Diff of the two buildlogs:
--
--- b1/build.log 2021-12-08 17:42:34.844436404 +0000
+++ b2/build.log 2021-12-08 17:56:54.754037715 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Dec 8 05:39:27 -12 2021
-I: pbuilder-time-stamp: 1638985167
+I: Current time: Wed Jan 11 14:05:46 +14 2023
+I: pbuilder-time-stamp: 1673395546
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
I: copying local configuration
@@ -17,7 +17,7 @@
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
-gpgv: Signature made Tue Feb 5 19:10:41 2019 -12
+gpgv: Signature made Wed Feb 6 21:10:41 2019 +14
gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.1+dfsg-2.1.dsc
@@ -29,136 +29,170 @@
dpkg-source: info: applying hdf5-1.10.0-support.patch
I: using fakeroot in build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/28320/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3430533/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos5-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
+Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
+Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
+Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/3430533/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3430533/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='amd64'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
- DISTRIBUTION=''
- HOME='/root'
- HOST_ARCH='amd64'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.0.3(1)-release'
+ BUILDDIR=/build
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
+ DIRSTACK=()
+ DISTRIBUTION=
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='e583b02c18c444e69d3fb050fe77e860'
- 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='28320'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=1ba8410c457f46faa0c78bc248dccdba
+ LANG=C
+ LANGUAGE=et_EE:et
+ LC_ALL=C
+ MACHTYPE=x86_64-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=3430533
PS4='+ '
- PWD='/'
- SHELL='/bin/bash'
- SHLVL='2'
- SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.dQxUtD8dWy/pbuilderrc_bgnf --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dQxUtD8dWy/b1 --logfile b1/build.log pbseqlib_5.3.1+dfsg-2.1.dsc'
- SUDO_GID='111'
- SUDO_UID='106'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://78.137.99.97:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.dQxUtD8dWy/pbuilderrc_j76A --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dQxUtD8dWy/b2 --logfile b2/build.log pbseqlib_5.3.1+dfsg-2.1.dsc'
+ SUDO_GID=110
+ SUDO_UID=105
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://85.184.249.68:3128
I: uname -a
- Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux
I: ls -l /bin
total 5116
- -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash
- -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2
- -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff
- -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep
- -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep
- -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep
- -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2
- -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore
- -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore
- -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat
- -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp
- -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod
- -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown
- -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp
- -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash
- -rwxr-xr-x 1 root root 109408 Feb 28 2019 date
- -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd
- -rwxr-xr-x 1 root root 93744 Feb 28 2019 df
- -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir
- -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg
- lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname
- lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname
- -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo
- -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep
- -rwxr-xr-x 1 root root 35424 Feb 28 2019 false
- -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep
- -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt
- -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount
- -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep
- -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip
- -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe
- -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip
- -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname
- -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln
- -rwxr-xr-x 1 root root 56760 Jul 26 2018 login
- -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls
- -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk
- -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir
- -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod
- -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp
- -rwxr-xr-x 1 root root 43008 Jan 9 2019 more
- -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount
- -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint
- -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv
- lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname
- lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5
- -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd
- lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash
- -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink
- -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm
- -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir
- -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts
- -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed
- lrwxrwxrwx 1 root root 4 Nov 7 09:58 sh -> dash
- -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep
- -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty
- -rwsr-xr-x 1 root root 63568 Jan 9 2019 su
- -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync
- -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar
- -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile
- -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch
- -rwxr-xr-x 1 root root 35424 Feb 28 2019 true
- -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server
- -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount
- -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname
- -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress
- -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir
- -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl
- -rwxr-xr-x 1 root root 946 Jan 21 2019 which
- lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname
- -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat
- -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp
- -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff
- -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep
- -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep
- -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce
- -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep
- -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless
- -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore
- -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew
-I: user script /srv/workspace/pbuilder/28320/tmp/hooks/D02_print_environment finished
+ -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash
+ -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2
+ -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff
+ -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep
+ -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep
+ -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep
+ -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2
+ -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore
+ -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore
+ -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat
+ -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp
+ -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod
+ -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown
+ -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp
+ -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash
+ -rwxr-xr-x 1 root root 109408 Mar 1 2019 date
+ -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd
+ -rwxr-xr-x 1 root root 93744 Mar 1 2019 df
+ -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir
+ -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname
+ -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo
+ -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep
+ -rwxr-xr-x 1 root root 35424 Mar 1 2019 false
+ -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep
+ -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt
+ -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount
+ -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep
+ -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip
+ -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe
+ -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip
+ -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname
+ -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln
+ -rwxr-xr-x 1 root root 56760 Jul 27 2018 login
+ -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls
+ -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk
+ -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir
+ -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod
+ -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp
+ -rwxr-xr-x 1 root root 43008 Jan 10 2019 more
+ -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount
+ -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint
+ -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname
+ lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5
+ -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd
+ lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash
+ -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink
+ -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm
+ -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir
+ -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts
+ -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed
+ lrwxrwxrwx 1 root root 4 Jan 11 14:05 sh -> bash
+ lrwxrwxrwx 1 root root 4 Dec 11 18:21 sh.distrib -> dash
+ -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep
+ -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty
+ -rwsr-xr-x 1 root root 63568 Jan 10 2019 su
+ -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync
+ -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar
+ -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile
+ -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch
+ -rwxr-xr-x 1 root root 35424 Mar 1 2019 true
+ -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server
+ -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount
+ -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname
+ -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress
+ -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir
+ -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl
+ -rwxr-xr-x 1 root root 946 Jan 22 2019 which
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname
+ -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat
+ -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp
+ -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff
+ -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep
+ -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep
+ -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce
+ -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep
+ -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless
+ -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore
+ -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew
+I: user script /srv/workspace/pbuilder/3430533/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -296,7 +330,7 @@
Get: 84 http://deb.debian.org/debian buster/main amd64 libpbbam0.19.0 amd64 0.19.0+dfsg-4 [551 kB]
Get: 85 http://deb.debian.org/debian buster/main amd64 libssl-dev amd64 1.1.1d-0+deb10u7 [1795 kB]
Get: 86 http://deb.debian.org/debian buster/main amd64 libpbbam-dev amd64 0.19.0+dfsg-4 [93.3 kB]
-Fetched 49.2 MB in 2s (32.0 MB/s)
+Fetched 49.2 MB in 2s (27.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libbsd0:amd64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19195 files and directories currently installed.)
@@ -666,7 +700,8 @@
fakeroot is already the newest version (1.23-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
-I: Running cd /build/pbseqlib-5.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbseqlib_5.3.1+dfsg-2.1_source.changes
+hostname: Name or service not known
+I: Running cd /build/pbseqlib-5.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pbseqlib_5.3.1+dfsg-2.1_source.changes
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 5.3.1+dfsg-2.1
dpkg-buildpackage: info: source distribution unstable
@@ -678,7 +713,7 @@
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg'
dh_auto_clean
- make -j15 clean
+ make -j16 clean
make[2]: Entering directory '/build/pbseqlib-5.3.1+dfsg'
make -C /build/pbseqlib-5.3.1+dfsg//pbdata clean
make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg/pbdata'
@@ -742,7 +777,7 @@
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/pbseqlib-5.3.1+dfsg'
dh_auto_build -- PREFIX_INC=..
- make -j15 "INSTALL=install --strip-program=true" PREFIX_INC=..
+ make -j16 "INSTALL=install --strip-program=true" PREFIX_INC=..
make[2]: Entering directory '/build/pbseqlib-5.3.1+dfsg'
make libpbdata
make[3]: Entering directory '/build/pbseqlib-5.3.1+dfsg'
@@ -779,6 +814,9 @@
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/AcqParams.cpp -o AcqParams.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/QualityTransform.cpp -o QualityTransform.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.o
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c metagenome/TitleTable.cpp -o TitleTable.o
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MetricField.cpp -o MetricField.o
In file included from reads/RegionAnnotations.cpp:3:
reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
@@ -790,9 +828,6 @@
reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c metagenome/TitleTable.cpp -o TitleTable.o
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MetricField.cpp -o MetricField.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c amos/AfgBasWriter.cpp -o AfgBasWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c alignment/CmpAlignment.cpp -o CmpAlignment.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c StringUtils.cpp -o StringUtils.o
@@ -815,6 +850,8 @@
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o
In file included from SMRTSequence.cpp:3:
SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
@@ -826,8 +863,6 @@
SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o
@@ -839,8 +874,6 @@
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ReadType.cpp -o ReadType.shared.o
In file included from reads/RegionAnnotations.cpp:3:
reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
@@ -852,6 +885,8 @@
reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ReadType.cpp -o ReadType.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o
@@ -913,11 +948,11 @@
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)':
HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
HDFFile.cpp: In member function 'void HDFFile::Open(std::__cxx11::string, unsigned int, const H5::FileAccPropList&)':
HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
} catch (FileIException e) {
@@ -925,6 +960,7 @@
HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
} catch (FileIException fileException) {
^~~~~~~~~~~~~
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
In file included from HDFAtom.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:174:16: required from here
@@ -958,16 +994,28 @@
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:183:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWWriter.cpp -o HDFZMWWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFNewBasReader.cpp -o HDFNewBasReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseWriter.cpp -o HDFPulseWriter.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o
HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()':
HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o
+In file included from ../hdf/BufferedHDFArray.hpp:217,
+ from ../hdf/HDFZMWMetricsWriter.hpp:7,
+ from HDFZMWMetricsWriter.cpp:3:
+../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]':
+HDFZMWMetricsWriter.cpp:54:27: required from here
+../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
+ } catch (H5::DataSetIException e) {
+ ^~~~~
+../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
+HDFZMWMetricsWriter.cpp:55:30: required from here
+../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFBaseCallsWriter.hpp:12,
@@ -1000,20 +1048,6 @@
HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
- from ../hdf/HDFArray.hpp:9,
- from ../hdf/HDFCmpExperimentGroup.hpp:10,
- from HDFCmpExperimentGroup.cpp:1:
-../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
-../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
-HDFCmpExperimentGroup.cpp:36:69: required from here
-../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
- } catch (H5::DataSetIException e) {
- ^~~~~
-../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]':
-../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
-HDFCmpExperimentGroup.cpp:199:72: required from here
-../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
-In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from HDFZMWWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]':
@@ -1025,15 +1059,18 @@
HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
- from ../hdf/HDFZMWMetricsWriter.hpp:7,
- from HDFZMWMetricsWriter.cpp:3:
-../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]':
-HDFZMWMetricsWriter.cpp:54:27: required from here
+ from ../hdf/HDFArray.hpp:9,
+ from ../hdf/HDFCmpExperimentGroup.hpp:10,
+ from HDFCmpExperimentGroup.cpp:1:
+../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
+../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
+HDFCmpExperimentGroup.cpp:36:69: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
-../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
-HDFZMWMetricsWriter.cpp:55:30: required from here
+../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]':
+../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
+HDFCmpExperimentGroup.cpp:199:72: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
@@ -1049,8 +1086,6 @@
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.o
@@ -1078,9 +1113,6 @@
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAtom.cpp -o HDFAtom.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o
In file included from HDFAtom.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:174:16: required from here
@@ -1114,11 +1146,15 @@
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:183:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWMetricsWriter.hpp:7,
from HDFZMWMetricsWriter.cpp:3:
@@ -1130,10 +1166,7 @@
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
HDFZMWMetricsWriter.cpp:55:30: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
-HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()':
-HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
- } catch (H5::Exception e) {
- ^
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.o
HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()':
HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
@@ -1151,6 +1184,25 @@
HDFBaseCallsWriter.cpp:350:35: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from ../hdf/BufferedHDFArray.hpp:217,
+ from ../hdf/HDFArray.hpp:9,
+ from ../hdf/HDFCmpExperimentGroup.hpp:10,
+ from HDFCmpExperimentGroup.cpp:1:
+../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
+../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
+HDFCmpExperimentGroup.cpp:36:69: required from here
+../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
+ } catch (H5::DataSetIException e) {
+ ^~~~~
+../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]':
+../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
+HDFCmpExperimentGroup.cpp:199:72: required from here
+../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o
+HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()':
+HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
+ } catch (H5::Exception e) {
+ ^
+In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFPulseCallsWriter.hpp:12,
from HDFPulseCallsWriter.cpp:5:
@@ -1165,20 +1217,9 @@
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]':
HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
-In file included from ../hdf/BufferedHDFArray.hpp:217,
- from ../hdf/HDFArray.hpp:9,
- from ../hdf/HDFCmpExperimentGroup.hpp:10,
- from HDFCmpExperimentGroup.cpp:1:
-../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
-../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
-HDFCmpExperimentGroup.cpp:36:69: required from here
-../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
- } catch (H5::DataSetIException e) {
- ^~~~~
-../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]':
-../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
-HDFCmpExperimentGroup.cpp:199:72: required from here
-../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
+g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from HDFZMWWriter.cpp:5:
@@ -1190,15 +1231,8 @@
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]':
HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
-g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o
-ar rc libpbihdf.a HDFAttributable.o BufferedHDFArray.o HDFRegionsWriter.o HDFScanDataReader.o HDFWriterBase.o HDFData.o DatasetCollection.o HDFFile.o HDFRegionTableReader.o HDFZMWMetricsWriter.o HDFAtom.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFBaseCallsWriter.o HDFCmpSupportedFields.o HDFZMWReader.o HDFZMWWriter.o HDFAlnInfoGroup.o HDFNewBasReader.o HDFAlnGroupGroup.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFScanDataWriter.o HDFBaxWriter.o HDFPulseH5Writer.o BufferedHDF2DArray.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
@@ -1213,6 +1247,7 @@
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
+ar rc libpbihdf.a HDFAttributable.o BufferedHDFArray.o HDFRegionsWriter.o HDFScanDataReader.o HDFWriterBase.o HDFData.o DatasetCollection.o HDFFile.o HDFRegionTableReader.o HDFZMWMetricsWriter.o HDFAtom.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFBaseCallsWriter.o HDFCmpSupportedFields.o HDFZMWReader.o HDFZMWWriter.o HDFAlnInfoGroup.o HDFNewBasReader.o HDFAlnGroupGroup.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFScanDataWriter.o HDFBaxWriter.o HDFPulseH5Writer.o BufferedHDF2DArray.o
g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -L../pbdata/ -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o BufferedHDFArray.shared.o HDFRegionsWriter.shared.o HDFScanDataReader.shared.o HDFWriterBase.shared.o HDFData.shared.o DatasetCollection.shared.o HDFFile.shared.o HDFRegionTableReader.shared.o HDFZMWMetricsWriter.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFPulseDataFile.shared.o HDFPulseCallsWriter.shared.o HDFBaseCallsWriter.shared.o HDFCmpSupportedFields.shared.o HDFZMWReader.shared.o HDFZMWWriter.shared.o HDFAlnInfoGroup.shared.o HDFNewBasReader.shared.o HDFAlnGroupGroup.shared.o HDFPulseWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFScanDataWriter.shared.o HDFBaxWriter.shared.o HDFPulseH5Writer.shared.o BufferedHDF2DArray.shared.o -lpbbam -lpbbam -lpbdata -lhdf5 -lhdf5_cpp
make[4]: Leaving directory '/build/pbseqlib-5.3.1+dfsg/hdf'
make[3]: Leaving directory '/build/pbseqlib-5.3.1+dfsg'
@@ -1248,18 +1283,12 @@
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/CCSIterator.cpp -o CCSIterator.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/BaseSequenceIO.cpp -o BaseSequenceIO.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/MatchPos.cpp -o MatchPos.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/ClusterList.cpp -o ClusterList.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool, bool)':
files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
} catch (std::exception e) {
^
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/BaseSequenceIO.cpp -o BaseSequenceIO.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o
In file included from ../alignment/files/ReaderAgglomerate.hpp:8,
from files/ReaderAgglomerate.cpp:1:
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]':
@@ -1289,6 +1318,12 @@
../hdf/HDFCCSReader.hpp:270:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/MatchPos.cpp -o MatchPos.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/ClusterList.cpp -o ClusterList.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/CmpFile.cpp -o CmpFile.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.o
@@ -1297,6 +1332,7 @@
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/Alignment.cpp -o Alignment.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/qsufsort.cpp -o qsufsort.o
+g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)':
files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=]
std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl;
@@ -1311,7 +1347,6 @@
files/ReaderAgglomerate.cpp:671:9: note: here
case FileType::Fourbit:
^~~~
-g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o
@@ -1754,24 +1789,24 @@
dh_strip
dh_makeshlibs
dh_shlibdeps
-dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libpbihdf/usr/lib/x86_64-linux-gnu/libpbihdf.so (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libblasr/usr/lib/x86_64-linux-gnu/libblasr.so (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dpkg-shlibdeps: warning: cannot find library libpbihdf.so needed by debian/libblasr/usr/lib/x86_64-linux-gnu/libblasr.so (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
+dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libpbihdf/usr/lib/x86_64-linux-gnu/libpbihdf.so (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.1+dfsg-2.1_all.deb'.
dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.1+dfsg-2.1_all.deb'.
-dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.1+dfsg-2.1_amd64.deb'.
dpkg-deb: building package 'libpbdata' in '../libpbdata_5.3.1+dfsg-2.1_amd64.deb'.
-dpkg-deb: building package 'libpbdata-dbgsym' in '../libpbdata-dbgsym_5.3.1+dfsg-2.1_amd64.deb'.
-dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.1+dfsg-2.1_amd64.deb'.
+dpkg-deb: building package 'libblasr' in '../libblasr_5.3.1+dfsg-2.1_amd64.deb'.
dpkg-deb: building package 'libpbihdf' in '../libpbihdf_5.3.1+dfsg-2.1_amd64.deb'.
-dpkg-deb: building package 'libpbihdf-dbgsym' in '../libpbihdf-dbgsym_5.3.1+dfsg-2.1_amd64.deb'.
dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.1+dfsg-2.1_amd64.deb'.
-dpkg-deb: building package 'libblasr' in '../libblasr_5.3.1+dfsg-2.1_amd64.deb'.
+dpkg-deb: building package 'libpbihdf-dbgsym' in '../libpbihdf-dbgsym_5.3.1+dfsg-2.1_amd64.deb'.
+dpkg-deb: building package 'libpbdata-dbgsym' in '../libpbdata-dbgsym_5.3.1+dfsg-2.1_amd64.deb'.
+dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.1+dfsg-2.1_all.deb'.
+dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.1+dfsg-2.1_amd64.deb'.
dpkg-deb: building package 'libblasr-dbgsym' in '../libblasr-dbgsym_5.3.1+dfsg-2.1_amd64.deb'.
+dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.1+dfsg-2.1_amd64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../pbseqlib_5.3.1+dfsg-2.1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1779,12 +1814,14 @@
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/3430533/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3430533/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/28320 and its subdirectories
-I: Current time: Wed Dec 8 05:42:34 -12 2021
-I: pbuilder-time-stamp: 1638985354
+I: removing directory /srv/workspace/pbuilder/3430533 and its subdirectories
+I: Current time: Wed Jan 11 14:20:02 +14 2023
+I: pbuilder-time-stamp: 1673396402