Diff of the two buildlogs: -- --- b1/build.log 2023-06-09 11:45:31.761290850 +0000 +++ b2/build.log 2023-06-09 11:49:22.663193797 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 8 23:27:22 -12 2023 -I: pbuilder-time-stamp: 1686310043 +I: Current time: Sat Jun 10 01:45:59 +14 2023 +I: pbuilder-time-stamp: 1686311159 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 [./survivor_1.0.7.orig.tar.gz] I: copying [./survivor_1.0.7-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 6 03:00:39 2022 -12 +gpgv: Signature made Wed Dec 7 05:00:39 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,135 +28,167 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16331/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/9907/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 Jun 10 01:46 /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/9907/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/9907/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='8a77545008bd41b7b00ac3df15f2604b' - 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='16331' - PS1='# ' - PS2='> ' + INVOCATION_ID=fe765f4e12fe4fbc89d6915b81f8af4f + 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=9907 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.JfcMPviT/pbuilderrc_KPAs --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.JfcMPviT/b1 --logfile b1/build.log survivor_1.0.7-4.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.JfcMPviT/pbuilderrc_8Bxp --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.JfcMPviT/b2 --logfile b2/build.log --extrapackages usrmerge survivor_1.0.7-4.dsc' + SUDO_GID=114 + SUDO_UID=108 + 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 wbq0 5.10.0-23-armmp #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/16331/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 Jun 10 01:46 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/9907/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +257,7 @@ Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] -Fetched 18.9 MB in 2s (8253 kB/s) +Fetched 18.9 MB in 0s (45.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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.) @@ -363,8 +395,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/survivor-1.0.7/ && 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 > ../survivor_1.0.7-4_source.changes +I: user script /srv/workspace/pbuilder/9907/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/9907/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/survivor-1.0.7/ && 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 > ../survivor_1.0.7-4_source.changes dpkg-buildpackage: info: source package survivor dpkg-buildpackage: info: source version 1.0.7-4 dpkg-buildpackage: info: source distribution unstable @@ -374,11 +417,11 @@ debian/rules clean dh clean --sourcedirectory=Debug dh_auto_clean -O--sourcedirectory=Debug - cd Debug && make -j3 clean -make[1]: Entering directory '/build/survivor-1.0.7/Debug' + cd Debug && make -j4 clean +make[1]: ingresso nella directory «/build/survivor-1.0.7/Debug» rm -rf ./src/vcfs/Annotate_vcf.o ./src/vcfs/Combine_3_VCF.o ./src/vcfs/Compoverlap_VCF.o ./src/vcfs/Detect_nested.o ./src/vcfs/Filter_vcf.o ./src/vcfs/Generate_distMat.o ./src/vcfs/Merge_VCF.o ./src/snp_overlap/Overlap_snps.o ./src/simulator/Error_scanner.o ./src/simulator/Eval_vcf.o ./src/simulator/Pac_Simulator.o ./src/simulator/SV_Simulator.o ./src/simulator/Sim_reads.o ./src/simulator/test_cov.o ./src/scrup_vcf/scrup_svs.o ./src/phasing/Phasing_vcf.o ./src/merge_vcf/IntervallTree.o ./src/merge_vcf/combine_svs.o ./src/convert/ConvertMQ0Bed.o ./src/convert/Convert_Assemblytics.o ./src/convert/Convert_Bionano.o ./src/convert/Convert_Honey_tails.o ./src/convert/Convert_MUMmer.o ./src/convert/Convert_Pindel.o ./src/convert/Convert_VCF_to_BED.o ./src/convert/Convert_hapcut2.o ./src/convert/Process_Coverage.o ./src/convert/Process_Lumpy.o ./src/convert/Update_bam_pacbio.o ./src/analysis_sv/GIAB_summary.o ./src/analysis_sv/MT_identifier.o ./src/analysis_sv/MUMmer_overlap.o ./src/analysis_sv/Select_samples.o ./src/analysis_sv/Simplify_SVs.o ./src/analysis_sv/Summ_mat.o ./src/CorrectAllele.o ./src/DetectDif.o ./src/Extract_Seq.o ./src/SURVIVOR.o ./src/Summarize_SV.o ./src/vcfs/Annotate_vcf.d ./src/vcfs/Combine_3_VCF.d ./src/vcfs/Compoverlap_VCF.d ./src/vcfs/Detect_nested.d ./src/vcfs/Filter_vcf.d ./src/vcfs/Generate_distMat.d ./src/vcfs/Merge_VCF.d ./src/snp_overlap/Overlap_snps.d ./src/simulator/Error_scanner.d ./src/simulator/Eval_vcf.d ./src/simulator/Pac_Simulator.d ./src/simulator/SV_Simulator.d ./src/simulator/Sim_reads.d ./src/simulator/test_cov.d ./src/scrup_vcf/scrup_svs.d ./src/phasing/Phasing_vcf.d ./src/merge_vcf/IntervallTree.d ./src/merge_vcf/combine_svs.d ./src/convert/ConvertMQ0Bed.d ./src/convert/Convert_Assemblytics.d ./src/convert/Convert_Bionano.d ./src/convert/Convert_Honey_tails.d ./src/convert/Convert_MUMmer.d ./src/convert/Convert_Pindel.d ./src/convert/Convert_VCF_to_BED.d ./src/convert/Convert_hapcut2.d ./src/convert/Process_Coverage.d ./src/convert/Process_Lumpy.d ./src/convert/Update_bam_pacbio.d ./src/analysis_sv/GIAB_summary.d ./src/analysis_sv/MT_identifier.d ./src/analysis_sv/MUMmer_overlap.d ./src/analysis_sv/Select_samples.d ./src/analysis_sv/Simplify_SVs.d ./src/analysis_sv/Summ_mat.d ./src/CorrectAllele.d ./src/DetectDif.d ./src/Extract_Seq.d ./src/SURVIVOR.d ./src/Summarize_SV.d SURVIVOR -make[1]: Leaving directory '/build/survivor-1.0.7/Debug' +make[1]: uscita dalla directory «/build/survivor-1.0.7/Debug» dh_autoreconf_clean -O--sourcedirectory=Debug dh_clean -O--sourcedirectory=Debug debian/rules binary @@ -387,17 +430,25 @@ dh_autoreconf -O--sourcedirectory=Debug dh_auto_configure -O--sourcedirectory=Debug dh_auto_build -O--sourcedirectory=Debug - cd Debug && make -j3 "INSTALL=install --strip-program=true" -make[1]: Entering directory '/build/survivor-1.0.7/Debug' + cd Debug && make -j4 "INSTALL=install --strip-program=true" +make[1]: ingresso nella directory «/build/survivor-1.0.7/Debug» Building file: ../src/vcfs/Annotate_vcf.cpp Building file: ../src/vcfs/Combine_3_VCF.cpp +Building file: ../src/vcfs/Compoverlap_VCF.cpp +Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Annotate_vcf.d" -MT"src/vcfs/Annotate_vcf.o" -o "src/vcfs/Annotate_vcf.o" "../src/vcfs/Annotate_vcf.cpp" Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Combine_3_VCF.d" -MT"src/vcfs/Combine_3_VCF.o" -o "src/vcfs/Combine_3_VCF.o" "../src/vcfs/Combine_3_VCF.cpp" -Building file: ../src/vcfs/Compoverlap_VCF.cpp -Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Compoverlap_VCF.d" -MT"src/vcfs/Compoverlap_VCF.o" -o "src/vcfs/Compoverlap_VCF.o" "../src/vcfs/Compoverlap_VCF.cpp" +Building file: ../src/vcfs/Detect_nested.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Detect_nested.d" -MT"src/vcfs/Detect_nested.o" -o "src/vcfs/Detect_nested.o" "../src/vcfs/Detect_nested.cpp" +Finished building: ../src/vcfs/Detect_nested.cpp + +Building file: ../src/vcfs/Filter_vcf.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Filter_vcf.d" -MT"src/vcfs/Filter_vcf.o" -o "src/vcfs/Filter_vcf.o" "../src/vcfs/Filter_vcf.cpp" In file included from /usr/include/c++/12/vector:70, from ../src/vcfs/../simulator/../vcfs/Merge_VCF.h:12, from ../src/vcfs/../simulator/Eval_vcf.h:12, @@ -413,45 +464,30 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/vcfs/Compoverlap_VCF.cpp - -Building file: ../src/vcfs/Detect_nested.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Detect_nested.d" -MT"src/vcfs/Detect_nested.o" -o "src/vcfs/Detect_nested.o" "../src/vcfs/Detect_nested.cpp" -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘void process_SV(std::vector, std::vector&, int, int, int)’ at ../src/vcfs/Combine_3_VCF.cpp:58:20: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/vcfs/Detect_nested.cpp - -Building file: ../src/vcfs/Filter_vcf.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Filter_vcf.d" -MT"src/vcfs/Filter_vcf.o" -o "src/vcfs/Filter_vcf.o" "../src/vcfs/Filter_vcf.cpp" ../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’: ../src/vcfs/Filter_vcf.cpp:18:13: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable] 18 | int lumpy = 0; | ^~~~~ -Finished building: ../src/vcfs/Combine_3_VCF.cpp +Finished building: ../src/vcfs/Compoverlap_VCF.cpp Building file: ../src/vcfs/Generate_distMat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Generate_distMat.d" -MT"src/vcfs/Generate_distMat.o" -o "src/vcfs/Generate_distMat.o" "../src/vcfs/Generate_distMat.cpp" +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = strvcfentry; _Alloc = std::allocator]’, + inlined from ‘void process_SV(std::vector, std::vector&, int, int, int)’ at ../src/vcfs/Combine_3_VCF.cpp:58:20: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/vcfs/Generate_distMat.cpp Building file: ../src/vcfs/Merge_VCF.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Merge_VCF.d" -MT"src/vcfs/Merge_VCF.o" -o "src/vcfs/Merge_VCF.o" "../src/vcfs/Merge_VCF.cpp" -Finished building: ../src/vcfs/Annotate_vcf.cpp +Finished building: ../src/vcfs/Combine_3_VCF.cpp Building file: ../src/snp_overlap/Overlap_snps.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/snp_overlap/Overlap_snps.d" -MT"src/snp_overlap/Overlap_snps.o" -o "src/snp_overlap/Overlap_snps.o" "../src/snp_overlap/Overlap_snps.cpp" -Finished building: ../src/vcfs/Filter_vcf.cpp - -Building file: ../src/simulator/Error_scanner.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp" ../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps(std::string, std::string, int, int, int, std::string)’: ../src/snp_overlap/Overlap_snps.cpp:192:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 192 | for (size_t i = start; i <= stop; i++) { @@ -471,13 +507,36 @@ ../src/snp_overlap/Overlap_snps.cpp:781:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { | ~~~~^~~~~~~~~~~~~~~~~~~~~ +Finished building: ../src/vcfs/Filter_vcf.cpp + +Building file: ../src/simulator/Error_scanner.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp" +In file included from /usr/include/c++/12/vector:70, + from ../src/snp_overlap/Overlap_snps.h:17, + from ../src/snp_overlap/Overlap_snps.cpp:8: +/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const strvcfentry&}; _Tp = strvcfentry; _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>:: + | ^~~~~~~~~~~~~~~~~~~ ../src/simulator/Error_scanner.cpp: In function ‘void computeAlignment(std::vector, char*, std::string, std::vector > >&, std::string)’: ../src/simulator/Error_scanner.cpp:173:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 173 | while (pos + 1 > error_mat.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~ +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 = strvcfentry; _Alloc = std::allocator]’, + inlined from ‘std::vector parse_random(std::string)’ at ../src/snp_overlap/Overlap_snps.cpp:354:20: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +Finished building: ../src/vcfs/Annotate_vcf.cpp + +Building file: ../src/simulator/Eval_vcf.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp" In file included from /usr/include/c++/12/vector:70, - from ../src/snp_overlap/Overlap_snps.h:17, - from ../src/snp_overlap/Overlap_snps.cpp:8: + from ../src/vcfs/Merge_VCF.h:12, + from ../src/vcfs/Merge_VCF.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const strvcfentry&}; _Tp = strvcfentry; _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>:: @@ -495,35 +554,6 @@ /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/vector:70, - from ../src/vcfs/Merge_VCF.h:12, - from ../src/vcfs/Merge_VCF.cpp:8: -/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const strvcfentry&}; _Tp = strvcfentry; _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 = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘std::vector parse_random(std::string)’ at ../src/snp_overlap/Overlap_snps.cpp:354:20: -/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/vector:64: -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘std::vector parse_vcf(std::string&, int)’ at ../src/vcfs/Merge_VCF.cpp:823:20: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/simulator/Error_scanner.cpp - -Building file: ../src/simulator/Eval_vcf.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp" -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘void merge_entries(std::string, int, std::vector&)’ at ../src/vcfs/Merge_VCF.cpp:866:23: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’: ../src/simulator/Eval_vcf.cpp:102:15: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable] 102 | float dv = 0; //"# high-quality variant pairs" @@ -540,21 +570,27 @@ ../src/simulator/Eval_vcf.cpp:106:13: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable] 106 | int rv = 0; | ^~ -Finished building: ../src/vcfs/Merge_VCF.cpp +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 = strvcfentry; _Alloc = std::allocator]’, + inlined from ‘std::vector parse_vcf(std::string&, int)’ at ../src/vcfs/Merge_VCF.cpp:823:20: +/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 = strvcfentry; _Alloc = std::allocator]’, + inlined from ‘void merge_entries(std::string, int, std::vector&)’ at ../src/vcfs/Merge_VCF.cpp:866:23: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +Finished building: ../src/simulator/Error_scanner.cpp Building file: ../src/simulator/Pac_Simulator.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Pac_Simulator.d" -MT"src/simulator/Pac_Simulator.o" -o "src/simulator/Pac_Simulator.o" "../src/simulator/Pac_Simulator.cpp" -Finished building: ../src/simulator/Pac_Simulator.cpp +Finished building: ../src/vcfs/Merge_VCF.cpp Building file: ../src/simulator/SV_Simulator.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp" -Finished building: ../src/snp_overlap/Overlap_snps.cpp - -Building file: ../src/simulator/Sim_reads.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Sim_reads.d" -MT"src/simulator/Sim_reads.o" -o "src/simulator/Sim_reads.o" "../src/simulator/Sim_reads.cpp" In file included from /usr/include/c++/12/vector:70, from ../src/simulator/../vcfs/Merge_VCF.h:12, from ../src/simulator/Eval_vcf.h:12, @@ -635,6 +671,11 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Finished building: ../src/snp_overlap/Overlap_snps.cpp + +Building file: ../src/simulator/Sim_reads.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Sim_reads.d" -MT"src/simulator/Sim_reads.o" -o "src/simulator/Sim_reads.o" "../src/simulator/Sim_reads.cpp" In file included from /usr/include/c++/12/vector:70, from ../src/simulator/Sim_reads.h:15, from ../src/simulator/Sim_reads.cpp:8: @@ -648,22 +689,22 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/simulator/Eval_vcf.cpp +Finished building: ../src/simulator/Pac_Simulator.cpp Building file: ../src/simulator/test_cov.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/test_cov.d" -MT"src/simulator/test_cov.o" -o "src/simulator/test_cov.o" "../src/simulator/test_cov.cpp" -Finished building: ../src/simulator/test_cov.cpp +Finished building: ../src/simulator/Sim_reads.cpp Building file: ../src/scrup_vcf/scrup_svs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/scrup_vcf/scrup_svs.d" -MT"src/scrup_vcf/scrup_svs.o" -o "src/scrup_vcf/scrup_svs.o" "../src/scrup_vcf/scrup_svs.cpp" -Finished building: ../src/simulator/Sim_reads.cpp +Finished building: ../src/simulator/Eval_vcf.cpp Building file: ../src/phasing/Phasing_vcf.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/phasing/Phasing_vcf.d" -MT"src/phasing/Phasing_vcf.o" -o "src/phasing/Phasing_vcf.o" "../src/phasing/Phasing_vcf.cpp" -Finished building: ../src/scrup_vcf/scrup_svs.cpp +Finished building: ../src/simulator/SV_Simulator.cpp Building file: ../src/merge_vcf/IntervallTree.cpp Invoking: Cross G++ Compiler @@ -675,17 +716,22 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ +Finished building: ../src/simulator/test_cov.cpp + +Building file: ../src/merge_vcf/combine_svs.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/combine_svs.d" -MT"src/merge_vcf/combine_svs.o" -o "src/merge_vcf/combine_svs.o" "../src/merge_vcf/combine_svs.cpp" +Finished building: ../src/scrup_vcf/scrup_svs.cpp + +Building file: ../src/convert/ConvertMQ0Bed.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/ConvertMQ0Bed.d" -MT"src/convert/ConvertMQ0Bed.o" -o "src/convert/ConvertMQ0Bed.o" "../src/convert/ConvertMQ0Bed.cpp" 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 = snp_str; _Alloc = std::allocator]’, inlined from ‘std::vector parse_hapcut2(std::string)’ at ../src/phasing/Phasing_vcf.cpp:57:20: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/phasing/Phasing_vcf.cpp - -Building file: ../src/merge_vcf/combine_svs.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/combine_svs.d" -MT"src/merge_vcf/combine_svs.o" -o "src/merge_vcf/combine_svs.o" "../src/merge_vcf/combine_svs.cpp" ../src/merge_vcf/combine_svs.cpp: In function ‘void print_GTs(std::ostringstream&, SVS_Node*)’: ../src/merge_vcf/combine_svs.cpp:213:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 213 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) { @@ -700,12 +746,7 @@ ../src/merge_vcf/combine_svs.cpp:688:31: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] 688 | short type = (*i)->type; | ^~~~ -Finished building: ../src/simulator/SV_Simulator.cpp - -Building file: ../src/convert/ConvertMQ0Bed.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/ConvertMQ0Bed.d" -MT"src/convert/ConvertMQ0Bed.o" -o "src/convert/ConvertMQ0Bed.o" "../src/convert/ConvertMQ0Bed.cpp" -Finished building: ../src/merge_vcf/IntervallTree.cpp +Finished building: ../src/phasing/Phasing_vcf.cpp Building file: ../src/convert/Convert_Assemblytics.cpp Invoking: Cross G++ Compiler @@ -715,6 +756,11 @@ Building file: ../src/convert/Convert_Bionano.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Bionano.d" -MT"src/convert/Convert_Bionano.o" -o "src/convert/Convert_Bionano.o" "../src/convert/Convert_Bionano.cpp" +Finished building: ../src/merge_vcf/IntervallTree.cpp + +Building file: ../src/convert/Convert_Honey_tails.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Honey_tails.d" -MT"src/convert/Convert_Honey_tails.o" -o "src/convert/Convert_Honey_tails.o" "../src/convert/Convert_Honey_tails.cpp" In file included from /usr/include/c++/12/vector:70, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, @@ -724,6 +770,21 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ +../src/convert/Convert_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector&)’: +../src/convert/Convert_Honey_tails.cpp:45:21: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] + 45 | int dist=0; + | ^~~~ +Finished building: ../src/merge_vcf/combine_svs.cpp + +Building file: ../src/convert/Convert_MUMmer.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_MUMmer.d" -MT"src/convert/Convert_MUMmer.o" -o "src/convert/Convert_MUMmer.o" "../src/convert/Convert_MUMmer.cpp" +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 = strvcfentry; _Alloc = std::allocator]’, + inlined from ‘void parse_assemblytics(std::string, int, std::vector&)’ at ../src/convert/Convert_Assemblytics.cpp:104:21: +/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 file included from /usr/include/c++/12/vector:70, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, @@ -733,62 +794,56 @@ /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:70, + from ../src/convert/../vcfs/Merge_VCF.h:12, + from ../src/convert/Process_Lumpy.h:11, + from ../src/convert/Convert_Honey_tails.h:12, + from ../src/convert/Convert_Honey_tails.cpp:7: +/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const strvcfentry&}; _Tp = strvcfentry; _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 = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘void parse_assemblytics(std::string, int, std::vector&)’ at ../src/convert/Convert_Assemblytics.cpp:104:21: + inlined from ‘void parse_Bionano(std::string, std::vector&)’ at ../src/convert/Convert_Bionano.cpp:122:20: /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/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘void parse_Bionano(std::string, std::vector&)’ at ../src/convert/Convert_Bionano.cpp:122:20: + inlined from ‘void parse_honey_tails(std::string, int, std::vector&)’ at ../src/convert/Convert_Honey_tails.cpp:75:21: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/convert/Convert_Assemblytics.cpp - -Building file: ../src/convert/Convert_Honey_tails.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Honey_tails.d" -MT"src/convert/Convert_Honey_tails.o" -o "src/convert/Convert_Honey_tails.o" "../src/convert/Convert_Honey_tails.cpp" In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = strvcfentry; _Alloc = std::allocator]’, inlined from ‘void parse_GC(std::string, std::vector&)’ at ../src/convert/Convert_Bionano.cpp:186:22: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/merge_vcf/combine_svs.cpp - -Building file: ../src/convert/Convert_MUMmer.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_MUMmer.d" -MT"src/convert/Convert_MUMmer.o" -o "src/convert/Convert_MUMmer.o" "../src/convert/Convert_MUMmer.cpp" -Finished building: ../src/convert/Convert_Bionano.cpp +Finished building: ../src/convert/Convert_Assemblytics.cpp Building file: ../src/convert/Convert_Pindel.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Pindel.d" -MT"src/convert/Convert_Pindel.o" -o "src/convert/Convert_Pindel.o" "../src/convert/Convert_Pindel.cpp" -../src/convert/Convert_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector&)’: -../src/convert/Convert_Honey_tails.cpp:45:21: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] - 45 | int dist=0; - | ^~~~ Finished building: ../src/convert/Convert_MUMmer.cpp Building file: ../src/convert/Convert_VCF_to_BED.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_VCF_to_BED.d" -MT"src/convert/Convert_VCF_to_BED.o" -o "src/convert/Convert_VCF_to_BED.o" "../src/convert/Convert_VCF_to_BED.cpp" -In file included from /usr/include/c++/12/vector:70, - from ../src/convert/../vcfs/Merge_VCF.h:12, - from ../src/convert/Process_Lumpy.h:11, - from ../src/convert/Convert_Honey_tails.h:12, - from ../src/convert/Convert_Honey_tails.cpp:7: -/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const strvcfentry&}; _Tp = strvcfentry; _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 = strvcfentry; _Alloc = std::allocator]’, - inlined from ‘void parse_honey_tails(std::string, int, std::vector&)’ at ../src/convert/Convert_Honey_tails.cpp:75:21: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +Finished building: ../src/convert/Convert_Honey_tails.cpp + +Building file: ../src/convert/Convert_hapcut2.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_hapcut2.d" -MT"src/convert/Convert_hapcut2.o" -o "src/convert/Convert_hapcut2.o" "../src/convert/Convert_hapcut2.cpp" +Finished building: ../src/convert/Convert_Bionano.cpp + +Building file: ../src/convert/Process_Coverage.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp" +../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’: +../src/convert/Convert_VCF_to_BED.cpp:348:20: warning: unknown escape sequence: '\/' + 348 | convert << "\tGT\t.\/."; + | ^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, @@ -798,26 +853,12 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ -../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’: -../src/convert/Convert_VCF_to_BED.cpp:348:20: warning: unknown escape sequence: '\/' - 348 | convert << "\tGT\t.\/."; - | ^~~~~~~~~~~~ -Finished building: ../src/convert/Convert_Honey_tails.cpp - -Building file: ../src/convert/Convert_hapcut2.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_hapcut2.d" -MT"src/convert/Convert_hapcut2.o" -o "src/convert/Convert_hapcut2.o" "../src/convert/Convert_hapcut2.cpp" In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {strvcfentry}; _Tp = strvcfentry; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = strvcfentry; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void parse_pindel(std::string, std::vector&, int, int)’ at ../src/convert/Convert_Pindel.cpp:121:22: /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Finished building: ../src/convert/Convert_Pindel.cpp - -Building file: ../src/convert/Process_Coverage.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp" In file included from /usr/include/c++/12/vector:70, from ../src/convert/../merge_vcf/combine_svs.h:16, from ../src/convert/Convert_VCF_to_BED.h:17, @@ -826,32 +867,27 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ +Finished building: ../src/convert/Process_Coverage.cpp + +Building file: ../src/convert/Process_Lumpy.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Lumpy.d" -MT"src/convert/Process_Lumpy.o" -o "src/convert/Process_Lumpy.o" "../src/convert/Process_Lumpy.cpp" 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 = strvcfentry; _Alloc = std::allocator]’, inlined from ‘std::vector parse_vcf_slim(std::string)’ at ../src/convert/Convert_VCF_to_BED.cpp:220:19: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -Finished building: ../src/convert/Process_Coverage.cpp - -Building file: ../src/convert/Process_Lumpy.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Lumpy.d" -MT"src/convert/Process_Lumpy.o" -o "src/convert/Process_Lumpy.o" "../src/convert/Process_Lumpy.cpp" Finished building: ../src/convert/Convert_hapcut2.cpp Building file: ../src/convert/Update_bam_pacbio.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Update_bam_pacbio.d" -MT"src/convert/Update_bam_pacbio.o" -o "src/convert/Update_bam_pacbio.o" "../src/convert/Update_bam_pacbio.cpp" -Finished building: ../src/convert/Convert_VCF_to_BED.cpp +Finished building: ../src/convert/Convert_Pindel.cpp Building file: ../src/analysis_sv/GIAB_summary.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/GIAB_summary.d" -MT"src/analysis_sv/GIAB_summary.o" -o "src/analysis_sv/GIAB_summary.o" "../src/analysis_sv/GIAB_summary.cpp" -Finished building: ../src/convert/Update_bam_pacbio.cpp - -Building file: ../src/analysis_sv/MT_identifier.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MT_identifier.d" -MT"src/analysis_sv/MT_identifier.o" -o "src/analysis_sv/MT_identifier.o" "../src/analysis_sv/MT_identifier.cpp" In file included from /usr/include/c++/12/vector:70, from ../src/analysis_sv/GIAB_summary.h:15, from ../src/analysis_sv/GIAB_summary.cpp:8: @@ -859,12 +895,17 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ +Finished building: ../src/convert/Update_bam_pacbio.cpp + +Building file: ../src/analysis_sv/MT_identifier.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MT_identifier.d" -MT"src/analysis_sv/MT_identifier.o" -o "src/analysis_sv/MT_identifier.o" "../src/analysis_sv/MT_identifier.cpp" Finished building: ../src/convert/Process_Lumpy.cpp Building file: ../src/analysis_sv/MUMmer_overlap.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MUMmer_overlap.d" -MT"src/analysis_sv/MUMmer_overlap.o" -o "src/analysis_sv/MUMmer_overlap.o" "../src/analysis_sv/MUMmer_overlap.cpp" -Finished building: ../src/analysis_sv/MT_identifier.cpp +Finished building: ../src/convert/Convert_VCF_to_BED.cpp Building file: ../src/analysis_sv/Select_samples.cpp Invoking: Cross G++ Compiler @@ -876,6 +917,11 @@ ../src/analysis_sv/MUMmer_overlap.cpp:61:21: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 61 | int len = 0; | ^~~ +Finished building: ../src/analysis_sv/MT_identifier.cpp + +Building file: ../src/analysis_sv/Simplify_SVs.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Simplify_SVs.d" -MT"src/analysis_sv/Simplify_SVs.o" -o "src/analysis_sv/Simplify_SVs.o" "../src/analysis_sv/Simplify_SVs.cpp" 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 = svstruct; _Alloc = std::allocator]’, inlined from ‘void summary_giab_old(std::string, std::string)’ at ../src/analysis_sv/GIAB_summary.cpp:311:16: @@ -884,47 +930,44 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/analysis_sv/Select_samples.cpp -Building file: ../src/analysis_sv/Simplify_SVs.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Simplify_SVs.d" -MT"src/analysis_sv/Simplify_SVs.o" -o "src/analysis_sv/Simplify_SVs.o" "../src/analysis_sv/Simplify_SVs.cpp" -Finished building: ../src/analysis_sv/MUMmer_overlap.cpp - Building file: ../src/analysis_sv/Summ_mat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Summ_mat.d" -MT"src/analysis_sv/Summ_mat.o" -o "src/analysis_sv/Summ_mat.o" "../src/analysis_sv/Summ_mat.cpp" -Finished building: ../src/analysis_sv/GIAB_summary.cpp - ../src/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector >, std::string&)’: ../src/analysis_sv/Simplify_SVs.cpp:54:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) { | ~~^~~~~~~~~~~~~ -Building file: ../src/CorrectAllele.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/CorrectAllele.d" -MT"src/CorrectAllele.o" -o "src/CorrectAllele.o" "../src/CorrectAllele.cpp" ../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map, std::vector > >)’: ../src/analysis_sv/Simplify_SVs.cpp:118:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, bool>::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 118 | if (count + 1 < entry.accessions.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -Finished building: ../src/analysis_sv/Summ_mat.cpp +Finished building: ../src/analysis_sv/MUMmer_overlap.cpp + +Building file: ../src/CorrectAllele.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/CorrectAllele.d" -MT"src/CorrectAllele.o" -o "src/CorrectAllele.o" "../src/CorrectAllele.cpp" +Finished building: ../src/analysis_sv/GIAB_summary.cpp Building file: ../src/DetectDif.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/DetectDif.d" -MT"src/DetectDif.o" -o "src/DetectDif.o" "../src/DetectDif.cpp" -Finished building: ../src/CorrectAllele.cpp +Finished building: ../src/analysis_sv/Summ_mat.cpp Building file: ../src/Extract_Seq.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Extract_Seq.d" -MT"src/Extract_Seq.o" -o "src/Extract_Seq.o" "../src/Extract_Seq.cpp" -Finished building: ../src/analysis_sv/Simplify_SVs.cpp +Finished building: ../src/DetectDif.cpp Building file: ../src/SURVIVOR.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/SURVIVOR.d" -MT"src/SURVIVOR.o" -o "src/SURVIVOR.o" "../src/SURVIVOR.cpp" -Finished building: ../src/DetectDif.cpp +Finished building: ../src/analysis_sv/Simplify_SVs.cpp Building file: ../src/Summarize_SV.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Summarize_SV.d" -MT"src/Summarize_SV.o" -o "src/Summarize_SV.o" "../src/Summarize_SV.cpp" +Finished building: ../src/CorrectAllele.cpp + ../src/Summarize_SV.cpp: In function ‘void summary_venn(std::string, bool, std::string)’: ../src/Summarize_SV.cpp:608:65: warning: format ‘%e’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] 608 | fprintf(file, "%e", 0); @@ -951,7 +994,7 @@ g++ -o SURVIVOR ./src/vcfs/Annotate_vcf.o ./src/vcfs/Combine_3_VCF.o ./src/vcfs/Compoverlap_VCF.o ./src/vcfs/Detect_nested.o ./src/vcfs/Filter_vcf.o ./src/vcfs/Generate_distMat.o ./src/vcfs/Merge_VCF.o ./src/snp_overlap/Overlap_snps.o ./src/simulator/Error_scanner.o ./src/simulator/Eval_vcf.o ./src/simulator/Pac_Simulator.o ./src/simulator/SV_Simulator.o ./src/simulator/Sim_reads.o ./src/simulator/test_cov.o ./src/scrup_vcf/scrup_svs.o ./src/phasing/Phasing_vcf.o ./src/merge_vcf/IntervallTree.o ./src/merge_vcf/combine_svs.o ./src/convert/ConvertMQ0Bed.o ./src/convert/Convert_Assemblytics.o ./src/convert/Convert_Bionano.o ./src/convert/Convert_Honey_tails.o ./src/convert/Convert_MUMmer.o ./src/convert/Convert_Pindel.o ./src/convert/Convert_VCF_to_BED.o ./src/convert/Convert_hapcut2.o ./src/convert/Process_Coverage.o ./src/convert/Process_Lumpy.o ./src/convert/Update_bam_pacbio.o ./src/analysis_sv/GIAB_summary.o ./src/analysis_sv/MT_identifier.o ./src/analysis_sv/MUMmer_overlap.o ./src/analysis_sv/Select_samples.o ./src/analysis_sv/Simplify_SVs.o ./src/analysis_sv/Summ_mat.o ./src/CorrectAllele.o ./src/DetectDif.o ./src/Extract_Seq.o ./src/SURVIVOR.o ./src/Summarize_SV.o -lz Finished building target: SURVIVOR -make[1]: Leaving directory '/build/survivor-1.0.7/Debug' +make[1]: uscita dalla directory «/build/survivor-1.0.7/Debug» dh_auto_test -O--sourcedirectory=Debug create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=Debug @@ -977,8 +1020,8 @@ dh_gencontrol -O--sourcedirectory=Debug dh_md5sums -O--sourcedirectory=Debug dh_builddeb -O--sourcedirectory=Debug -dpkg-deb: building package 'survivor' in '../survivor_1.0.7-4_armhf.deb'. -dpkg-deb: building package 'survivor-dbgsym' in '../survivor-dbgsym_1.0.7-4_armhf.deb'. +dpkg-deb: generazione del pacchetto "survivor" in "../survivor_1.0.7-4_armhf.deb". +dpkg-deb: generazione del pacchetto "survivor-dbgsym" in "../survivor-dbgsym_1.0.7-4_armhf.deb". dpkg-genbuildinfo --build=binary -O../survivor_1.0.7-4_armhf.buildinfo dpkg-genchanges --build=binary -O../survivor_1.0.7-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -986,12 +1029,14 @@ 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/9907/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/9907/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/16331 and its subdirectories -I: Current time: Thu Jun 8 23:45:27 -12 2023 -I: pbuilder-time-stamp: 1686311127 +I: removing directory /srv/workspace/pbuilder/9907 and its subdirectories +I: Current time: Sat Jun 10 01:49:15 +14 2023 +I: pbuilder-time-stamp: 1686311355