~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C +overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': +overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 258 | fgets(line, 1024, F); + | ~~~~~^~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+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] + 479 | #warning do we need to check for contained too? + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C +overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)': +overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 430 | FILE *BAT = openOutput(outputPrefix, "ovlbat"); + | ^~~~~~~~ +overlapInCore/overlapInCorePartition.C:431:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 431 | FILE *JOB = openOutput(outputPrefix, "ovljob"); + | ^~~~~~~~ +overlapInCore/overlapInCorePartition.C:432:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 432 | FILE *OPT = openOutput(outputPrefix, "ovlopt"); + | ^~~~~~~~ +overlapInCore/overlapInCorePartition.C:445:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 445 | renameToFinal(outputPrefix, "ovlbat"); + | ^~~~~~~~ +overlapInCore/overlapInCorePartition.C:446:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 446 | renameToFinal(outputPrefix, "ovljob"); + | ^~~~~~~~ +overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 447 | renameToFinal(outputPrefix, "ovlopt"); + | ^~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C +overlapInCore/overlapImport.C: In function 'int main(int, char**)': +overlapInCore/overlapImport.C:158:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 158 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +overlapInCore/overlapImport.C:161:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 161 | err.push_back("ERROR: no input overlap files supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C +overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 274 | 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] + 304 | fgets(S, 1024, in->file()); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': +overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | fgets(line, lineMax, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapPair.C: In function 'void* recomputeOverlaps(void*)': overlapInCore/overlapPair.C:429:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | if (extendAlignment(bRead, bbgn, bend, blen, "B", bID, @@ -2591,41 +2592,42 @@ overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 587 | aRead, abgn, aend, alen, "Ab3", aID, | ^~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C +mhap/mhapConvert.C: In function 'int main(int, char**)': +mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] + 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~ + | | + | int +mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] +mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] +mhap/mhapConvert.C:158:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 11 has type 'int' [-Wformat=] +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C +minimap/mmapConvert.C: In function 'int main(int, char**)': +minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] + 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~ + | | + | int +minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] +minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] +minimap/mmapConvert.C:139:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C -haplotyping/splitHaplotype.C: In function 'void outputReadBatch(void*, void*)': -haplotyping/splitHaplotype.C:707:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 707 | ">%s\n", s->_names[ii].string()); - | ^~~~~~~ -haplotyping/splitHaplotype.C: In function 'int main(int, char**)': -haplotyping/splitHaplotype.C:771:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 771 | err.push_back("No input sequences supplied with either (-S) or (-R).\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -haplotyping/splitHaplotype.C:773:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 773 | err.push_back("Only one type of input reads (-S or -R) supported.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -haplotyping/splitHaplotype.C:775:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 775 | err.push_back("Not enough haplotypes (-H) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C -overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)': -overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 77 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)': overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 480 | readsIn .generatePlots(outputPrefix, "inputReads", 250); @@ -2654,12 +2656,16 @@ overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 504 | trim3.generatePlots(outputPrefix, "trim3", 25); | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C In file included from overlapBasedTrimming/trimReads.C:31: overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | system(N); | ~~~~~~^~~ +haplotyping/splitHaplotype.C: In function 'void outputReadBatch(void*, void*)': +haplotyping/splitHaplotype.C:707:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 707 | ">%s\n", s->_names[ii].string()); + | ^~~~~~~ correction/falconsense.C: In function 'int main(int, char**)': correction/falconsense.C:359:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 359 | err.push_back("ERROR: no seqStore input (-S) supplied.\n"); @@ -2667,8 +2673,38 @@ correction/falconsense.C:362:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 362 | err.push_back("ERROR: no corStore input (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C +haplotyping/splitHaplotype.C: In function 'int main(int, char**)': +haplotyping/splitHaplotype.C:771:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 771 | err.push_back("No input sequences supplied with either (-S) or (-R).\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +haplotyping/splitHaplotype.C:773:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 773 | err.push_back("Only one type of input reads (-S or -R) supported.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +haplotyping/splitHaplotype.C:775:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 775 | err.push_back("Not enough haplotypes (-H) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)': +overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 77 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C +correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': +correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 70 | for (fgets(L, 1024, R); + | ~~~~~^~~~~~~~~~~~ +correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 72 | fgets(L, 1024, R)) { + | ~~~~~^~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C overlapAlign/computeOverlapAlignment.C: In member function 'void maComputation::computeOverlapAlignment(uint32, uint32, double, uint32, uint32)': overlapAlign/computeOverlapAlignment.C:581:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 581 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into @@ -2694,36 +2730,20 @@ overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 720 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends. | ^~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C -correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': -correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 70 | for (fgets(L, 1024, R); - | ~~~~~^~~~~~~~~~~~ -correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 72 | fgets(L, 1024, R)) { - | ~~~~~^~~~~~~~~~~~ -bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] - 486 | #warning deviationGraph hard coded - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)': overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID); | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C overlapErrorAdjustment/findErrors-Dump.C: In function 'int main(int, char**)': overlapErrorAdjustment/findErrors-Dump.C:66:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 66 | char *typeName[13] = { "IDENT", @@ -2761,11 +2781,36 @@ overlapErrorAdjustment/findErrors-Dump.C:77:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 77 | "EXTENSION", | ^~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C +bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] + 486 | #warning deviationGraph hard coded + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+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:91:37: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] + 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); + | ^~~~ +bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument + 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from bogart/AS_BAT_Logging.H:41, + from bogart/AS_BAT_Logging.C:38: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4115 bytes into a destination of size 4096 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C bogart/bogart.C: In function 'int main(int, char**)': bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n"); @@ -2782,15 +2827,48 @@ bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 736 | writeTigsToStore(contigs, prefix, "ctg", true); | ^~~~~ bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 756 | writeTigsToStore(unitigs, prefix, "utg", true); | ^~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C +bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': +bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)': +bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false); + | ^~~~~ +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C @@ -2798,26 +2876,6 @@ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C -bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': -bogart/AS_BAT_Logging.C:91:37: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] - 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); - | ^~~~ -bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument - 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from bogart/AS_BAT_Logging.H:41, - from bogart/AS_BAT_Logging.C:38: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 12 and 4115 bytes into a destination of size 4096 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)': -bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false); - | ^~~~~ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/reproducible-path/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C cp -pf pipelines/canu.pl /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/canu chmod +x /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/canu @@ -2836,29 +2894,6 @@ cp -pf pipelines/canu/Execution.pm /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/SequenceStore.pm /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ -bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': -bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int -bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int cp -pf pipelines/canu/Grid_Cloud.pm /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/site_perl/canu/ @@ -2893,57 +2928,6 @@ utgcns/utgcns.C:890:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 890 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gfa/alignGFA.C: In function 'bool checkRecord(bedRecord*, sequences&, sequences&, sequences&, bool, bool)': -gfa/alignGFA.C:507:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 507 | success &= checkRecord_align("ALL", - | ^~~~~ -gfa/alignGFA.C:535:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 535 | success &= checkRecord_align("LEFT", - | ^~~~~~ -gfa/alignGFA.C:541:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 541 | success &= checkRecord_align("RIGHT", - | ^~~~~~~ -gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, double, uint32)': -gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0"); - | ^~~~~~~~~~~~~ -gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': -gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 162 | system(Pfile); - | ~~~~~~^~~~~~~ -gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] - 140 | sprintf(Pname, "plot-%s-%s", Aname, Bname); - | ^~ ~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from gfa/alignGFA.C:30: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 8199 bytes into a destination of size 4097 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gfa/alignGFA.C:141:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] - 141 | sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname); - | ^~ ~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from gfa/alignGFA.C:30: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 10 and 8202 bytes into a destination of size 4097 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gfa/alignGFA.C:160:27: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=] - 160 | sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname); - | ^~ ~~~~~ -In file included from /usr/include/stdio.h:867, - from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, - from gfa/alignGFA.C:30: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 13 and 8205 bytes into a destination of size 4097 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': bogus/bogusUtil.C:125:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets(inLine, 1024, inFile); // (file paths) @@ -2983,6 +2967,20 @@ bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 327 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gfa/alignGFA.C: In function 'bool checkRecord(bedRecord*, sequences&, sequences&, sequences&, bool, bool)': +gfa/alignGFA.C:507:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 507 | success &= checkRecord_align("ALL", + | ^~~~~ +gfa/alignGFA.C:535:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 535 | success &= checkRecord_align("LEFT", + | ^~~~~~ +gfa/alignGFA.C:541:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 541 | success &= checkRecord_align("RIGHT", + | ^~~~~~~ +gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, double, uint32)': +gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0"); + | ^~~~~~~~~~~~~ ar rv /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/libcanu.a /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/edlib.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/logging.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqCache.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadData.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o ar: creating /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib/libcanu.a a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.o @@ -3028,7 +3026,11 @@ a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o +a - /build/reprogfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': +gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 162 | system(Pfile); + | ~~~~~~^~~~~~~ +ducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o a - /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o @@ -3061,6 +3063,39 @@ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu +gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] + 140 | sprintf(Pname, "plot-%s-%s", Aname, Bname); + | ^~ ~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from gfa/alignGFA.C:30: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 8199 bytes into a destination of size 4097 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gfa/alignGFA.C:141:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] + 141 | sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname); + | ^~ ~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from gfa/alignGFA.C:30: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 10 and 8202 bytes into a destination of size 4097 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gfa/alignGFA.C:160:27: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=] + 160 | sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname); + | ^~ ~~~~~ +In file included from /usr/include/stdio.h:867, + from /build/reproducible-path/canu-2.0+dfsg/src/AS_global.H:67, + from gfa/alignGFA.C:30: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 13 and 8205 bytes into a destination of size 4097 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu @@ -3098,10 +3133,10 @@ g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu +g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.o -lcanu g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu -g++ -o /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.0+dfsg/Linux-amd64/lib /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.o -lcanu Success! canu installed in /build/reproducible-path/canu-2.0+dfsg/Linux-amd64/bin/canu @@ -3144,8 +3179,8 @@ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ -dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-1_amd64.deb'. +dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../canu_2.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3153,12 +3188,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/341593/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/341593/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/2645341 and its subdirectories -I: Current time: Thu Aug 7 05:00:43 -12 2025 -I: pbuilder-time-stamp: 1754586043 +I: removing directory /srv/workspace/pbuilder/341593 and its subdirectories +I: Current time: Sat Jul 6 00:53:23 +14 2024 +I: pbuilder-time-stamp: 1720176803