Sun Jun 11 01:04:45 UTC 2023 I: starting to build idba/bookworm/amd64 on jenkins on '2023-06-11 01:04'
Sun Jun 11 01:04:45 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/737/console.log
Sun Jun 11 01:04:45 UTC 2023 I: Downloading source for bookworm/idba=1.1.3-8
--2023-06-11 01:04:45-- http://cdn-fastly.deb.debian.org/debian/pool/main/i/idba/idba_1.1.3-8.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2022 (2.0K) [text/prs.lines.tag]
Saving to: ‘idba_1.1.3-8.dsc’
0K . 100% 78.8M=0s
2023-06-11 01:04:45 (78.8 MB/s) - ‘idba_1.1.3-8.dsc’ saved [2022/2022]
Sun Jun 11 01:04:45 UTC 2023 I: idba_1.1.3-8.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: idba
Binary: idba, idba-extra
Architecture: any
Version: 1.1.3-8
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/loneknightpy/idba
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/idba
Vcs-Git: https://salsa.debian.org/med-team/idba.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libgtest-dev <!nocheck>, python3 <!nocheck>
Package-List:
idba deb science optional arch=any
idba-extra deb science optional arch=any
Checksums-Sha1:
cf673154a9696215648177f0bc43b9cc25feaf26 446227 idba_1.1.3.orig.tar.gz
895352f0b6cbf98d8f9fa02df13f9c80807f2fbe 263136 idba_1.1.3-8.debian.tar.xz
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89c37bdd6d8b98b75c81ff5347bf12b53fdc31b97cbb06021aa742636873daef 263136 idba_1.1.3-8.debian.tar.xz
Files:
41fe7eabdcfaea677558f3e4baeb2ea8 446227 idba_1.1.3.orig.tar.gz
69a68d8d6501e6ff89cfafeab18e7273 263136 idba_1.1.3-8.debian.tar.xz
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Sun Jun 11 01:04:45 UTC 2023 I: Checking whether the package is not for us
Sun Jun 11 01:04:45 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net.
Sun Jun 11 01:04:45 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net.
Sun Jun 11 01:17:47 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Aug 15 01:50:49 -12 2025
I: pbuilder-time-stamp: 1755265849
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 Sat Nov 5 08:30:52 2022 -12
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/3715227/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='583692f5ecd5468abc1b9bcc5f007b1b'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3715227'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/pbuilderrc_Mbj2 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/b1 --logfile b1/build.log idba_1.1.3-8.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos5-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/3715227/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 (27.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
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(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.
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I: Building the package
I: Running cd /build/idba-1.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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
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dh binary
dh_update_autotools_config
dh_autoreconf
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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')
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automake: You are advised to start using 'subdir-objects' option throughout your
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bin/Makefile.am:20: warning: source file '$(top_srcdir)/src/tools/split_fa.cpp' is in a subdirectory,
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bin/Makefile.am:26: warning: source file '$(top_srcdir)/src/release/validate_contigs_blat.cpp' is in a subdirectory,
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bin/Makefile.am:22: warning: source file '$(top_srcdir)/src/tools/validate_reads_blat.cpp' is in a subdirectory,
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lib/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/basic/math.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
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lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/log.cpp' is in a subdirectory,
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lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/utils.cpp' is in a subdirectory,
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lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/short_sequence.cpp' is in a subdirectory,
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lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_writer.cpp' is in a subdirectory,
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lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_io.cpp' is in a subdirectory,
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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,
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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... /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 -j16
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
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
../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/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_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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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/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
| ^~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~
../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 ../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
| ^~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~
../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 ../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
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
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
| ^~~~~~~~~~~~~~
../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];
| ^~~~~~
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
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 filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_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 split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp
../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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../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]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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_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_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
| ^~~~~~~~~~~~~~
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/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)
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../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";
| ^
../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 validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_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 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
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
../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]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../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++ -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
../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());
| ~~~~~~^~~~~~~~~~~~~
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
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 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 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 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 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 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 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 idba_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 idba_tran_test idba_tran_test.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 && 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 -j16 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'
/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'
/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-dbgsym' in '../idba-dbgsym_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-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: 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/3715227 and its subdirectories
I: Current time: Fri Aug 15 02:03:47 -12 2025
I: pbuilder-time-stamp: 1755266627
Sun Jun 11 01:17:47 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Sun Jun 11 01:17:47 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Sun Jun 11 01:21:48 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Sun Jun 11 01:21:49 UTC 2023 I: idba_1.1.3-8_amd64.changes:
Format: 1.8
Date: Sat, 05 Nov 2022 21:27:52 +0100
Source: idba
Binary: idba idba-dbgsym idba-extra idba-extra-dbgsym
Architecture: amd64
Version: 1.1.3-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
idba - iterative De Bruijn Graph short read assemblers
idba-extra - iterative De Bruijn Graph short read assemblers (extra tools)
Changes:
idba (1.1.3-8) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Fix dh_missingwq
Checksums-Sha1:
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33063ba9243980db71be63d5fc0fd9166e0d4558 9681836 idba-extra-dbgsym_1.1.3-8_amd64.deb
94fc7bbffb411d8edde1ddad3398efa6dbafaa8e 397616 idba-extra_1.1.3-8_amd64.deb
0f2ba222221f5c5aae30dffd618970d416668fed 6100 idba_1.1.3-8_amd64.buildinfo
9f95de0c8852685ced81c96ba126c596dc8ddc39 642368 idba_1.1.3-8_amd64.deb
Checksums-Sha256:
4376a58a0e991f79ce6997491c46cd7499dd16f4edf851fa6c9c6cc044d94b38 13414828 idba-dbgsym_1.1.3-8_amd64.deb
d74935f15871c2722a5f0392b157b53f5bddc46b64e3245da95a8c04d77b30e1 9681836 idba-extra-dbgsym_1.1.3-8_amd64.deb
6db087f62ef484409ea4811a27cc7af6eabcbae751ae0dd0750f535a86cc6fb0 397616 idba-extra_1.1.3-8_amd64.deb
50efb01f915eea7c34a7bef2e9bec107088e87ffd8ad5ded1b5e1b4c15367122 6100 idba_1.1.3-8_amd64.buildinfo
88388239210ca7043c4afa092980af3995aac4dbf0abda9abb2fd693fb2d513e 642368 idba_1.1.3-8_amd64.deb
Files:
5aa1c2ac92e6e89c03eba86d04ae4426 13414828 debug optional idba-dbgsym_1.1.3-8_amd64.deb
dfe05357777cde0b0ab44e726d6de3b6 9681836 debug optional idba-extra-dbgsym_1.1.3-8_amd64.deb
d919db5b2fd6609d1845468d41402687 397616 science optional idba-extra_1.1.3-8_amd64.deb
431a38bb61e8508f14f1273850bccad2 6100 science optional idba_1.1.3-8_amd64.buildinfo
8079916ea8382656551f52bc39ce9b21 642368 science optional idba_1.1.3-8_amd64.deb
Sun Jun 11 01:21:53 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/idba_1.1.3-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/idba_1.1.3-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/idba_1.1.3-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/b1/idba_1.1.3-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8KOaPtZ9/b2/idba_1.1.3-8_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 2.063s)
2.063s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.266s)
0.266s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Sun Jun 11 01:21:56 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jun 11 01:21:56 UTC 2023 I: idba from bookworm built successfully and reproducibly on amd64.
Sun Jun 11 01:21:57 UTC 2023 I: Submitting .buildinfo files to external archives:
Sun Jun 11 01:21:57 UTC 2023 I: Submitting 8.0K b1/idba_1.1.3-8_amd64.buildinfo.asc
Sun Jun 11 01:21:59 UTC 2023 I: Submitting 8.0K b2/idba_1.1.3-8_amd64.buildinfo.asc
Sun Jun 11 01:22:00 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jun 11 01:22:00 UTC 2023 I: Done submitting .buildinfo files.
Sun Jun 11 01:22:00 UTC 2023 I: Removing signed idba_1.1.3-8_amd64.buildinfo.asc files:
removed './b1/idba_1.1.3-8_amd64.buildinfo.asc'
removed './b2/idba_1.1.3-8_amd64.buildinfo.asc'