I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 11 15:17:49 +14 2023
I: pbuilder-time-stamp: 1686446269
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [idba_1.1.3-8.dsc]
I: copying [./idba_1.1.3.orig.tar.gz]
I: copying [./idba_1.1.3-8.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Nov 6 10:30:52 2022 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./idba_1.1.3-8.dsc: no acceptable signature found
dpkg-source: info: extracting idba in idba-1.1.3
dpkg-source: info: unpacking idba_1.1.3.orig.tar.gz
dpkg-source: info: unpacking idba_1.1.3-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying install_all_idba_flavours.patch
dpkg-source: info: applying use-atomic-for-mips.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying use_debian_packaged_googletest.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3053281/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jun 11 15:17 /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/3053281/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/3053281/tmp/hooks/D02_print_environment starting
I: set
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]="x86_64-pc-linux-gnu")
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=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 '
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=2fb23556f9604f5ba00f507130a56518
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=3053281
PS4='+ '
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.8KOaPtZ9/pbuilderrc_E7Em --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.8KOaPtZ9/b2 --logfile b2/build.log --extrapackages usrmerge idba_1.1.3-8.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://78.137.99.97:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 21 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 21 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 121904 Sep 21 2022 date
-rwxr-xr-x 1 root root 89240 Sep 21 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 21 2022 df
-rwxr-xr-x 1 root root 151344 Sep 21 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 24 00:02 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 43856 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 35664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt
-rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount
-rwxr-xr-x 1 root root 203152 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 98136 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 72824 Sep 21 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 24 02:40 login
-rwxr-xr-x 1 root root 151344 Sep 21 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk
-rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 24 00:02 more
-rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount
-rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint
-rwxr-xr-x 1 root root 142968 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 43952 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 21 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 9 Jun 11 15:17 sh -> /bin/bash
-rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 21 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 24 00:02 su
-rwxr-xr-x 1 root root 39824 Sep 21 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 21 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 21 2022 true
-rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount
-rwxr-xr-x 1 root root 43888 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 24 00:02 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/3053281/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), libgtest-dev, python3
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19591 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on libgtest-dev; however:
Package libgtest-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgtest-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.1 MB of archives. After unpacking 100 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 googletest all 1.12.1-0.2 [506 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 libgtest-dev amd64 1.12.1-0.2 [240 kB]
Fetched 25.1 MB in 1s (32.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal: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 ... 19591 files and directories currently installed.)
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
(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 ... 19907 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:amd64.
Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ...
Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:amd64.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ...
Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
(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 ... 20341 files and directories currently installed.)
Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.2_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package googletest.
Preparing to unpack .../31-googletest_1.12.1-0.2_all.deb ...
Unpacking googletest (1.12.1-0.2) ...
Selecting previously unselected package libgtest-dev:amd64.
Preparing to unpack .../32-libgtest-dev_1.12.1-0.2_amd64.deb ...
Unpacking libgtest-dev:amd64 (1.12.1-0.2) ...
Setting up media-types (10.0.0) ...
Setting up libpipeline1:amd64 (1.5.7-1) ...
Setting up libicu72:amd64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:amd64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up googletest (1.12.1-0.2) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up autoconf (2.71-3) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:amd64 (0.188-2.1) ...
Setting up readline-common (8.2-1.3) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libgtest-dev:amd64 (1.12.1-0.2) ...
Setting up libtool (2.4.7-5) ...
Setting up libreadline8:amd64 (8.2-1.3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
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: user script /srv/workspace/pbuilder/3053281/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/3053281/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/idba-1.1.3/ && 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 > ../idba_1.1.3-8_source.changes
dpkg-buildpackage: info: source package idba
dpkg-buildpackage: info: source version 1.1.3-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:7: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:7: the top level
configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:429: AM_INIT_AUTOMAKE is expanded from...
configure.ac:8: the top level
configure.ac:30: warning: AC_OUTPUT should be used without arguments.
configure.ac:30: You should run autoupdate.
configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
bin/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
bin/Makefile.am:9: warning: source file '$(top_srcdir)/src/tools/fa2fq.cpp' is in a subdirectory,
bin/Makefile.am:9: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least one source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
bin/Makefile.am:19: warning: source file '$(top_srcdir)/src/tools/filter_blat.cpp' is in a subdirectory,
bin/Makefile.am:19: but option 'subdir-objects' is disabled
bin/Makefile.am:17: warning: source file '$(top_srcdir)/src/tools/filter_contigs.cpp' is in a subdirectory,
bin/Makefile.am:17: but option 'subdir-objects' is disabled
bin/Makefile.am:33: warning: source file '$(top_srcdir)/src/release/filterfa.cpp' is in a subdirectory,
bin/Makefile.am:33: but option 'subdir-objects' is disabled
bin/Makefile.am:25: warning: source file '$(top_srcdir)/src/release/fq2fa.cpp' is in a subdirectory,
bin/Makefile.am:25: but option 'subdir-objects' is disabled
bin/Makefile.am:34: warning: source file '$(top_srcdir)/src/release/idba.cpp' is in a subdirectory,
bin/Makefile.am:34: but option 'subdir-objects' is disabled
bin/Makefile.am:30: warning: source file '$(top_srcdir)/src/release/idba_hybrid.cpp' is in a subdirectory,
bin/Makefile.am:30: but option 'subdir-objects' is disabled
bin/Makefile.am:29: warning: source file '$(top_srcdir)/src/release/idba_tran.cpp' is in a subdirectory,
bin/Makefile.am:29: but option 'subdir-objects' is disabled
bin/Makefile.am:13: warning: source file '$(top_srcdir)/src/tools/idba_tran_test.cpp' is in a subdirectory,
bin/Makefile.am:13: but option 'subdir-objects' is disabled
bin/Makefile.am:27: warning: source file '$(top_srcdir)/src/release/idba_ud.cpp' is in a subdirectory,
bin/Makefile.am:27: but option 'subdir-objects' is disabled
bin/Makefile.am:31: warning: source file '$(top_srcdir)/src/release/parallel_blat.cpp' is in a subdirectory,
bin/Makefile.am:31: but option 'subdir-objects' is disabled
bin/Makefile.am:18: warning: source file '$(top_srcdir)/src/tools/parallel_rna_blat.cpp' is in a subdirectory,
bin/Makefile.am:18: but option 'subdir-objects' is disabled
bin/Makefile.am:12: warning: source file '$(top_srcdir)/src/tools/print_graph.cpp' is in a subdirectory,
bin/Makefile.am:12: but option 'subdir-objects' is disabled
bin/Makefile.am:28: warning: source file '$(top_srcdir)/src/release/raw_n50.cpp' is in a subdirectory,
bin/Makefile.am:28: but option 'subdir-objects' is disabled
bin/Makefile.am:14: warning: source file '$(top_srcdir)/src/tools/sample_reads.cpp' is in a subdirectory,
bin/Makefile.am:14: but option 'subdir-objects' is disabled
bin/Makefile.am:7: warning: source file '$(top_srcdir)/src/tools/scaffold.cpp' is in a subdirectory,
bin/Makefile.am:7: but option 'subdir-objects' is disabled
bin/Makefile.am:6: warning: source file '$(top_srcdir)/src/tools/shuffle_reads.cpp' is in a subdirectory,
bin/Makefile.am:6: but option 'subdir-objects' is disabled
bin/Makefile.am:36: warning: source file '$(top_srcdir)/src/release/sim_reads.cpp' is in a subdirectory,
bin/Makefile.am:36: but option 'subdir-objects' is disabled
bin/Makefile.am:32: warning: source file '$(top_srcdir)/src/release/sim_reads_tran.cpp' is in a subdirectory,
bin/Makefile.am:32: but option 'subdir-objects' is disabled
bin/Makefile.am:15: warning: source file '$(top_srcdir)/src/tools/sort_psl.cpp' is in a subdirectory,
bin/Makefile.am:15: but option 'subdir-objects' is disabled
bin/Makefile.am:16: warning: source file '$(top_srcdir)/src/tools/sort_reads.cpp' is in a subdirectory,
bin/Makefile.am:16: but option 'subdir-objects' is disabled
bin/Makefile.am:20: warning: source file '$(top_srcdir)/src/tools/split_fa.cpp' is in a subdirectory,
bin/Makefile.am:20: but option 'subdir-objects' is disabled
bin/Makefile.am:23: warning: source file '$(top_srcdir)/src/tools/split_fq.cpp' is in a subdirectory,
bin/Makefile.am:23: but option 'subdir-objects' is disabled
bin/Makefile.am:35: warning: source file '$(top_srcdir)/src/release/split_scaffold.cpp' is in a subdirectory,
bin/Makefile.am:35: but option 'subdir-objects' is disabled
bin/Makefile.am:21: warning: source file '$(top_srcdir)/src/tools/test.cpp' is in a subdirectory,
bin/Makefile.am:21: but option 'subdir-objects' is disabled
bin/Makefile.am:8: warning: source file '$(top_srcdir)/src/tools/validate_component.cpp' is in a subdirectory,
bin/Makefile.am:8: but option 'subdir-objects' is disabled
bin/Makefile.am:26: warning: source file '$(top_srcdir)/src/release/validate_contigs_blat.cpp' is in a subdirectory,
bin/Makefile.am:26: but option 'subdir-objects' is disabled
bin/Makefile.am:11: warning: source file '$(top_srcdir)/src/tools/validate_contigs_mummer.cpp' is in a subdirectory,
bin/Makefile.am:11: but option 'subdir-objects' is disabled
bin/Makefile.am:22: warning: source file '$(top_srcdir)/src/tools/validate_reads_blat.cpp' is in a subdirectory,
bin/Makefile.am:22: but option 'subdir-objects' is disabled
bin/Makefile.am:10: warning: source file '$(top_srcdir)/src/tools/validate_rna.cpp' is in a subdirectory,
bin/Makefile.am:10: but option 'subdir-objects' is disabled
lib/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/basic/math.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/hash_aligner.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/options_description.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/log.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/utils.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/blat_record.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/short_sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_reader.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_writer.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_io.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/compact_sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph_branch_group.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/scaffold_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph_branch_group.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_info.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/local_assembler.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/assembly_utility.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
lib/Makefile.am:68: but option 'subdir-objects' is disabled
lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest-all.cc' is in a subdirectory,
lib/Makefile.am:68: but option 'subdir-objects' is disabled
test/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
test/Makefile.am:11: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:11: but option 'subdir-objects' is disabled
test/Makefile.am:11: warning: source file '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' is in a subdirectory,
test/Makefile.am:11: but option 'subdir-objects' is disabled
test/Makefile.am:8: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:8: but option 'subdir-objects' is disabled
test/Makefile.am:8: warning: source file '$(top_srcdir)/src/test/bit_edges_unittest.cpp' is in a subdirectory,
test/Makefile.am:8: but option 'subdir-objects' is disabled
test/Makefile.am:6: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:6: but option 'subdir-objects' is disabled
test/Makefile.am:6: warning: source file '$(top_srcdir)/src/test/compact_sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:6: but option 'subdir-objects' is disabled
test/Makefile.am:17: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:17: but option 'subdir-objects' is disabled
test/Makefile.am:17: warning: source file '$(top_srcdir)/src/test/hash_map_unittest.cpp' is in a subdirectory,
test/Makefile.am:17: but option 'subdir-objects' is disabled
test/Makefile.am:10: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:10: but option 'subdir-objects' is disabled
test/Makefile.am:10: warning: source file '$(top_srcdir)/src/test/hash_set_unittest.cpp' is in a subdirectory,
test/Makefile.am:10: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/test/hash_table_unittest.cpp' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:13: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:13: but option 'subdir-objects' is disabled
test/Makefile.am:13: warning: source file '$(top_srcdir)/src/test/histgram_unittest.cpp' is in a subdirectory,
test/Makefile.am:13: but option 'subdir-objects' is disabled
test/Makefile.am:9: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:9: but option 'subdir-objects' is disabled
test/Makefile.am:9: warning: source file '$(top_srcdir)/src/test/kmer_unittest.cpp' is in a subdirectory,
test/Makefile.am:9: but option 'subdir-objects' is disabled
test/Makefile.am:14: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:14: but option 'subdir-objects' is disabled
test/Makefile.am:14: warning: source file '$(top_srcdir)/src/test/managed_list_unittest.cpp' is in a subdirectory,
test/Makefile.am:14: but option 'subdir-objects' is disabled
test/Makefile.am:15: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:15: but option 'subdir-objects' is disabled
test/Makefile.am:15: warning: source file '$(top_srcdir)/src/test/sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:15: but option 'subdir-objects' is disabled
test/Makefile.am:16: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:16: but option 'subdir-objects' is disabled
test/Makefile.am:16: warning: source file '$(top_srcdir)/src/test/short_sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:16: but option 'subdir-objects' is disabled
test/Makefile.am:12: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:12: but option 'subdir-objects' is disabled
test/Makefile.am:12: warning: source file '$(top_srcdir)/src/test/vertex_status_unittest.cpp' is in a subdirectory,
test/Makefile.am:12: but option 'subdir-objects' is disabled
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/idba-1.1.3'
dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" LIBS=" -latomic"
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" "LIBS= -latomic"
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ranlib... ranlib
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for an ANSI C-conforming const... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for sqrt... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating lib/Makefile
config.status: creating test/Makefile
config.status: creating script/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/build/idba-1.1.3'
dh_auto_build
make -j15
make[1]: Entering directory '/build/idba-1.1.3'
make all-recursive
make[2]: Entering directory '/build/idba-1.1.3'
Making all in lib
make[3]: Entering directory '/build/idba-1.1.3/lib'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp
../src/misc/log.cpp: In destructor 'LogProcess::~LogProcess()':
../src/misc/log.cpp:78:13: warning: 'throw' will always call 'terminate' [-Wterminate]
78 | throw runtime_error("cannot kill log process");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/misc/log.cpp:78:13: note: in C++11 destructors default to 'noexcept'
In file included from ../src/container/hash_map.h:14,
from ../src/misc/hash_aligner.h:14,
from ../src/misc/hash_aligner.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/functional:49,
from ../src/basic/functional.h:13,
from ../src/container/hash_map.h:13:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)':
../src/misc/log.cpp:122:14: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result]
122 | write(log_thread.out_fd, line, len);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/graph/contig_graph_branch_group.h:15,
from ../src/graph/contig_graph_branch_group.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/graph/contig_graph_branch_group.h:13:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/graph/hash_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/hash_graph.h:15:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/graph/scaffold_graph.h:19,
from ../src/graph/scaffold_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/graph/scaffold_graph.h:14:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/graph/contig_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/contig_graph.h:14:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/assembly/local_assembler.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/assembly/assembly_utility.h:17,
from ../src/assembly/local_assembler.h:13:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/graph/hash_graph_branch_group.h:14,
from ../src/graph/hash_graph_branch_group.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/hash_graph.h:15:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)':
../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
488 | bool flag = false;
| ^~~~
../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable]
489 | int aligned[2] = {0};
| ^~~~~~~
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/assembly/assembly_utility.cpp:14:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/assembly/assembly_utility.h:17,
from ../src/assembly/assembly_utility.cpp:9:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque<ContigGraphVertexAdaptor>&, std::deque<ContigGraphVertexAdaptor>&)':
../src/graph/contig_graph.cpp:1391:30: warning: variable 'end' set but not used [-Wunused-but-set-variable]
1391 | ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component);
| ^~~
In file included from ../gtest_src/gtest/gtest-all.cc:39:
../gtest_src/gtest/gtest.h: In static member function 'static const char* testing::internal::String::CloneCString(const char*)':
../gtest_src/gtest/gtest.h:2672:17: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2672 | return strncpy(dest, src, n);
| ^
../gtest_src/gtest/gtest-all.cc:2155:39: note: length computed here
2155 | NULL : CloneString(c_str, strlen(c_str));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
rm -f libgtest.a
ar cru libgtest.a gtest_main.o gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
rm -f libassembly.a
ar cru libassembly.a math.o hash_aligner.o options_description.o log.o utils.o blat_record.o short_sequence.o sequence_reader.o sequence_writer.o sequence_io.o sequence.o compact_sequence.o contig_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph.o hash_graph_branch_group.o contig_info.o local_assembler.o assembly_utility.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
make[3]: Leaving directory '/build/idba-1.1.3/lib'
Making all in bin
make[3]: Entering directory '/build/idba-1.1.3/bin'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/tools/print_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/contig_graph.h:14:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/release/idba_hybrid.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba_hybrid.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/tools/validate_rna.cpp: In function 'int main(int, char**)':
../src/tools/validate_rna.cpp:396:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
396 | fscanf(flist, "%s %lf", buf, &coverage[i]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)':
../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
218 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
219 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
220 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
221 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
222 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/release/idba_ud.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba_ud.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp
../src/tools/validate_component.cpp: In function 'int main(int, char**)':
../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable]
141 | int ref_id = dict[record.ref_name];
| ^~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/tools/idba_tran_test.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/tools/idba_tran_test.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/release/idba_tran.cpp:22:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba_tran.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/tools/scaffold.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/tools/scaffold.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/release/idba.cpp:23:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp
../src/release/idba_tran.cpp: In function 'void FindIsoforms(ContigGraphPath&, std::deque<ContigGraphPath>&, ContigGraph&, std::deque<ContigGraphPath>&)':
../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
241 | if (flag && path.size() > option.min_transcript)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/release/idba_tran.cpp: In function 'void Assemble(HashGraph&)':
../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
523 | if (transcripts[i].size() >= option.min_transcript)
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp
../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const std::string&)':
../src/tools/parallel_rna_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
47 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const std::string&)':
../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
53 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void Append(const std::string&, const std::string&)':
../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
59 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const std::string&)':
../src/tools/parallel_rna_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
96 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp
../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive
6 | #include "graph/contig_graph.h";
| ^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp
../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive
7 | #include "sequence/sequence.h";
| ^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/tools/test.cpp:6:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/tools/test.cpp:1:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp
../src/release/parallel_blat.cpp: In function 'void CreateFile(const std::string&)':
../src/release/parallel_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
47 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void RemoveFile(const std::string&)':
../src/release/parallel_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
53 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void Append(const std::string&, const std::string&)':
../src/release/parallel_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
59 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void RunBlat(const std::string&)':
../src/release/parallel_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
96 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)':
../src/release/validate_contigs_blat.cpp:388:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
388 | fscanf(flist, "%s %lf", buf, &coverage[i]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic
../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)':
../src/release/sim_reads_tran.cpp:89:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
89 | fscanf(flist, "%s %lf", buf, &weight[i]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic
make[3]: Leaving directory '/build/idba-1.1.3/bin'
Making all in test
make[3]: Entering directory '/build/idba-1.1.3/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/idba-1.1.3/test'
Making all in script
make[3]: Entering directory '/build/idba-1.1.3/script'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/idba-1.1.3/script'
make[3]: Entering directory '/build/idba-1.1.3'
make[3]: Leaving directory '/build/idba-1.1.3'
make[2]: Leaving directory '/build/idba-1.1.3'
make[1]: Leaving directory '/build/idba-1.1.3'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/idba-1.1.3'
# /usr/bin/make unittest
export PATH=/build/idba-1.1.3/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path && cd test && /usr/bin/make check
make[2]: Entering directory '/build/idba-1.1.3/test'
/usr/bin/make compact_sequence_unittest hash_table_unittest bit_edges_unittest kmer_unittest hash_set_unittest atomic_integer_unittest vertex_status_unittest histgram_unittest managed_list_unittest sequence_unittest short_sequence_unittest hash_map_unittest
make[3]: Entering directory '/build/idba-1.1.3/test'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence_unittest.o `test -f '../src/test/compact_sequence_unittest.cpp' || echo './'`../src/test/compact_sequence_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o compact_sequence_unittest gtest_main.o compact_sequence_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_table_unittest.o `test -f '../src/test/hash_table_unittest.cpp' || echo './'`../src/test/hash_table_unittest.cpp
In file included from ../src/container/hash_table.h:23,
from ../src/test/hash_table_unittest.cpp:11:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from ../src/test/hash_table_unittest.cpp:9:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_table_unittest gtest_main.o hash_table_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bit_edges_unittest.o `test -f '../src/test/bit_edges_unittest.cpp' || echo './'`../src/test/bit_edges_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o bit_edges_unittest gtest_main.o bit_edges_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o kmer_unittest.o `test -f '../src/test/kmer_unittest.cpp' || echo './'`../src/test/kmer_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o kmer_unittest gtest_main.o kmer_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_set_unittest.o `test -f '../src/test/hash_set_unittest.cpp' || echo './'`../src/test/hash_set_unittest.cpp
In file included from ../src/container/hash_set.h:13,
from ../src/test/hash_set_unittest.cpp:12:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from ../src/test/hash_set_unittest.cpp:10:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_set_unittest gtest_main.o hash_set_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atomic_integer_unittest.o `test -f '../src/test/atomic_integer_unittest.cpp' || echo './'`../src/test/atomic_integer_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o atomic_integer_unittest gtest_main.o atomic_integer_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vertex_status_unittest.o `test -f '../src/test/vertex_status_unittest.cpp' || echo './'`../src/test/vertex_status_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vertex_status_unittest gtest_main.o vertex_status_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o histgram_unittest.o `test -f '../src/test/histgram_unittest.cpp' || echo './'`../src/test/histgram_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o histgram_unittest gtest_main.o histgram_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o managed_list_unittest.o `test -f '../src/test/managed_list_unittest.cpp' || echo './'`../src/test/managed_list_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o managed_list_unittest gtest_main.o managed_list_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_unittest.o `test -f '../src/test/sequence_unittest.cpp' || echo './'`../src/test/sequence_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequence_unittest gtest_main.o sequence_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence_unittest.o `test -f '../src/test/short_sequence_unittest.cpp' || echo './'`../src/test/short_sequence_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o short_sequence_unittest gtest_main.o short_sequence_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_map_unittest.o `test -f '../src/test/hash_map_unittest.cpp' || echo './'`../src/test/hash_map_unittest.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/test/hash_map_unittest.cpp:11:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from ../src/test/hash_map_unittest.cpp:9:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_map_unittest gtest_main.o hash_map_unittest.o ../lib/libassembly.a -lgtest -latomic
make[3]: Leaving directory '/build/idba-1.1.3/test'
/usr/bin/make check-TESTS
make[3]: Entering directory '/build/idba-1.1.3/test'
make[4]: Entering directory '/build/idba-1.1.3/test'
PASS: compact_sequence_unittest
PASS: hash_table_unittest
PASS: bit_edges_unittest
PASS: kmer_unittest
PASS: hash_set_unittest
PASS: atomic_integer_unittest
PASS: vertex_status_unittest
PASS: histgram_unittest
PASS: managed_list_unittest
PASS: sequence_unittest
PASS: short_sequence_unittest
PASS: hash_map_unittest
============================================================================
Testsuite summary for idba 1.1.3
============================================================================
# TOTAL: 12
# PASS: 12
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/build/idba-1.1.3/test'
make[3]: Leaving directory '/build/idba-1.1.3/test'
make[2]: Leaving directory '/build/idba-1.1.3/test'
make[1]: Leaving directory '/build/idba-1.1.3'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_installdirs
dh_auto_install
make -j15 install DESTDIR=/build/idba-1.1.3/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/idba-1.1.3'
Making install in lib
make[2]: Entering directory '/build/idba-1.1.3/lib'
make[3]: Entering directory '/build/idba-1.1.3/lib'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/idba-1.1.3/lib'
make[2]: Leaving directory '/build/idba-1.1.3/lib'
Making install in bin
make[2]: Entering directory '/build/idba-1.1.3/bin'
make[3]: Entering directory '/build/idba-1.1.3/bin'
/usr/bin/mkdir -p '/build/idba-1.1.3/debian/tmp/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c idba idba_ud idba_tran idba_hybrid '/build/idba-1.1.3/debian/tmp/usr/bin'
make[3]: Leaving directory '/build/idba-1.1.3/bin'
make[2]: Leaving directory '/build/idba-1.1.3/bin'
Making install in test
make[2]: Entering directory '/build/idba-1.1.3/test'
make[3]: Entering directory '/build/idba-1.1.3/test'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/idba-1.1.3/test'
make[2]: Leaving directory '/build/idba-1.1.3/test'
Making install in script
make[2]: Entering directory '/build/idba-1.1.3/script'
make[3]: Entering directory '/build/idba-1.1.3/script'
/usr/bin/mkdir -p '/build/idba-1.1.3/debian/tmp/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/build/idba-1.1.3/debian/tmp/usr/bin'
make[3]: Leaving directory '/build/idba-1.1.3/script'
make[2]: Leaving directory '/build/idba-1.1.3/script'
make[2]: Entering directory '/build/idba-1.1.3'
make[3]: Entering directory '/build/idba-1.1.3'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/idba-1.1.3'
make[2]: Leaving directory '/build/idba-1.1.3'
make[1]: Leaving directory '/build/idba-1.1.3'
debian/rules override_dh_install
make[1]: Entering directory '/build/idba-1.1.3'
dh_install
# for the moment the role of these scripts is totally unknown but they do not seem to be necessary
mv debian/idba/usr/bin/*.py debian/idba/usr/lib/idba/
mv debian/idba/usr/bin/validate_blat* debian/idba/usr/lib/idba/
make[1]: Leaving directory '/build/idba-1.1.3'
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'idba' in '../idba_1.1.3-8_amd64.deb'.
dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_amd64.deb'.
dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-8_amd64.deb'.
dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-8_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../idba_1.1.3-8_amd64.buildinfo
dpkg-genchanges --build=binary -O../idba_1.1.3-8_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
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/3053281/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/3053281/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/3053281 and its subdirectories
I: Current time: Sun Jun 11 15:21:48 +14 2023
I: pbuilder-time-stamp: 1686446508