Diff of the two buildlogs:
--
--- b1/build.log 2023-05-07 01:31:29.373647216 +0000
+++ b2/build.log 2023-05-07 03:19:04.326509104 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Sat May 6 12:56:30 -12 2023
-I: pbuilder-time-stamp: 1683420990
+I: Current time: Sun May 7 15:34:21 +14 2023
+I: pbuilder-time-stamp: 1683423261
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 [./vt_0.57721+ds.orig.tar.xz]
I: copying [./vt_0.57721+ds-3.debian.tar.xz]
I: Extracting source
-gpgv: Signature made Tue Nov 10 04:13:34 2020 -12
+gpgv: Signature made Wed Nov 11 06:13:34 2020 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
@@ -32,135 +32,167 @@
dpkg-source: info: applying 0002-hts-1.11.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/12314/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/6752/tmp/hooks/D01_modify_environment starting
+debug: Running on cbxi4b.
+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 7 15:35 /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/6752/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/6752/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='e928b93de7d644d595b503acd6699478'
- 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='12314'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=d8b37150ff5d41d2989e2ccbb8c5d232
+ 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=6752
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.VqoBUjYo/pbuilderrc_L1Pb --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.VqoBUjYo/b1 --logfile b1/build.log vt_0.57721+ds-3.dsc'
- SUDO_GID='114'
- SUDO_UID='108'
- 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.VqoBUjYo/pbuilderrc_o1ND --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.VqoBUjYo/b2 --logfile b2/build.log --extrapackages usrmerge vt_0.57721+ds-3.dsc'
+ SUDO_GID=116
+ SUDO_UID=112
+ 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 virt64a 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 5.10.0-22-armmp #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l 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/12314/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 7 15:35 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/6752/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -334,7 +366,7 @@
Get: 112 http://deb.debian.org/debian bookworm/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 113 http://deb.debian.org/debian bookworm/main armhf r-base-core armhf 4.2.2.20221110-2 [25.6 MB]
Get: 114 http://deb.debian.org/debian bookworm/main armhf r-mathlib armhf 4.2.2.20221110-2 [2239 kB]
-Fetched 74.4 MB in 6s (13.5 MB/s)
+Fetched 74.4 MB in 10s (7721 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package readline-common.
(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 ... 19329 files and directories currently installed.)
@@ -823,8 +855,19 @@
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/vt-0.57721+ds/ && 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 > ../vt_0.57721+ds-3_source.changes
+I: user script /srv/workspace/pbuilder/6752/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/6752/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/vt-0.57721+ds/ && 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 > ../vt_0.57721+ds-3_source.changes
dpkg-buildpackage: info: source package vt
dpkg-buildpackage: info: source version 0.57721+ds-3
dpkg-buildpackage: info: source distribution unstable
@@ -834,7 +877,7 @@
debian/rules clean
dh clean
dh_auto_clean
- make -j3 clean
+ make -j4 clean
make[1]: Entering directory '/build/vt-0.57721+ds'
rm -rf vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o
make[1]: Leaving directory '/build/vt-0.57721+ds'
@@ -845,11 +888,12 @@
dh_autoreconf
dh_auto_configure
dh_auto_build
- make -j3 "INSTALL=install --strip-program=true"
+ make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/vt-0.57721+ds'
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ahmm.o -c ahmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o align.o -c align.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o allele.o -c allele.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_1000g.o -c annotate_1000g.cpp
ahmm.cpp: In member function 'void AHMM::collect_statistics(int32_t, int32_t, int32_t)':
ahmm.cpp:687:35: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
687 | rflank_start[MODEL] = NAN;
@@ -912,7 +956,6 @@
ahmm.cpp:753:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
753 | rflank_end[READ] = NAN;
| ^~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_1000g.o -c annotate_1000g.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_indels.o -c annotate_indels.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_indels2.o -c annotate_indels2.cpp
@@ -926,6 +969,8 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_synced_reader.o -c bcf_synced_reader.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bed.o -c bed.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_motif_picker.o -c candidate_motif_picker.cpp
bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)':
bcf_ordered_writer.cpp:162:114: warning: format '%d' expects argument of type 'int', but argument 8 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
162 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n",
@@ -960,12 +1005,11 @@
bcf_ordered_writer.cpp:261:30: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
261 | bcf_write(file, hdr, buffer.back());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bed.o -c bed.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_motif_picker.o -c candidate_motif_picker.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_region_extractor.o -c candidate_region_extractor.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o cat.o -c cat.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o chmm.o -c chmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o complex_genotyping_record.o -c complex_genotyping_record.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_concordance.o -c compute_concordance.cpp
chmm.cpp: In member function 'void CHMM::clear_statistics()':
chmm.cpp:1106:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
1106 | lflank_start[MODEL] = NAN;
@@ -1015,7 +1059,6 @@
chmm.cpp:1121:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
1121 | motif_xid = NAN;
| ^~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_concordance.o -c compute_concordance.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features.o -c compute_features.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features2.o -c compute_features2.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_rl_dist.o -c compute_rl_dist.cpp
@@ -1028,7 +1071,6 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose2.o -c decompose2.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose_blocksub.o -c decompose_blocksub.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o discover.o -c discover.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o duplicate.o -c duplicate.cpp
In file included from bcf_ordered_reader.h:27,
from program.h:32,
from discover.h:27,
@@ -1042,6 +1084,7 @@
| ^~~~~~~~~~~~
discover.cpp:355:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
355 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o duplicate.o -c duplicate.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimate.o -c estimate.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimator.o -c estimator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o extract_vntrs.o -c extract_vntrs.cpp
@@ -1050,12 +1093,12 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o flank_detector.o -c flank_detector.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_aligner.o -c fuzzy_aligner.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_partition.o -c fuzzy_partition.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o gencode.o -c gencode.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genome_interval.o -c genome_interval.cpp
fuzzy_partition.cpp: In member function 'void {anonymous}::Igor::initialize()':
fuzzy_partition.cpp:153:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
153 | bcf_hdr_sync(odr->hdr);
| ~~~~~~~~~~~~^~~~~~~~~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o gencode.o -c gencode.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genome_interval.o -c genome_interval.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotype.o -c genotype.cpp
In file included from bam_ordered_reader.h:27,
from genotype.h:27,
@@ -1072,15 +1115,16 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotyping_record.o -c genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ghmm.o -c ghmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hts_utils.o -c hts_utils.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hfilter.o -c hfilter.cpp
hts_utils.cpp: In function 'void bcf_hdr_print(bcf_hdr_t*)':
hts_utils.cpp:406:33: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
406 | if ( h->dirty ) bcf_hdr_sync(h);
| ~~~~~~~~~~~~^~~
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hfilter.o -c hfilter.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_annotator.o -c indel_annotator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_genotyping_record.o -c indel_genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o index.o -c index.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o info2tab.o -c info2tab.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval_tree.o -c interval_tree.cpp
info2tab.cpp: In member function 'void {anonymous}::Igor::info2tab()':
info2tab.cpp:278:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
278 | fprintf(out, "%s\t%d", bcf_get_chrom(h, v), bcf_get_pos1(v));
@@ -1088,9 +1132,9 @@
| |
| int
| %lld
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval_tree.o -c interval_tree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval.o -c interval.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lfhmm.o -c lfhmm.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm.o -c lhmm.cpp
lfhmm.cpp: In member function 'void LFHMM::collect_statistics(int32_t, int32_t, int32_t)':
lfhmm.cpp:761:33: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
761 | rflank_end[MODEL] = NAN;
@@ -1144,7 +1188,6 @@
lfhmm.cpp:884:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
884 | rflank_end[READ] = NAN;
| ^~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm.o -c lhmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm1.o -c lhmm1.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o liftover.o -c liftover.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o log_tool.o -c log_tool.cpp
@@ -1201,6 +1244,7 @@
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge.o -c merge.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_candidate_variants.o -c merge_candidate_variants.cpp
In file included from /usr/include/c++/12/vector:70,
from utils.h:33,
from log_tool.h:30,
@@ -1216,7 +1260,6 @@
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_candidate_variants.o -c merge_candidate_variants.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_genotypes.o -c merge_genotypes.cpp
merge_genotypes.cpp: In member function 'void {anonymous}::Igor::initialize()':
merge_genotypes.cpp:215:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
@@ -1238,7 +1281,6 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o normalize.o -c normalize.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o nuclear_pedigree.o -c nuclear_pedigree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp
ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector<GenomeInterval>&)':
ordered_bcf_overlap_matcher.cpp:34:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
34 | bcf_hdr_sync(odr->hdr);
@@ -1247,6 +1289,7 @@
ordered_bcf_overlap_matcher.cpp:52:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
52 | bcf_hdr_sync(odr->hdr);
| ~~~~~~~~~~~~^~~~~~~~~~
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o partition.o -c partition.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste.o -c paste.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp
@@ -1263,15 +1306,16 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_indels.o -c profile_indels.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_len.o -c profile_len.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_mendelian.o -c profile_mendelian.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_na12878.o -c profile_na12878.cpp
profile_mendelian.cpp: In member function 'void {anonymous}::Igor::initialize()':
profile_mendelian.cpp:191:25: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
191 | bcf_hdr_sync(odw->hdr);
| ~~~~~~~~~~~~^~~~~~~~~~
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_na12878.o -c profile_na12878.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_snps.o -c profile_snps.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_vntrs.o -c profile_vntrs.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o program.o -c program.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o read_filter.o -c read_filter.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o reference_sequence.o -c reference_sequence.cpp
In file included from read_filter.h:30,
from read_filter.cpp:24:
read_filter.cpp: In member function 'bool ReadFilter::filter_read(bam_hdr_t*, bam1_t*)':
@@ -1283,58 +1327,10 @@
| ^~~~~~~~~~~~
read_filter.cpp:95:91: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
95 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o reference_sequence.o -c reference_sequence.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm.o -c rfhmm.cpp
-rfhmm.cpp: In member function 'void RFHMM::clear_statistics()':
-rfhmm.cpp:833:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 833 | lflank_start[MODEL] = NAN;
- | ^~~
-rfhmm.cpp:834:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 834 | lflank_start[READ] = NAN;
- | ^~~
-rfhmm.cpp:835:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 835 | lflank_end[MODEL] = NAN;
- | ^~~
-rfhmm.cpp:836:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 836 | lflank_end[READ] = NAN;
- | ^~~
-rfhmm.cpp:837:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 837 | motif_start[MODEL] = NAN;
- | ^~~
-rfhmm.cpp:838:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 838 | motif_start[READ] = NAN;
- | ^~~
-rfhmm.cpp:839:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 839 | motif_end[MODEL] = NAN;
- | ^~~
-rfhmm.cpp:840:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 840 | motif_end[READ] = NAN;
- | ^~~
-rfhmm.cpp:841:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 841 | rflank_start[MODEL] = NAN;
- | ^~~
-rfhmm.cpp:842:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 842 | rflank_start[READ] = NAN;
- | ^~~
-rfhmm.cpp:843:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 843 | rflank_end[MODEL] = NAN;
- | ^~~
-rfhmm.cpp:844:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 844 | rflank_end[READ] = NAN;
- | ^~~
-rfhmm.cpp:845:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 845 | motif_count = NAN;
- | ^~~
-rfhmm.cpp:846:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 846 | exact_motif_count = NAN;
- | ^~~
-rfhmm.cpp:847:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 847 | motif_m = NAN;
- | ^~~
-rfhmm.cpp:848:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
- 848 | motif_xid = NAN;
- | ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm_x.o -c rfhmm_x.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rminfo.o -c rminfo.cpp
+g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o seq.o -c seq.cpp
rfhmm_x.cpp: In member function 'void RFHMM_X::clear_statistics()':
rfhmm_x.cpp:928:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
928 | lflank_start[MODEL] = NAN;
@@ -1384,8 +1380,55 @@
rfhmm_x.cpp:943:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
943 | motif_xid = NAN;
| ^~~
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rminfo.o -c rminfo.cpp
-g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o seq.o -c seq.cpp
+rfhmm.cpp: In member function 'void RFHMM::clear_statistics()':
+rfhmm.cpp:833:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 833 | lflank_start[MODEL] = NAN;
+ | ^~~
+rfhmm.cpp:834:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 834 | lflank_start[READ] = NAN;
+ | ^~~
+rfhmm.cpp:835:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 835 | lflank_end[MODEL] = NAN;
+ | ^~~
+rfhmm.cpp:836:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 836 | lflank_end[READ] = NAN;
+ | ^~~
+rfhmm.cpp:837:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 837 | motif_start[MODEL] = NAN;
+ | ^~~
+rfhmm.cpp:838:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 838 | motif_start[READ] = NAN;
+ | ^~~
+rfhmm.cpp:839:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 839 | motif_end[MODEL] = NAN;
+ | ^~~
+rfhmm.cpp:840:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 840 | motif_end[READ] = NAN;
+ | ^~~
+rfhmm.cpp:841:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 841 | rflank_start[MODEL] = NAN;
+ | ^~~
+rfhmm.cpp:842:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 842 | rflank_start[READ] = NAN;
+ | ^~~
+rfhmm.cpp:843:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 843 | rflank_end[MODEL] = NAN;
+ | ^~~
+rfhmm.cpp:844:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 844 | rflank_end[READ] = NAN;
+ | ^~~
+rfhmm.cpp:845:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 845 | motif_count = NAN;
+ | ^~~
+rfhmm.cpp:846:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 846 | exact_motif_count = NAN;
+ | ^~~
+rfhmm.cpp:847:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 847 | motif_m = NAN;
+ | ^~~
+rfhmm.cpp:848:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
+ 848 | motif_xid = NAN;
+ | ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o set_ref.o -c set_ref.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o snp_genotyping_record.o -c snp_genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sort.o -c sort.cpp
@@ -1416,7 +1459,7 @@
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o -lz -lpthread -lbz2 -llzma -lcurl -lcrypto -lhts -lpcre2-8 -lsvm -lRmath -lR
make[1]: Leaving directory '/build/vt-0.57721+ds'
dh_auto_test
- make -j3 test
+ make -j4 test
make[1]: Entering directory '/build/vt-0.57721+ds'
test/test.sh
++++++++++++++++++++++
@@ -1468,8 +1511,8 @@
dh_gencontrol
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'vt' in '../vt_0.57721+ds-3_armhf.deb'.
dpkg-deb: building package 'vt-dbgsym' in '../vt-dbgsym_0.57721+ds-3_armhf.deb'.
+dpkg-deb: building package 'vt' in '../vt_0.57721+ds-3_armhf.deb'.
dpkg-deb: building package 'vt-examples' in '../vt-examples_0.57721+ds-3_all.deb'.
dpkg-genbuildinfo --build=binary -O../vt_0.57721+ds-3_armhf.buildinfo
dpkg-genchanges --build=binary -O../vt_0.57721+ds-3_armhf.changes
@@ -1478,12 +1521,14 @@
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/6752/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/6752/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/12314 and its subdirectories
-I: Current time: Sat May 6 13:31:25 -12 2023
-I: pbuilder-time-stamp: 1683423085
+I: removing directory /srv/workspace/pbuilder/6752 and its subdirectories
+I: Current time: Sun May 7 17:18:57 +14 2023
+I: pbuilder-time-stamp: 1683429537