Diff of the two buildlogs: -- --- b1/build.log 2023-05-29 04:49:51.428393934 +0000 +++ b2/build.log 2023-05-29 05:00:17.897007649 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 28 16:29:50 -12 2023 -I: pbuilder-time-stamp: 1685334590 +I: Current time: Mon May 29 18:51:03 +14 2023 +I: pbuilder-time-stamp: 1685335863 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./canu_2.0+dfsg.orig.tar.xz] I: copying [./canu_2.0+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Oct 28 08:38:47 2021 -12 +gpgv: Signature made Fri Oct 29 10:38:47 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,167 @@ dpkg-source: info: applying remove-deprecated-sysctl.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1343/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 May 29 18:51 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='1bf589266f774ae8ab00f52922f71cf2' - 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='1343' - PS1='# ' - PS2='> ' + INVOCATION_ID=260c6215efc24974b26b18a53ea08a08 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1803 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.nbiCOcZF/pbuilderrc_V7wK --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nbiCOcZF/b1 --logfile b1/build.log canu_2.0+dfsg-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.nbiCOcZF/pbuilderrc_hLK6 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nbiCOcZF/b2 --logfile b2/build.log --extrapackages usrmerge canu_2.0+dfsg-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1343/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 29 18:51 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -279,7 +311,7 @@ Get: 74 http://deb.debian.org/debian bookworm/main armhf libmeryl-dev armhf 0~20150903+r2013-8+b3 [60.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libssw-java armhf 1.1-13 [19.1 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf mhap all 2.1.3+dfsg-3 [160 kB] -Fetched 99.0 MB in 10s (9749 kB/s) +Fetched 99.0 MB in 9s (11.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:armhf. (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 ... 19324 files and directories currently installed.) @@ -758,10 +790,17 @@ Reading package lists... Building dependency tree... Reading state information... +usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../canu_2.0+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../canu_2.0+dfsg-2_source.changes dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -785,20 +824,21 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-2.0+dfsg' dh_auto_build - cd src && make -j3 "INSTALL=install --strip-program=true" + cd src && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/canu-2.0+dfsg/src' WARNING: WARNING: g++ 12 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: -Building for 'Linux' '5.10.0-23-armmp-lpae' as 'armv7l' into '/build/canu-2.0+dfsg/Linux-armv7l/{bin,obj}'. +Building for 'Linux' '5.10.0-23-arm64' as 'aarch64' into '/build/canu-2.0+dfsg/Linux-aarch64/{bin,obj}'. Using '/usr/bin/g++' version '12'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'. -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C Building release v2.0 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C utility/files.C: In function 'void writeToFile(void*, const char*, uint64, uint64, FILE*)': utility/files.C:89:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n", @@ -932,9 +972,9 @@ utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 684 | fgets(line, FILENAME_MAX, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | read(_fd, _data, _length); @@ -943,7 +983,6 @@ utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | write(_fd, _data, _length), close(_fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C utility/logging.C: In member function 'void logFileInstance::rotate()': utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); @@ -1012,11 +1051,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C In file included from utility/kmers.H:32, from utility/kmers.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -1026,15 +1064,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from utility/kmers.H:32, - from utility/kmers-reader.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1090,6 +1119,40 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C +utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] + 58 | #warning how to set prefix size for streaming operations? + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C +In file included from utility/kmers.H:32, + from utility/kmers-reader.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers.H:32, + from utility/kmers-writer-block.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from utility/kmers.H:32, + from utility/kmers-writer.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1211,37 +1274,95 @@ | ~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C -utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': -utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from utility/kmers.H:29: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)' at utility/kmers-reader.C:143:11: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] - 58 | #warning how to set prefix size for streaming operations? - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C -In file included from utility/kmers.H:32, - from utility/kmers-writer.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-writer-block.C: In member function 'void kmerCountBlockWriter::mergeBatches(uint32)': +utility/kmers-writer-block.C:325:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 326 | oi, ii, prefix, inBlocks[ii].prefix()); + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-writer-block.C:325:96: warning: format '%lx' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 326 | oi, ii, prefix, inBlocks[ii].prefix()); + | ~~~~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers-writer-block.C:370:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); + | ~~^ ~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +utility/kmers-writer-block.C:370:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1329,6 +1450,22 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %016llx +utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': +utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from utility/kmers.H:29: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)' at utility/kmers-reader.C:143:11: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ 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); @@ -1354,16 +1491,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from utility/kmers.H:32, - from utility/kmers-writer-block.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1419,95 +1547,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-writer-block.C: In member function 'void kmerCountBlockWriter::mergeBatches(uint32)': -utility/kmers-writer-block.C:325:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 326 | oi, ii, prefix, inBlocks[ii].prefix()); - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-writer-block.C:325:96: warning: format '%lx' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 326 | oi, ii, prefix, inBlocks[ii].prefix()); - | ~~~~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers-writer-block.C:370:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); - | ~~^ ~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/kmers-writer-block.C:370:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu In file included from /usr/include/c++/12/map:60, from utility/kmers.H:34: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': @@ -1525,16 +1564,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C -In file included from utility/kmers.H:32, - from utility/kmers-statistics.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void kmerCountStatistics::addValue(uint64)' at utility/kmers.H:356:21, inlined from 'void kmerCountBlockWriter::mergeBatches(uint32)' at utility/kmers-writer-block.C:395:31: @@ -1545,6 +1575,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void kmerCountStatistics::addValue(uint64)' at utility/kmers.H:356:21, + inlined from 'void kmerCountBlockWriter::addBlock(uint64, uint64, uint64*, uint32*)' at utility/kmers-writer-block.C:139:29: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In file included from utility/kmers.H:32, + from utility/kmers-statistics.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1600,17 +1651,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void kmerCountStatistics::addValue(uint64)' at utility/kmers.H:356:21, - inlined from 'void kmerCountBlockWriter::addBlock(uint64, uint64, uint64*, uint32*)' at utility/kmers-writer-block.C:139:29: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C In file included from utility/kmers.H:32, from utility/kmers-exact.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -1620,7 +1660,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -1921,12 +1960,12 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C 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"; @@ -1940,12 +1979,12 @@ utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 260 | args[4] = "--output"; | ^~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/falconConsensus.H:75, - from correction/falconConsensus-alignTag.C:73: + from correction/falconConsensus.C:73: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -1956,7 +1995,7 @@ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/falconConsensus.H:75, - from correction/falconConsensus.C:73: + from correction/falconConsensus-alignTag.C:73: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -1964,8 +2003,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -1977,6 +2017,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)': stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases); @@ -1995,9 +2036,8 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)': stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 109 | buffer->writeIFFchunk("BLOB"); @@ -2026,8 +2066,6 @@ stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 132 | buffer->closeIFFchunk("BLOB"); | ^~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C In file included from stores/sqStoreBlob.C:26: In function 'void makeBlobName(char*, uint32, char*)', inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: @@ -2075,8 +2113,65 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C +stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] + 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING + | ^~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C +stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()': +stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] + 82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::readInfo8(char*)': +stores/sqStoreInfo.C:229:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 229 | fprintf(stderr, "sqStore_loadInfo()-- Error: Unsupported historical version %lu detected.\n", _sqVersion); + | ~~^ ~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +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); + | ^~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:204:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 204 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); @@ -2184,9 +2279,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] - 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING - | ^~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:225:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 225 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawc", _storePath, V); @@ -2420,59 +2512,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()': -stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] - 82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::readInfo8(char*)': -stores/sqStoreInfo.C:229:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 229 | fprintf(stderr, "sqStore_loadInfo()-- Error: Unsupported historical version %lu detected.\n", _sqVersion); - | ~~^ ~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -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/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", @@ -2506,11 +2545,7 @@ | ~~~~~~~~~~~~ | | | int -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C -stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] - 71 | #warning not failing if a valid store - | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C stores/ovStore.C: In member function 'void ovStore::testStore(bool)': stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n", @@ -2534,6 +2569,10 @@ | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C +stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] + 71 | #warning not failing if a valid store + | ^~~~~~~ In file included from stores/ovStore.C:59: stores/ovStore.H: In constructor 'ovStore::ovStore(const char*, sqStore*)': stores/ovStore.H:77:39: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] @@ -2565,6 +2604,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C stores/ovStoreWriter.C: 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); @@ -2641,7 +2681,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': stores/ovStore.H:79:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 79 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); @@ -2688,7 +2727,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C stores/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); @@ -2793,7 +2832,28 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +In file included from stores/ovStore.H:43, + from stores/ovStoreFile.C:47: +stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': +stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); + | ^~~ +In file included from /usr/include/stdio.h:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from stores/ovStore.H:37: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'ovFileOCW::ovFileOCW(sqStore*, const char*)' at stores/ovStoreFile.H:89:15, + inlined from 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)' at stores/ovStoreFile.C:221:47: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'int' [-Wformat=] 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", @@ -2826,6 +2886,15 @@ | | | int In file included from stores/tgTig.H:36, + from stores/tgTig.C:34: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStore.C:44: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -2835,25 +2904,21 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from stores/ovStore.H:43, - from stores/ovStoreFile.C:47: -stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': -stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); - | ^~~ -In file included from /usr/include/stdio.h:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from stores/ovStore.H:37: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'ovFileOCW::ovFileOCW(sqStore*, const char*)' at stores/ovStoreFile.H:89:15, - inlined from 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)' at stores/ovStoreFile.C:221:47: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'void tgTig::dumpLayout(FILE*, bool)': +stores/tgTig.C:547:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 547 | fprintf(stderr, "ERROR: _bases length %ld\n", strlen(_bases)); + | ~~^ ~~~~~~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': +stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': +stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:191:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); @@ -2905,6 +2970,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': +stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ +stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 690 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStoreEntry*&, uint32&, uint32)': stores/tgStore.C:594:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); @@ -2985,18 +3057,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C -In file included from stores/tgTig.H:36, - from stores/tgTig.C:34: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu In file included from stores/tgTig.H:36, from stores/tgTigSizeAnalysis.H:41, from stores/tgTigSizeAnalysis.C:42: @@ -3007,31 +3067,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -stores/tgTig.C: In member function 'void tgTig::dumpLayout(FILE*, bool)': -stores/tgTig.C:547:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 547 | fprintf(stderr, "ERROR: _bases length %ld\n", strlen(_bases)); - | ~~^ ~~~~~~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -stores/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", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/tgTigMultiAlignDisplay.C:42: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu stores/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); @@ -3048,18 +3083,22 @@ 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++; - | ~~~~~^~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgTigMultiAlignDisplay.C:42: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, @@ -3071,12 +3110,13 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -3089,10 +3129,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C In file included from utgcns/libNDalign/NDalign.C:36: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -3138,8 +3177,10 @@ utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 838 | display("NDalign::realignBackward()-- ", displayAlign); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C In file included from /usr/include/c++/12/set:60, from utility/strings.H:37, from stores/ovOverlap.H:45, @@ -3179,7 +3220,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void NDalign::fastFindMersB(bool)' at utgcns/libNDalign/NDalign.C:364:28: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -3207,15 +3247,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C gfa/gfa.C: In member function 'void gfaSequence::load(char*)': gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 123 | findGFAtokenI(_features, "LN:i:", _length); | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C 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"); @@ -3223,7 +3264,6 @@ 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/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C stores/ovStoreConfig.C: In member function 'void ovStoreConfig::assignReadsToSlices(sqStore*, uint64, uint64)': stores/ovStoreConfig.C:288:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 288 | fprintf(stderr, "ERROR: expected %u slices, generated %u instead. %lu overlaps per slice allowed.\n", @@ -3251,8 +3291,6 @@ stores/ovStoreConfig.C:385:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 385 | err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C stores/ovStoreBucketizer.C: In function 'int main(int, char**)': stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 139 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); @@ -3266,6 +3304,9 @@ stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C 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"); @@ -3273,19 +3314,6 @@ stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 170 | err.push_back("ERROR: no slice number (-F) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C -stores/ovStoreIndexer.C: In function 'int main(int, char**)': -stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 80 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreIndexer.C:83:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 83 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 86 | err.push_back("ERROR: No config (-C) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/ovStoreDump.C:56: @@ -3296,6 +3324,16 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +stores/ovStoreIndexer.C: In function 'int main(int, char**)': +stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 80 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreIndexer.C:83:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 83 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] + 86 | err.push_back("ERROR: No config (-C) supplied.\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/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"); @@ -3306,12 +3344,8 @@ stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from utgcns/libpbutgcns/AlnGraphBoost.C:68: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C In file included from stores/ovStoreStats.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -3341,36 +3375,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'const std::vector AlnGraphBoost::bestPath()' at utgcns/libpbutgcns/AlnGraphBoost.C:458:23: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'const std::vector AlnGraphBoost::bestPath()' at utgcns/libpbutgcns/AlnGraphBoost.C:474:57: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'const std::vector AlnGraphBoost::bestPath()' at utgcns/libpbutgcns/AlnGraphBoost.C:486:24: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C stores/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); @@ -3378,7 +3383,12 @@ stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C +In file included from /usr/include/c++/12/map:60, + from utgcns/libpbutgcns/AlnGraphBoost.C:68: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -3434,6 +3444,35 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'const std::vector AlnGraphBoost::bestPath()' at utgcns/libpbutgcns/AlnGraphBoost.C:458:23: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'const std::vector AlnGraphBoost::bestPath()' at utgcns/libpbutgcns/AlnGraphBoost.C:474:57: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'const std::vector AlnGraphBoost::bestPath()' at utgcns/libpbutgcns/AlnGraphBoost.C:486:24: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C stores/sqStoreDumpMetaData.C: In function 'void dumpReads(sqStore*, uint32, uint32, sqRead_which)': stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n", @@ -3458,7 +3497,6 @@ | | | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from utility/arrays.H:33, @@ -3473,43 +3511,8 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': -sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] - 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); - | ~~^ - | | - | long unsigned int - | %llu -sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); - | ~~^ ~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector)': -sequence/sequence-summarize.C:120:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] - 120 | fprintf(stdout, "%lu\n", lengths[ii]); - | ~~^ - | | - | long unsigned int - | %llu -sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': -sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ - | | - | std::vector::size_type {aka unsigned int} -sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ - | | - | std::vector::size_type {aka unsigned int} -sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ - | | - | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C In file included from /usr/include/c++/12/vector:70, from utility/files.H:36, from stores/sqStore.H:38, @@ -3552,6 +3555,58 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgStoreCompress.C:45: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': +sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] + 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); + | ~~^ + | | + | long unsigned int + | %llu +sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); + | ~~^ ~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector)': +sequence/sequence-summarize.C:120:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] + 120 | fprintf(stdout, "%lu\n", lengths[ii]); + | ~~^ + | | + | long unsigned int + | %llu +sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': +sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ + | | + | std::vector::size_type {aka unsigned int} +sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ + | | + | std::vector::size_type {aka unsigned int} +sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ + | | + | std::vector::size_type {aka unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C +stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] + 675 | #warning replace this with genericStatistics + | ^~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from utility/arrays.H:33, @@ -3613,6 +3668,16 @@ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from stores/tgTig.H:36, + from stores/tgTigSizeAnalysis.H:41, + from stores/tgTigSizeAnalysis.C:42: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = less]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'void doSummarize_dumpLengths(std::vector)' at sequence/sequence-summarize.C:117:7: @@ -3626,7 +3691,6 @@ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -3637,80 +3701,7 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from stores/tgStoreCompress.C:45: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, - inlined from 'void doSummarize_lengthHistogram(std::vector, uint64, bool)' at sequence/sequence-summarize.C:130:7: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, - inlined from 'void doSummarize_lengthHistogram(std::vector, uint64, bool)' at sequence/sequence-summarize.C:130:7: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] - 675 | #warning replace this with genericStatistics - | ^~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void doSummarize(std::vector&, summarizeParameters&)' at sequence/sequence-summarize.C:380:26: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void doSummarize(std::vector&, summarizeParameters&)' at sequence/sequence-summarize.C:409:28: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/tgStoreDump.C:55: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgTigSizeAnalysis.H:41, - from stores/tgTigSizeAnalysis.C:42: + from stores/tgStoreLoad.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -3736,7 +3727,7 @@ | ^~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from stores/tgStoreLoad.C:33: + from stores/tgStoreDump.C:55: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -3754,8 +3745,57 @@ stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C +stores/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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, + inlined from 'void doSummarize_lengthHistogram(std::vector, uint64, bool)' at sequence/sequence-summarize.C:130:7: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, + inlined from 'void doSummarize_lengthHistogram(std::vector, uint64, bool)' at sequence/sequence-summarize.C:130:7: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void doSummarize(std::vector&, summarizeParameters&)' at sequence/sequence-summarize.C:380:26: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void doSummarize(std::vector&, summarizeParameters&)' at sequence/sequence-summarize.C:409:28: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStoreFilter.C:45: @@ -3768,23 +3808,6 @@ | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, - from stores/tgTigDisplay.C:33: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C -stores/loadTrimmedReads.C: In function 'int main(int, char**)': -stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] - 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadErates.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, from stores/loadCorrectedReads.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -3808,11 +3831,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/tgTigDisplay.C:33: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadErates.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] 261 | #warning HARD CODED NUMBER OF FILES! | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C 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"); @@ -3823,6 +3857,10 @@ stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stores/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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -3934,6 +3972,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -3945,6 +3986,61 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +meryl/meryl.C: In function 'int main(int, char**)': +meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /build/canu-2.0+dfsg/src/AS_global.H:67, + from meryl/meryl.H:49: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:331:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/meryl.C: In function 'int main(int, char**)': +meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString); + | ^~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:332:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/meryl.C: In function 'int main(int, char**)': +meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString); + | ^~~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:333:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/meryl.C: In function 'int main(int, char**)': +meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=] + 594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString); + | ^~ ~~~~~~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int main(int, char**)' at meryl/meryl.C:594:15: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 + 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 56 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4016,7 +4112,6 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, from meryl/meryl.H:49: meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': @@ -4040,7 +4135,7 @@ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylInput.C:26: + from meryl/merylOp-count.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4048,6 +4143,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4059,128 +4155,10 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ~^~~~~~~~~~~~~~~~~~ -meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 52 | if (_stream) return("meryl-database"); - | ~^~~~~~~~~~~~~~~~~ -meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | if (_sequence) return("sequence-file"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | if (_store) return("canu-seqStore"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 58 | return("invalid-input"); - | ~^~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /build/canu-2.0+dfsg/src/AS_global.H:67, - from meryl/meryl.H:49: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:331:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString); - | ^~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:332:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString); - | ^~~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:333:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/meryl.C: In function 'int main(int, char**)': -meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=] - 594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString); - | ^~ ~~~~~~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int main(int, char**)' at meryl/meryl.C:594:15: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 - 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 56 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp-count.C:26: + from meryl/merylInput.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4188,17 +4166,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ @@ -4243,17 +4210,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-countSimple.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4270,61 +4226,6 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': -utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - | ~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~~~^ - | | - | long unsigned int - | %016llx - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu - 595 | prefix, - 596 | _blockPrefix, _blockPosition, _numKmers, - | ~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} -utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", - | ~~~^ - | | - | long unsigned int - | %8llu -...... - 597 | AS_UTL_ftell(F), _numKmers + nKmers); - | ~~~~~~~~~~~~~~~~~~ - | | - | uint64 {aka long long unsigned int} meryl/merylOp-count.C: In function 'uint64 findMaxInputSizeForMemorySize(uint32, uint64)': meryl/merylOp-count.C:69:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 69 | fprintf(stderr, "For memory size %lu bytes\n", memSize); @@ -4460,17 +4361,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from meryl/merylInput.H:30, - from meryl/meryl.H:51, - from meryl/merylOp-histogram.C:26: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu meryl/merylOp-count.C: In member function 'void merylOperation::count(uint32, uint64, uint32, uint64)': meryl/merylOp-count.C:603:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 603 | fprintf(stderr, "Used %3.3f GB out of %3.3f GB to store %12lu kmers.\n", @@ -4483,6 +4373,61 @@ | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4499,6 +4444,17 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp-countSimple.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4554,6 +4510,22 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ~^~~~~~~~~~~~~~~~~~ +meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 52 | if (_stream) return("meryl-database"); + | ~^~~~~~~~~~~~~~~~~ +meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | if (_sequence) return("sequence-file"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | if (_store) return("canu-seqStore"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 58 | return("invalid-input"); + | ~^~~~~~~~~~~~~~~~ meryl/merylOp-countSimple.C: In member function 'void merylOperation::countSimple()': meryl/merylOp-countSimple.C:107:76: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 107 | fprintf(stderr, "Increasing to %u-bit storage (for kmer 0x%016lx).\n", @@ -4586,35 +4558,19 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %016llx -meryl/merylInput.H: In member function 'char* merylInput::inputType()': -meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 51 | if (_operation) return("meryl-operation"); - | ~^~~~~~~~~~~~~~~~~~ -meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 52 | if (_stream) return("meryl-database"); - | ~^~~~~~~~~~~~~~~~~ -meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | if (_sequence) return("sequence-file"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | if (_store) return("canu-seqStore"); - | ~^~~~~~~~~~~~~~~~ -meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 58 | return("invalid-input"); - | ~^~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] 98 | #warning "need to decide whic direction we're going?" | ^~~~~~~ meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] 116 | #warning "rounding issues in word-frequency!" | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp-nextMer.C:26: + from meryl/merylOp-histogram.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4622,10 +4578,11 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, - from meryl/merylOp.C:26: + from meryl/merylOp-nextMer.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); @@ -4688,6 +4645,77 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': +utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + | ~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~~~^ + | | + | long unsigned int + | %016llx + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu + 595 | prefix, + 596 | _blockPrefix, _blockPosition, _numKmers, + | ~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", + | ~~~^ + | | + | long unsigned int + | %8llu +...... + 597 | AS_UTL_ftell(F), _numKmers + nKmers); + | ~~~~~~~~~~~~~~~~~~ + | | + | uint64 {aka long long unsigned int} +meryl/merylInput.H: In member function 'char* merylInput::inputType()': +meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 51 | if (_operation) return("meryl-operation"); + | ~^~~~~~~~~~~~~~~~~~ +meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 52 | if (_stream) return("meryl-database"); + | ~^~~~~~~~~~~~~~~~~ +meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | if (_sequence) return("sequence-file"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | if (_store) return("canu-seqStore"); + | ~^~~~~~~~~~~~~~~~ +meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 58 | return("invalid-input"); + | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -4740,6 +4768,17 @@ | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} +In file included from utility/kmers.H:32, + from meryl/merylInput.H:30, + from meryl/meryl.H:51, + from meryl/merylOp.C:26: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4811,6 +4850,7 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C In file included from utility/kmers.H:32, from meryl/meryl-import.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -4820,7 +4860,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4911,7 +4950,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, @@ -4923,6 +4962,7 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -4978,15 +5018,6 @@ | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from utility/kmers.H:32, - from meryl/meryl-lookup.C:28: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); @@ -5003,7 +5034,35 @@ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence.C +In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, + from meryl/meryl.H:49: +meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': +meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]' +meryl/merylCountArray.C:396:16: required from here +utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] + 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' + 41 | _s2 = suffix & uint64MASK(32); + | ^~~~~~~~~~ +meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]': +meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]' +meryl/merylCountArray.C:397:16: required from here +utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] + 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' + 41 | _s2 = suffix & uint64MASK(32); + | ^~~~~~~~~~ +In file included from utility/kmers.H:32, + from meryl/meryl-lookup.C:28: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", @@ -5146,26 +5205,7 @@ meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 289 | err.push_back("No report-type (-existence, etc) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, - from meryl/meryl.H:49: -meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': -meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]' -meryl/merylCountArray.C:396:16: required from here -utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] - 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' - 41 | _s2 = suffix & uint64MASK(32); - | ^~~~~~~~~~ -meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]': -meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]' -meryl/merylCountArray.C:397:16: required from here -utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] - 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' - 41 | _s2 = suffix & uint64MASK(32); - | ^~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C 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"); @@ -5241,15 +5281,15 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)': sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 92 | ">random%08 " F_U64P "\n", nSeqs); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C 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()); @@ -5265,6 +5305,15 @@ sequence/sequence-sample.C:417:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 417 | AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); | ^~~~~~~ +In file included from sequence/sequence-shiftregister.C:31: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C In file included from /usr/include/c++/12/vector:70, from utility/strings.H:38, from /build/canu-2.0+dfsg/src/sequence/sequence.H:32, @@ -5273,9 +5322,61 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from sequence/sequence-shiftregister-emit-fast.C:29: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +sequence/sequence-shiftregister-emit-fast.C: In function 'void emitShiftRegisterFast(shiftRegisterParameters&)': +sequence/sequence-shiftregister-emit-fast.C:52:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 52 | fprintf(stderr, "Emitting %lu bases, plus an extra %u.\n", srPar.length - srPar.order - 1 - 1, srPar.order - 1); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +sequence/sequence-shiftregister-emit-fast.C:53:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 53 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr)); + | ~~~~^ ~~~~~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %0*llo +sequence/sequence-shiftregister-emit-fast.C:54:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 54 | fprintf(stderr, " cyclen %lu\n", cyclen); + | ~~^ ~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +sequence/sequence-shiftregister-emit-fast.C:55:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 55 | fprintf(stderr, " cycmax %lu\n", cycmax); + | ~~^ ~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +sequence/sequence-shiftregister-emit-fast.C:56:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 56 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv)); + | ~~~~^ ~~~~~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %0*llo +sequence/sequence-shiftregister-emit-fast.C:57:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 57 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax)); + | ~~~~^ ~~~~~~~~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %0*llo +sequence/sequence-shiftregister-emit-fast.C:58:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 58 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask)); + | ~~~~^ ~~~~~~~~~~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %0*llo /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {seqEntry}; _Tp = seqEntry; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -5317,14 +5418,7 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from sequence/sequence-shiftregister.C:31: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const seqEntry&, const seqEntry&)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'void doSample_sample(sampleParameters&, uint64, uint64, std::vector&)' at sequence/sequence-sample.C:118:7: @@ -5357,66 +5451,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void doSample_single(std::vector&, sampleParameters&)' at sequence/sequence-sample.C:398:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C -In file included from sequence/sequence-shiftregister-emit-fast.C:29: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -sequence/sequence-shiftregister-emit-fast.C: In function 'void emitShiftRegisterFast(shiftRegisterParameters&)': -sequence/sequence-shiftregister-emit-fast.C:52:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 52 | fprintf(stderr, "Emitting %lu bases, plus an extra %u.\n", srPar.length - srPar.order - 1 - 1, srPar.order - 1); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -sequence/sequence-shiftregister-emit-fast.C:53:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 53 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr)); - | ~~~~^ ~~~~~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %0*llo -sequence/sequence-shiftregister-emit-fast.C:54:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 54 | fprintf(stderr, " cyclen %lu\n", cyclen); - | ~~^ ~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -sequence/sequence-shiftregister-emit-fast.C:55:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 55 | fprintf(stderr, " cycmax %lu\n", cycmax); - | ~~^ ~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -sequence/sequence-shiftregister-emit-fast.C:56:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 56 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv)); - | ~~~~^ ~~~~~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %0*llo -sequence/sequence-shiftregister-emit-fast.C:57:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 57 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax)); - | ~~~~^ ~~~~~~~~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %0*llo -sequence/sequence-shiftregister-emit-fast.C:58:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 58 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask)); - | ~~~~^ ~~~~~~~~~~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %0*llo In file included from sequence/sequence-shiftregister-search-fast.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -5496,8 +5535,6 @@ | ~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C In file included from sequence/sequence-shiftregister-search-slow.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -5542,6 +5579,10 @@ | ~~~~~~ | | | uint64 {aka long long unsigned int} +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C 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); @@ -5575,7 +5616,6 @@ | ~~~~~~~~ | | | uint64 {aka long long unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); @@ -5612,7 +5652,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5642,6 +5681,19 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/sqCache.H:30, + from overlapInCore/overlapInCore.H:66, + from overlapInCore/overlapInCore-Build_Hash_Index.C:67: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -5656,6 +5708,10 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': +overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 258 | fgets(line, 1024, F); + | ~~~~~^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from utility/strings.H:38, from /build/canu-2.0+dfsg/src/sequence/sequence.H:32: @@ -5665,6 +5721,7 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -5727,18 +5784,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore-Build_Hash_Index.C:67: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void doSummarize(std::vector&, summarizeParameters&)' at sequence/sequence-summarize.C:380:26: @@ -5751,12 +5796,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C -overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': -overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 258 | fgets(line, 1024, F); - | ~~~~~^~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5781,9 +5820,10 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -5796,18 +5836,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from stores/sqCache.H:30, - from overlapInCore/overlapInCore.H:66, - from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu overlapInCore/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"); @@ -5827,10 +5855,20 @@ overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 447 | renameToFinal(outputPrefix, "ovlopt"); | ^~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from stores/sqCache.H:30, + from overlapInCore/overlapInCore.H:66, + from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C 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? | ^~~~~~~ @@ -5847,6 +5885,9 @@ overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, @@ -5858,10 +5899,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -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, @@ -5899,8 +5936,12 @@ overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 587 | aRead, abgn, aend, alen, "Ab3", aID, | ^~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C +overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': +overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | fgets(line, lineMax, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C mhap/mhapConvert.C: In function 'int main(int, char**)': mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", @@ -5934,19 +5975,6 @@ | ~~~~~~~~~~~~~~~ | | | int -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from wtdbg/wtdbgConvert.C:33: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu minimap/mmapConvert.C: In function 'int main(int, char**)': minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", @@ -5980,8 +6008,19 @@ | ~~~~~~~~~~~~~~~ | | | int -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from wtdbg/wtdbgConvert.C:33: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/generateCorrectionLayouts.C:37: @@ -6040,15 +6079,6 @@ | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} -In file included from /usr/include/c++/12/set:60, - from utility/strings.H:37, - from stores/ovOverlap.H:45, - from stores/ovStore.H:42, - from wtdbg/wtdbgConvert.C:31: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, @@ -6060,6 +6090,17 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C +In file included from /usr/include/c++/12/set:60, + from utility/strings.H:37, + from stores/ovOverlap.H:45, + from stores/ovStore.H:42, + from wtdbg/wtdbgConvert.C:31: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61, from stores/tgTig.H:38: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', @@ -6071,25 +6112,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int main(int, char**)' at wtdbg/wtdbgConvert.C:237:37: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int main(int, char**)' at wtdbg/wtdbgConvert.C:243:37: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/filterCorrectionLayouts.C:29: @@ -6100,8 +6122,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -6113,18 +6133,24 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from utgcns/stashContains.H:35, - from utgcns/stashContains.C:30: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'int main(int, char**)' at wtdbg/wtdbgConvert.C:237:37: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'int main(int, char**)' at wtdbg/wtdbgConvert.C:243:37: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ correction/falconsense.C: In function 'void generateFalconConsensus(falconConsensus*, tgTig*, sqCache*, std::map&, bool, uint32)': correction/falconsense.C:207:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 207 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem); @@ -6152,6 +6178,20 @@ correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fgets(L, 1024, R)) { | ~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from utgcns/stashContains.H:35, + from utgcns/stashContains.C:30: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu In file included from correction/errorEstimate.C:34: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] @@ -6181,9 +6221,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C In file included from utility/kmers.H:32, from haplotyping/splitHaplotype.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': @@ -6288,6 +6325,9 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %12llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C 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); @@ -6321,16 +6361,14 @@ overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | system(N); | ~~~~~~^~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C 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"); @@ -6346,6 +6384,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -6357,7 +6397,6 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C 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 @@ -6394,8 +6433,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, @@ -6407,10 +6446,8 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from utility/arrays.H:33, @@ -6448,12 +6485,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 266 | _GLIBCXX_MOVE(__value), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C 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", @@ -6491,14 +6528,16 @@ overlapErrorAdjustment/findErrors-Dump.C:77:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 77 | "EXTENSION", | ^~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)': overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID); | ^~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/bogart.C:46: @@ -6552,8 +6591,8 @@ bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 756 | writeTigsToStore(unitigs, prefix, "utg", true); | ^~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_AssemblyGraph.C:28: @@ -6615,22 +6654,6 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C -In file included from /usr/include/c++/12/vector:70, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_AssemblyGraph.C:26: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BestPlacement&}; _Tp = BestPlacement; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BestPlacement; _Alloc = std::allocator]', - inlined from '_ZN13AssemblyGraph10buildGraphEPKcdR9TigVector._omp_fn.0' at bogart/AS_BAT_AssemblyGraph.C:359:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from utility/arrays.H:33, @@ -6641,11 +6664,31 @@ /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C +In file included from /usr/include/c++/12/vector:70, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_AssemblyGraph.C:26: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BestPlacement&}; _Tp = BestPlacement; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] + 486 | #warning deviationGraph hard coded + | ^~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BestPlacement; _Alloc = std::allocator]', + inlined from '_ZN13AssemblyGraph10buildGraphEPKcdR9TigVector._omp_fn.0' at bogart/AS_BAT_AssemblyGraph.C:359:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -6665,10 +6708,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C -bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] - 486 | #warning deviationGraph hard coded - | ^~~~~~~ In file included from /usr/include/c++/12/vector:70, from utility/files.H:36, from stores/ovStore.H:38, @@ -6679,6 +6718,37 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from bogart/AS_BAT_Unitig.H:49, + from bogart/AS_BAT_AssemblyGraph.H:32, + from bogart/AS_BAT_CreateUnitigs.C:29: +utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': +utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu +utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); + | ~~^ ~~~~~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); + | ~~^ ~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu +utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); + | ~~^ ~~~~~~~~~ + | | | + | | uint64 {aka long long unsigned int} + | long unsigned int + | %llu In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void BestOverlapGraph::findErrorRateThreshold()' at bogart/AS_BAT_BestOverlapGraph.C:178:46: @@ -6741,38 +6811,7 @@ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_CreateUnitigs.C:29: -utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': -utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); - | ~~^ ~~~~~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); - | ~~^ ~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); - | ~~^ ~~~~~~~~~ - | | | - | | uint64 {aka long long unsigned int} - | long unsigned int - | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_DetectSpurs.C:31: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -6803,9 +6842,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_DropDeadEnds.C:29: @@ -6867,6 +6907,10 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)': +bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false); + | ^~~~~ bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': bogart/AS_BAT_Logging.C:91:37: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); @@ -6887,14 +6931,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __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/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_MergeOrphans.C:35: + from bogart/AS_BAT_AssemblyGraph.H:32, + from bogart/AS_BAT_MarkRepeatReads.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6923,32 +6962,17 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': -bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int -bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] - 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", - | ~~^ - | | - | long int - | %d - 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, - 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, - | ~~~~~~~~~~~~~~ - | | - | int +bogart/AS_BAT_MarkRepeatReads.C: In function 'uint32 splitTig(TigVector&, Unitig*, std::vector&, Unitig**, int32*, uint32*, uint32*, bool)': +bogart/AS_BAT_MarkRepeatReads.C:170:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] + 170 | fprintf(stderr, "Failed to place read %u at %d-%d with %lu BPs:\n", frg.ident, frgbgn, frgend, BP.size()); + | ~~^ ~~~~~~~~~ + | | | + | long unsigned int std::vector::size_type {aka unsigned int} + | %u +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_AssemblyGraph.H:32, - from bogart/AS_BAT_MarkRepeatReads.C:29: + from bogart/AS_BAT_OptimizePositions.C:44: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -6977,36 +7001,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -bogart/AS_BAT_MarkRepeatReads.C: In function 'uint32 splitTig(TigVector&, Unitig*, std::vector&, Unitig**, int32*, uint32*, uint32*, bool)': -bogart/AS_BAT_MarkRepeatReads.C:170:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] - 170 | fprintf(stderr, "Failed to place read %u at %d-%d with %lu BPs:\n", frg.ident, frgbgn, frgend, BP.size()); - | ~~^ ~~~~~~~~~ - | | | - | long unsigned int std::vector::size_type {aka unsigned int} - | %u -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C -In file included from /usr/include/c++/12/vector:70, - from utility/files.H:36, - from stores/ovStore.H:38, - from bogart/AS_BAT_ReadInfo.H:30, - from bogart/AS_BAT_MergeOrphans.C:30: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = overlapPlacement; _Alloc = std::allocator]', - inlined from 'void assignReadsToTargets(Unitig*, std::vector*, std::vector)' at bogart/AS_BAT_MergeOrphans.C:736:40: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = overlapPlacement; _Alloc = std::allocator]', - inlined from '_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEdd._omp_fn.0' at bogart/AS_BAT_MergeOrphans.C:420:27: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from bogart/AS_BAT_Unitig.H:49, - from bogart/AS_BAT_OptimizePositions.C:44: + from bogart/AS_BAT_MergeOrphans.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); @@ -7035,7 +7031,30 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C +bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': +bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] + 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", + | ~~^ + | | + | long int + | %d + 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, + 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, + | ~~~~~~~~~~~~~~ + | | + | int +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Outputs.C:47: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7076,9 +7095,29 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C +In file included from /usr/include/c++/12/vector:70, + from utility/files.H:36, + from stores/ovStore.H:38, + from bogart/AS_BAT_ReadInfo.H:30, + from bogart/AS_BAT_MergeOrphans.C:30: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const overlapPlacement&}; _Tp = overlapPlacement; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = overlapPlacement; _Alloc = std::allocator]', + inlined from 'void assignReadsToTargets(Unitig*, std::vector*, std::vector)' at bogart/AS_BAT_MergeOrphans.C:736:40: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = overlapPlacement; _Alloc = std::allocator]', + inlined from '_Z24findOrphanReadPlacementsR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEdd._omp_fn.0' at bogart/AS_BAT_MergeOrphans.C:420:27: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_OverlapCache.C:49: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7169,7 +7208,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C In file included from /usr/include/c++/12/vector:70, from utility/files.H:36, from stores/ovStore.H:38, @@ -7179,14 +7218,13 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = overlapPlacement; _Alloc = std::allocator]', inlined from 'bool placeReadUsingOverlaps(TigVector&, Unitig*, uint32, std::vector&, uint32)' at bogart/AS_BAT_PlaceReadUsingOverlaps.C:681:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PopulateUnitig.C:42: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7217,6 +7255,9 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PromoteToSingleton.C:40: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7247,9 +7288,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SetParentAndHang.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7280,6 +7319,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SplitDiscontinuous.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7310,8 +7350,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_TigGraph.C:28: @@ -7396,6 +7436,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ @@ -7403,8 +7444,7 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig_AddRead.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': @@ -7465,9 +7505,8 @@ | | uint64 {aka long long unsigned int} | long unsigned int | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/utgcns.C:46: @@ -7578,6 +7617,33 @@ utgcns/utgcns.C:890:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 890 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/algorithm:61, + from utility/arrays.H:33, + from /build/canu-2.0+dfsg/src/AS_global.H:105, + from bogus/bogusUtil.H:42, + from bogus/bogus.C:38: +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/bits/stl_algo.h:60: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = genomeAlignment; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) @@ -7617,47 +7683,7 @@ bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 327 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from utility/files.H:36, - from bogus/bogusUtil.H:44, - from bogus/bogusUtil.C:43: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const genomeAlignment&}; _Tp = genomeAlignment; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = genomeAlignment; _Alloc = std::allocator]', - inlined from 'void addAlignment(std::vector&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)' at bogus/bogusUtil.C:102:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/algorithm:61, - from utility/arrays.H:33, - from /build/canu-2.0+dfsg/src/AS_global.H:105, - from bogus/bogusUtil.H:42, - from bogus/bogus.C:38: -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/12/bits/stl_algo.h:60: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = genomeAlignment; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/12/bits/stl_algo.h:1932:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | __sort(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -7688,18 +7714,20 @@ /usr/include/c++/12/bits/stl_algo.h:4853:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4853 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from utility/files.H:36, + from bogus/bogusUtil.H:44, + from bogus/bogusUtil.C:43: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const genomeAlignment&}; _Tp = genomeAlignment; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = genomeAlignment; _Alloc = std::allocator]', - inlined from 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)' at bogus/bogusUtil.C:271:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = genomeAlignment; _Alloc = std::allocator]', - inlined from 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)' at bogus/bogusUtil.C:197:21: + inlined from 'void addAlignment(std::vector&, int32, int32, int32, bool, int32, int32, double, int32, int32, int32)' at bogus/bogusUtil.C:102:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, @@ -7711,7 +7739,46 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = genomeAlignment; _Alloc = std::allocator]', + inlined from 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)' at bogus/bogusUtil.C:271:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = genomeAlignment; _Alloc = std::allocator]', + inlined from 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)' at bogus/bogusUtil.C:197:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C +cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-aarch64/bin/canu +chmod +x /build/canu-2.0+dfsg/Linux-aarch64/bin/canu +cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-aarch64/bin/canu-time +chmod +x /build/canu-2.0+dfsg/Linux-aarch64/bin/canu-time +echo > /build/canu-2.0+dfsg/Linux-aarch64/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." +chmod -x /build/canu-2.0+dfsg/Linux-aarch64/bin/canu.defaults +cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-aarch64/share/sequence/ultra-long-nanopore +cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-aarch64/share/sequence/pacbio +cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-aarch64/share/sequence/pacbio-hifi +cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from gfa/alignGFA.C:32: @@ -7722,6 +7789,12 @@ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu +cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-aarch64/lib/site_perl/canu/ +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C 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", @@ -7740,13 +7813,17 @@ gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | system(Pfile); | ~~~~~~^~~~~~~ -cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-armv7l/bin/canu -chmod +x /build/canu-2.0+dfsg/Linux-armv7l/bin/canu -cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-armv7l/bin/canu-time -chmod +x /build/canu-2.0+dfsg/Linux-armv7l/bin/canu-time -echo > /build/canu-2.0+dfsg/Linux-armv7l/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." -chmod -x /build/canu-2.0+dfsg/Linux-armv7l/bin/canu.defaults -cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-armv7l/share/sequence/ultra-long-nanopore +In file included from stores/tgTig.H:36, + from stores/tgStore.H:43, + from utgcns/unitigConsensus.H:67, + from utgcns/unitigConsensus.C:74: +utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': +utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] + 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); + | ~~^ ~~~~~~~~ + | | | + | long unsigned int uint64 {aka long long unsigned int} + | %llu gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] 140 | sprintf(Pname, "plot-%s-%s", Aname, Bname); | ^~ ~~~~~ @@ -7788,166 +7865,128 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-armv7l/share/sequence/pacbio -cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-armv7l/share/sequence/pacbio-hifi -cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-armv7l/lib/site_perl/canu/ -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C -In file included from stores/tgTig.H:36, - from stores/tgStore.H:43, - from utgcns/unitigConsensus.H:67, - from utgcns/unitigConsensus.C:74: -utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': -utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] - 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); - | ~~^ ~~~~~~~~ - | | | - | long unsigned int uint64 {aka long long unsigned int} - | %llu -ar rv /build/canu-2.0+dfsg/Linux-armv7l/lib/libcanu.a /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -ar: creating /build/canu-2.0+dfsg/Linux-armv7l/lib/libcanu.a -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/AS_global.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/edlib.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-buffered.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-compressed.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/files-memoryMapped.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/logging.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/strings.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/system-stackTrace.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sequence.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-reader.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-block.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-writer-stream.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-statistics.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/kmers-exact.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/bits.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/hexDump.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/md5.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/mt19937ar.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/objectStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/speedCounter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utility/sweatShop.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/computeGlobalScore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqCache.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqLibrary.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadData.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqReadDataWriter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreBlob.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreConstructor.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/sqStoreInfo.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovOverlap.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreWriter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFilter.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreFile.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/ovStoreHistogram.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgStore.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTig.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/stores/libsnappy/snappy.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/gfa.o -a - /build/canu-2.0+dfsg/Linux-armv7l/obj/lib/libcanu.a/gfa/bed.o -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/dumpBlob -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/dumpBlob/stores/dumpBlob.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreBuild -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreConfig -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreBucketizer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreSorter -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib /build/canu-2.0+dfsg/Linux-armv7l/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu -g++ -o /build/canu-2.0+dfsg/Linux-armv7l/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-armv7l/lib 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/build/canu-2.0+dfsg/Linux-aarch64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/bogus/bogus/bogusUtil.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu +g++ -o /build/canu-2.0+dfsg/Linux-aarch64/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-aarch64/lib /build/canu-2.0+dfsg/Linux-aarch64/obj/bin/alignGFA/gfa/alignGFA.o -lcanu Success! -canu installed in /build/canu-2.0+dfsg/Linux-armv7l/bin/canu +canu installed in /build/canu-2.0+dfsg/Linux-aarch64/bin/canu make[2]: Leaving directory '/build/canu-2.0+dfsg/src' builddir=*-*/; \ find $builddir \ @@ -7983,9 +8022,9 @@ dh_makeshlibs -a -O--sourcedirectory=src/ dh_shlibdeps -a -O--sourcedirectory=src/ dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapInCore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogart contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapPair contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/bogart contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/canu/usr/lib/canu/bin/overlapInCore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src/ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ @@ -7999,12 +8038,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1803/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1803/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/1343 and its subdirectories -I: Current time: Sun May 28 16:49:39 -12 2023 -I: pbuilder-time-stamp: 1685335779 +I: removing directory /srv/workspace/pbuilder/1803 and its subdirectories +I: Current time: Mon May 29 19:00:10 +14 2023 +I: pbuilder-time-stamp: 1685336410