I: pbuilder: network access will be disabled during build
I: Current time: Tue Apr 14 08:22:34 +14 2026
I: pbuilder-time-stamp: 1776104554
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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: using eatmydata during job
I: Copying source file
I: copying [sortmerna_4.3.7-2.dsc]
I: copying [./sortmerna_4.3.7.orig.tar.gz]
I: copying [./sortmerna_4.3.7-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./sortmerna_4.3.7-2.dsc: unsupported subcommand
dpkg-source: info: extracting sortmerna in sortmerna-4.3.7
dpkg-source: info: unpacking sortmerna_4.3.7.orig.tar.gz
dpkg-source: info: unpacking sortmerna_4.3.7-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying concurrentqueue.h.patch
dpkg-source: info: applying gcc-13.patch
dpkg-source: info: applying pyhon3.12-syntax.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/D01_modify_environment starting
debug: Running on ionos16-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Apr 13 18:22 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=cbce236ecf3e456697dca36ecdda0d48
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=10443
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.clwSIEJt/pbuilderrc_OufC --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.clwSIEJt/b2 --logfile b2/build.log sortmerna_4.3.7-2.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/10443/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: i386
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), dh-sequence-python3, python3-all, cmake, librocksdb-dev (>= 6.25.3), libgflags-dev, libsnappy-dev, libzstd-dev, rapidjson-dev, libconcurrentqueue-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19769 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 dh-sequence-python3; however:
Package dh-sequence-python3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-all; however:
Package python3-all is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on librocksdb-dev (>= 6.25.3); however:
Package librocksdb-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgflags-dev; however:
Package libgflags-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsnappy-dev; however:
Package libsnappy-dev is not installed.
pbuilder-satisfydepends-dummy depends on libzstd-dev; however:
Package libzstd-dev is not installed.
pbuilder-satisfydepends-dummy depends on rapidjson-dev; however:
Package rapidjson-dev is not installed.
pbuilder-satisfydepends-dummy depends on libconcurrentqueue-dev; however:
Package libconcurrentqueue-dev 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libconcurrentqueue-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgflags-dev{a} libgflags2.2{a} libgnutls30t64{a} libgssapi-krb5-2{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblz4-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librocksdb-dev{a} librocksdb9.10{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsnappy-dev{a} libsnappy1v5{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} libxxhash-dev{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 87 newly installed, 0 to remove and 0 not upgraded.
Need to get 60.9 MB of archives. After unpacking 232 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 13.0.0 [29.3 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 python3 i386 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-7 [66.0 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-7 [876 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-7 [301 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 cmake-data all 3.31.6-1 [2268 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 41 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.8-1 [110 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-9 [20.8 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-9 [61.2 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.8.0-1 [78.7 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.12.1-3 [415 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 librhash1 i386 1.4.5-1 [144 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 libuv1t64 i386 1.50.0-2 [163 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 cmake i386 3.31.6-1 [13.1 MB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-4 [539 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 64 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 67 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 69 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20250308 [115 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 libconcurrentqueue-dev i386 1.0.4+ds-2 [60.1 kB]
Get: 76 http://deb.debian.org/debian unstable/main i386 libgflags2.2 i386 2.2.2-2 [84.1 kB]
Get: 77 http://deb.debian.org/debian unstable/main i386 libgflags-dev i386 2.2.2-2 [102 kB]
Get: 78 http://deb.debian.org/debian unstable/main i386 libxxhash-dev i386 0.8.3-2 [88.0 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 liblz4-dev i386 1.10.0-4 [89.3 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 libsnappy1v5 i386 1.2.1-1+b1 [31.3 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 librocksdb9.10 i386 9.10.0-1 [4193 kB]
Get: 82 http://deb.debian.org/debian unstable/main i386 libsnappy-dev i386 1.2.1-1+b1 [46.2 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 libzstd-dev i386 1.5.6+dfsg-2 [354 kB]
Get: 84 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 librocksdb-dev i386 9.10.0-1 [5869 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.13.2-2 [1044 B]
Get: 87 http://deb.debian.org/debian unstable/main i386 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB]
Fetched 60.9 MB in 1s (90.5 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:i386.
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(Reading database ... 19769 files and directories currently installed.)
Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ...
Unpacking libpython3.13-minimal:i386 (3.13.2-1) ...
Selecting previously unselected package libexpat1:i386.
Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ...
Unpacking libexpat1:i386 (2.6.4-1) ...
Selecting previously unselected package python3.13-minimal.
Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ...
Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
Setting up libexpat1:i386 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.2-1) ...
Selecting previously unselected package python3-minimal.
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(Reading database ... 20103 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.13.2-2_i386.deb ...
Unpacking python3-minimal (3.13.2-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_13.0.0_all.deb ...
Unpacking media-types (13.0.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../2-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../3-tzdata_2025a-2_all.deb ...
Unpacking tzdata (2025a-2) ...
Selecting previously unselected package libffi8:i386.
Preparing to unpack .../4-libffi8_3.4.7-1_i386.deb ...
Unpacking libffi8:i386 (3.4.7-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../5-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:i386.
Preparing to unpack .../6-libreadline8t64_8.2-6_i386.deb ...
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
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Current default time zone: 'Etc/UTC'
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/sortmerna-4.3.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sortmerna_4.3.7-2_source.changes
dpkg-buildpackage: info: source package sortmerna
dpkg-buildpackage: info: source version 4.3.7-2
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 i386
debian/rules clean
dh clean --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: dh_auto_clean --buildsystem=cmake
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: dh_auto_configure --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build -- -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.13 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.13/config-3.13-i386-linux-gnu/libpython3.13.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.13 -DPython_EXECUTABLE=/usr/bin/python3.13 -DPython_LIBRARY=/usr/lib/python3.13/config-3.13-i386-linux-gnu/libpython3.13.so -DPython_INCLUDE_DIR=/usr/include/python3.13 -DPython3_EXECUTABLE=/usr/bin/python3.13 -DPython3_LIBRARY=/usr/lib/python3.13/config-3.13-i386-linux-gnu/libpython3.13.so -DPython3_INCLUDE_DIR=/usr/include/python3.13
cd .pybuild/cpython3_3.13/build && PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.13 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.13/config-3.13-i386-linux-gnu/libpython3.13.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.13 -DPython_EXECUTABLE=/usr/bin/python3.13 -DPython_LIBRARY=/usr/lib/python3.13/config-3.13-i386-linux-gnu/libpython3.13.so -DPython_INCLUDE_DIR=/usr/include/python3.13 -DPython3_EXECUTABLE=/usr/bin/python3.13 -DPython3_LIBRARY=/usr/lib/python3.13/config-3.13-i386-linux-gnu/libpython3.13.so -DPython3_INCLUDE_DIR=/usr/include/python3.13 ../../..
-- The CXX compiler identification is GNU 14.2.0
-- The C compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find Git (missing: GIT_EXECUTABLE)
parsing version file: include/version.h
PROJECT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build
CMAKE_CXX_COMPILER_ID = GNU
CMAKE_CONFIGURATION_TYPES =
CMAKE_HOST_SYSTEM_NAME = Linux
CMAKE_HOST_SYSTEM_VERSION = 6.1.0-31-amd64
CMAKE_HOST_SYSTEM = Linux-6.1.0-31-amd64
CMAKE_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build
CMAKE_CURRENT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build
RUNTIME_OUTPUT_DIRECTORY_RELEASE =
CMAKE_CXX_FLAGS_DEBUG: -g
CMAKE_C_FLAGS_DEBUG: -g
CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG
EXTRA_CXX_FLAGS_RELEASE:
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.3.1")
searching ZLIB in default locations
ZLIB::ZLIB LOCATION: /usr/lib/i386-linux-gnu/libz.so
ZLIB::ZLIB LOCATION_DEBUG: /usr/lib/i386-linux-gnu/libz.so
searching RocksDB in default locations
CMAKE_MODULE_PATH: /build/reproducible-path/sortmerna-4.3.7/cmake/modules/
-- Found BZip2: /usr/lib/i386-linux-gnu/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found lz4: /usr/lib/i386-linux-gnu/liblz4.so
-- Found zstd: /usr/lib/i386-linux-gnu/libzstd.so
RocksDB found
Using Shared RocksDB lib
RocksDB::rocksdb-shared LOCATION: /usr/lib/i386-linux-gnu/librocksdb.so.9.10.0
RocksDB::rocksdb-shared LOCATION_DEBUG: /usr/lib/i386-linux-gnu/librocksdb.so.9.10.0
RocksDB::rocksdb-shared transitive link dependencies:
rocksdb transitive link dependencies AFTER modification: /usr/lib/i386-linux-gnu/libz.so;Threads::Threads
SMR Objects transitive link dependencies: alp;RocksDB::rocksdb-shared;ZLIB::ZLIB
SMR Objects COMPILE_OPT: COMPILE_OPT-NOTFOUND COMPILE_FLG: COMPILE_FLG-NOTFOUND
package_config_destination: /usr/cmake/sortmerna
-- Configuring done (0.8s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
PYTHON_EXECUTABLE
PYTHON_INCLUDE_DIR
PYTHON_LIBRARY
Python3_EXECUTABLE
Python3_INCLUDE_DIR
Python3_LIBRARY
Python_EXECUTABLE
Python_INCLUDE_DIR
Python_LIBRARY
-- Build files have been written to: /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: dh_auto_build --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --
cd .pybuild/cpython3_3.13/build && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
/usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.7 -B/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/CMakeFiles /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/depend
make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/depend
make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/CMakeFiles/build_version.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/build
make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/build
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
[ 1%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -MF CMakeFiles/cmph.dir/bdz_ph.c.o.d -o CMakeFiles/cmph.dir/bdz_ph.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bdz_ph.c
[ 4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o
[ 2%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_localmaxstatutil.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -MF CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bmz8.c
[ 7%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o
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/usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++17 -MD -MT CMakeFiles/build_version.dir/build_version.cpp.o -MF CMakeFiles/build_version.dir/build_version.cpp.o.d -o CMakeFiles/build_version.dir/build_version.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/build_version.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogproblim.cpp
[ 9%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprob.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogprob.cpp
[ 11%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o
[ 12%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o
[ 14%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o
[ 15%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -MF CMakeFiles/alp.dir/njn_ioutil.cpp.o.d -o CMakeFiles/alp.dir/njn_ioutil.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_ioutil.cpp
[ 16%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -MF CMakeFiles/cmph.dir/bdz.c.o.d -o CMakeFiles/cmph.dir/bdz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bdz.c
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstat.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_localmaxstat.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -MF CMakeFiles/cmph.dir/bmz.c.o.d -o CMakeFiles/cmph.dir/bmz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bmz.c
[ 18%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogprobproto.cpp
[ 19%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o
[ 21%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_localmaxstatmatrix.cpp
[ 28%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o
[ 28%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o
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cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_random.cpp
[ 28%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o
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cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -MF CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alignment_evaluer.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o -MF CMakeFiles/cmph.dir/brz.c.o.d -o CMakeFiles/cmph.dir/brz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/brz.c
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -MF CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alp_data.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alp.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o -MF CMakeFiles/cmph.dir/buffer_entry.c.o.d -o CMakeFiles/cmph.dir/buffer_entry.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/buffer_entry.c
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o -MF CMakeFiles/cmph.dir/buffer_manager.c.o.d -o CMakeFiles/cmph.dir/buffer_manager.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/buffer_manager.c
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o -MF CMakeFiles/alp.dir/sls_alp_regression.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_regression.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alp_regression.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o -MF CMakeFiles/cmph.dir/chd.c.o.d -o CMakeFiles/cmph.dir/chd.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/chd.c
/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
4 | const char* sortmerna_build_compile_date = __DATE__;
| ^~~~~~~~
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cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o -MF CMakeFiles/smr_objs.dir/alignment.cpp.o.d -o CMakeFiles/smr_objs.dir/alignment.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/alignment.cpp
[ 57%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/bitvector.cpp
[ 59%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -MF CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o.d -o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp
[ 61%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o
[ 61%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o
[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o
[ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o
[ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o -MF CMakeFiles/smr_objs.dir/izlib.cpp.o.d -o CMakeFiles/smr_objs.dir/izlib.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp
[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o -MF CMakeFiles/smr_objs.dir/index.cpp.o.d -o CMakeFiles/smr_objs.dir/index.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o -MF CMakeFiles/smr_objs.dir/indexdb.cpp.o.d -o CMakeFiles/smr_objs.dir/indexdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp
[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o
[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o
[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o -MF CMakeFiles/smr_objs.dir/summary.cpp.o.d -o CMakeFiles/smr_objs.dir/summary.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/summary.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o -MF CMakeFiles/smr_objs.dir/kseq_load.cpp.o.d -o CMakeFiles/smr_objs.dir/kseq_load.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kseq_load.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o -MF CMakeFiles/smr_objs.dir/output.cpp.o.d -o CMakeFiles/smr_objs.dir/output.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/output.cpp
[ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o
[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o CMakeFiles/smr_objs.dir/readfeed.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp
[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o
[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o -MF CMakeFiles/smr_objs.dir/processor.cpp.o.d -o CMakeFiles/smr_objs.dir/processor.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/processor.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp
[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp
[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/references.cpp
[ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/refstats.cpp
[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o
[ 84%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -MF CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o.d -o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/traverse_bursttrie.cpp
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o -MF CMakeFiles/smr_objs.dir/util.cpp.o.d -o CMakeFiles/smr_objs.dir/util.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/util.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp:243:29: warning: this statement may fall through [-Wimplicit-fallthrough=]
243 | ret = Z_DATA_ERROR; /* and fall through */
| ^
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp:244:17: note: here
244 | case Z_DATA_ERROR:
| ^~~~
[ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o -MF CMakeFiles/smr_objs.dir/otumap.cpp.o.d -o CMakeFiles/smr_objs.dir/otumap.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/otumap.cpp
[ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o -MF CMakeFiles/smr_objs.dir/report.cpp.o.d -o CMakeFiles/smr_objs.dir/report.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function 'void Readfeed::init(std::vector<std::__cxx11::basic_string<char> >&, const int&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter 'dbg' [-Wunused-parameter]
105 | void Readfeed::init(std::vector<std::string>& readfiles, const int& dbg)
| ~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::loadReadByIdx(Read&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:187:37: warning: unused parameter 'read' [-Wunused-parameter]
187 | bool Readfeed::loadReadByIdx(Read & read)
| ~~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::loadReadById(Read&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:271:35: warning: unused parameter 'read' [-Wunused-parameter]
271 | bool Readfeed::loadReadById(Read& read)
| ~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::hasnext(std::ifstream&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:553:39: warning: unused parameter 'ifs' [-Wunused-parameter]
553 | bool Readfeed::hasnext(std::ifstream& ifs)
| ~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function 'bool Readfeed::define_format(const int&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:857:36: warning: comparison is always false due to limited range of data type [-Wtype-limits]
857 | if (str[i] > 127 || str[i] < 0) {
[ 88%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_base.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp
[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o -MF CMakeFiles/smr_objs.dir/report_fastx.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fastx.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fastx.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp:915:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function]
915 | void help()
| ^~~~
[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_other.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_other.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp: In member function 'void Index::load(uint32_t, uint32_t, std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&, Refstats&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp:211:58: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
211 | ((NodeElement *&)dst) += 4;
| ^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
257 | ((NodeElement *&)dst) += 4;
| ^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter]
58 | int KeyValueDatabase::clear(std::string dbpath)
| ~~~~~~~~~~~~^~~~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:250:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
250 | if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' [-Wunused-parameter]
317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd)
| ~~~~~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter]
317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd)
| ~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter]
540 | void Read::unmarshallJson(KeyValueDatabase & kvdb)
| ~~~~~~~~~~~~~~~~~~~^~~~
In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:47:
/build/reproducible-path/sortmerna-4.3.7/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)':
/build/reproducible-path/sortmerna-4.3.7/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter]
92 | void threadEntry(int i)
| ~~~~^
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_log(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:284:42: warning: unused parameter 'val' [-Wunused-parameter]
284 | void Runopts::opt_log(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_denovo_otu(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:290:49: warning: unused parameter 'val' [-Wunused-parameter]
290 | void Runopts::opt_denovo_otu(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_otu_map(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:295:46: warning: unused parameter 'val' [-Wunused-parameter]
295 | void Runopts::opt_otu_map(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_print_all_reads(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:300:54: warning: unused parameter 'val' [-Wunused-parameter]
300 | void Runopts::opt_print_all_reads(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_pid(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:305:42: warning: unused parameter 'val' [-Wunused-parameter]
305 | void Runopts::opt_pid(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:310:45: warning: unused parameter 'val' [-Wunused-parameter]
310 | void Runopts::opt_paired(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired_in(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:324:48: warning: unused parameter 'val' [-Wunused-parameter]
324 | void Runopts::opt_paired_in(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired_out(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:329:49: warning: unused parameter 'val' [-Wunused-parameter]
329 | void Runopts::opt_paired_out(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_out2(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:338:43: warning: unused parameter 'val' [-Wunused-parameter]
338 | void Runopts::opt_out2(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sout(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:343:43: warning: unused parameter 'val' [-Wunused-parameter]
343 | void Runopts::opt_sout(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_fastx(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:471:44: warning: unused parameter 'val' [-Wunused-parameter]
471 | void Runopts::opt_fastx(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sam(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:484:42: warning: unused parameter 'val' [-Wunused-parameter]
484 | void Runopts::opt_sam(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
[ 92%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o -MF CMakeFiles/smr_objs.dir/report_blast.cpp.o.d -o CMakeFiles/smr_objs.dir/report_blast.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_blast.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_no_best(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:593:46: warning: unused parameter 'val' [-Wunused-parameter]
593 | void Runopts::opt_no_best(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:292:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
292 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_edges(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:636:15: warning: unused variable 'end' [-Wunused-variable]
636 | char *end = 0;
| ^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_full_search(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:651:50: warning: unused parameter 'val' [-Wunused-parameter]
651 | void Runopts::opt_full_search(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_SQ(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:661:41: warning: unused parameter 'val' [-Wunused-parameter]
661 | void Runopts::opt_SQ(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp:39:25: warning: unused parameter 'opts' [-Wunused-parameter]
39 | Report::Report(Runopts& opts) : pid_str(std::to_string(getpid())), is_zip(false) {}
| ~~~~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_version(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:740:46: warning: unused parameter 'val' [-Wunused-parameter]
740 | void Runopts::opt_version(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_unknown(char**, int&, char*)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:750:34: warning: unused parameter 'argv' [-Wunused-parameter]
750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt)
| ~~~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:750:45: warning: unused parameter 'narg' [-Wunused-parameter]
750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt)
| ~~~~~^~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_F(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:784:40: warning: unused parameter 'val' [-Wunused-parameter]
784 | void Runopts::opt_F(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_R(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:798:40: warning: unused parameter 'val' [-Wunused-parameter]
798 | void Runopts::opt_R(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_h(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:812:40: warning: unused parameter 'val' [-Wunused-parameter]
812 | void Runopts::opt_h(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_v(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:819:40: warning: unused parameter 'val' [-Wunused-parameter]
819 | void Runopts::opt_v(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_dbg_put_db(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:937:49: warning: unused parameter 'val' [-Wunused-parameter]
937 | void Runopts::opt_dbg_put_db(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
[ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o -MF CMakeFiles/smr_objs.dir/report_denovo.cpp.o.d -o CMakeFiles/smr_objs.dir/report_denovo.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_denovo.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_cmd(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:980:42: warning: unused parameter 'val' [-Wunused-parameter]
980 | void Runopts::opt_cmd(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_tmpdir(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1036:45: warning: unused parameter 'val' [-Wunused-parameter]
1036 | void Runopts::opt_tmpdir(const std::string &val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_align(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1193:44: warning: unused parameter 'val' [-Wunused-parameter]
1193 | void Runopts::opt_align(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_filter(const std::string&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1198:45: warning: unused parameter 'val' [-Wunused-parameter]
1198 | void Runopts::opt_filter(const std::string& val)
| ~~~~~~~~~~~~~~~~~~~^~~
In file included from /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:40,
from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp:52:
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
171 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ'
221 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT'
43 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1368:50: warning: unused parameter 'dryrun' [-Wunused-parameter]
1368 | void Runopts::process(int argc, char**argv, bool dryrun)
| ~~~~~^~~~~~
In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:41:
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp: At global scope:
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
171 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ'
221 | __KSEQ_READ
| ^~~~~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT'
43 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
[ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o -MF CMakeFiles/smr_objs.dir/report_biom.cpp.o.d -o CMakeFiles/smr_objs.dir/report_biom.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp
[ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o -MF CMakeFiles/smr_objs.dir/report_sam.cpp.o.d -o CMakeFiles/smr_objs.dir/report_sam.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_sam.cpp
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp: In member function 'void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp:201:123: warning: unused parameter 'dbg' [-Wunused-parameter]
201 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg)
| ~~~~~~~~~~~^~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)':
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter]
41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts)
| ~~~~~~~~~~^~~~~~~~
/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:52: warning: unused parameter 'opts' [-Wunused-parameter]
41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts)
| ~~~~~~~~~^~~~
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
[ 97%] Built target smr_objs
make -f src/sortmerna/CMakeFiles/sortmerna.dir/build.make src/sortmerna/CMakeFiles/sortmerna.dir/depend
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/src/sortmerna /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna/CMakeFiles/sortmerna.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make -f src/sortmerna/CMakeFiles/sortmerna.dir/build.make src/sortmerna/CMakeFiles/sortmerna.dir/build
make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
[ 98%] Building CXX object src/sortmerna/CMakeFiles/sortmerna.dir/main.cpp.o
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/sortmerna.dir/main.cpp.o -MF CMakeFiles/sortmerna.dir/main.cpp.o.d -o CMakeFiles/sortmerna.dir/main.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/main.cpp
[100%] Linking CXX executable sortmerna
cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/src/sortmerna && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortmerna.dir/link.txt --verbose=1
collect2 version 14.2.0
/usr/bin/ld -plugin /usr/libexec/gcc/i686-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/cc80gwKp.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o sortmerna /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/14 -L/usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/14/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/14/../../.. -v -z relro -z now --dependency-file=CMakeFiles/sortmerna.dir/link.d CMakeFiles/sortmerna.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o CMakeFiles/smr_objs.dir/alignment.cpp.o CMakeFiles/smr_objs.dir/bitvector.cpp.o CMakeFiles/smr_objs.dir/cmd.cpp.o CMakeFiles/smr_objs.dir/izlib.cpp.o CMakeFiles/smr_objs.dir/index.cpp.o CMakeFiles/smr_objs.dir/indexdb.cpp.o CMakeFiles/smr_objs.dir/kseq_load.cpp.o CMakeFiles/smr_objs.dir/kvdb.cpp.o CMakeFiles/smr_objs.dir/options.cpp.o CMakeFiles/smr_objs.dir/output.cpp.o CMakeFiles/smr_objs.dir/summary.cpp.o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o CMakeFiles/smr_objs.dir/processor.cpp.o CMakeFiles/smr_objs.dir/read.cpp.o CMakeFiles/smr_objs.dir/readfeed.cpp.o CMakeFiles/smr_objs.dir/readstats.cpp.o CMakeFiles/smr_objs.dir/references.cpp.o CMakeFiles/smr_objs.dir/refstats.cpp.o CMakeFiles/smr_objs.dir/ssw.c.o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o CMakeFiles/smr_objs.dir/util.cpp.o CMakeFiles/smr_objs.dir/otumap.cpp.o CMakeFiles/smr_objs.dir/report.cpp.o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o CMakeFiles/smr_objs.dir/report_fastx.cpp.o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o CMakeFiles/smr_objs.dir/report_blast.cpp.o CMakeFiles/smr_objs.dir/report_denovo.cpp.o CMakeFiles/smr_objs.dir/report_biom.cpp.o CMakeFiles/smr_objs.dir/report_sam.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /usr/lib/i386-linux-gnu/librocksdb.so.9.10.0 -ldl /usr/lib/i386-linux-gnu/libz.so -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/14/crtendS.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crtn.o
GNU ld (GNU Binutils for Debian) 2.44
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sortmerna.dir/link.d CMakeFiles/sortmerna.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o CMakeFiles/smr_objs.dir/alignment.cpp.o CMakeFiles/smr_objs.dir/bitvector.cpp.o CMakeFiles/smr_objs.dir/cmd.cpp.o CMakeFiles/smr_objs.dir/izlib.cpp.o CMakeFiles/smr_objs.dir/index.cpp.o CMakeFiles/smr_objs.dir/indexdb.cpp.o CMakeFiles/smr_objs.dir/kseq_load.cpp.o CMakeFiles/smr_objs.dir/kvdb.cpp.o CMakeFiles/smr_objs.dir/options.cpp.o CMakeFiles/smr_objs.dir/output.cpp.o CMakeFiles/smr_objs.dir/summary.cpp.o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o CMakeFiles/smr_objs.dir/processor.cpp.o CMakeFiles/smr_objs.dir/read.cpp.o CMakeFiles/smr_objs.dir/readfeed.cpp.o CMakeFiles/smr_objs.dir/readstats.cpp.o CMakeFiles/smr_objs.dir/references.cpp.o CMakeFiles/smr_objs.dir/refstats.cpp.o CMakeFiles/smr_objs.dir/ssw.c.o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o CMakeFiles/smr_objs.dir/util.cpp.o CMakeFiles/smr_objs.dir/otumap.cpp.o CMakeFiles/smr_objs.dir/report.cpp.o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o CMakeFiles/smr_objs.dir/report_fastx.cpp.o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o CMakeFiles/smr_objs.dir/report_blast.cpp.o CMakeFiles/smr_objs.dir/report_denovo.cpp.o CMakeFiles/smr_objs.dir/report_biom.cpp.o CMakeFiles/smr_objs.dir/report_sam.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o -o sortmerna ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /usr/lib/i386-linux-gnu/librocksdb.so.9.10.0 -ldl /usr/lib/i386-linux-gnu/libz.so
make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
[100%] Built target sortmerna
make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: dh_auto_test --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install --destdir=debian/sortmerna/ -O--buildsystem=pybuild
I: pybuild base:311: dh_auto_install --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --destdir=/build/reproducible-path/sortmerna-4.3.7/debian/sortmerna --
cd .pybuild/cpython3_3.13/build && make -j21 install DESTDIR=/build/reproducible-path/sortmerna-4.3.7/debian/sortmerna AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
/usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.7 -B/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/bin/sortmerna
-- Installing: /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake
-- Installing: /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake
make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.13/build'
dh_install -O--buildsystem=pybuild
debian/rules execute_after_dh_install
make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7'
find debian -name cmake -type d | xargs rm -rvf
removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake'
removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake'
removed directory 'debian/sortmerna/usr/cmake/sortmerna'
removed directory 'debian/sortmerna/usr/cmake'
make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7'
dh_installdocs -O--buildsystem=pybuild
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dh_installexamples -O--buildsystem=pybuild
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make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7'
# Convert example files to Unicode.
set -e \
; cd /build/reproducible-path/sortmerna-4.3.7/tests/sortmerna/ \
; for cxxfile in *.cpp \
; do iconv -f ISO-8859-15 -t UTF-8 \
< ${cxxfile} \
> /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/share/doc/sortmerna/examples/${cxxfile} \
; done
make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7'
dh_installman -O--buildsystem=pybuild
dh_python3 -O--buildsystem=pybuild
dh_installsystemduser -O--buildsystem=pybuild
dh_lintian -O--buildsystem=pybuild
dh_perl -O--buildsystem=pybuild
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make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7'
find debian/sortmerna -name '*.sh' -exec chmod -v +x '{}' ';'
mode of 'debian/sortmerna/usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x)
find debian/sortmerna -name '*.py' -exec chmod -v -x '{}' ';'
mode of 'debian/sortmerna/usr/share/sortmerna/scripts/run.py' retained as 0644 (rw-r--r--)
make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7'
dh_missing -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
dh_gencontrol -O--buildsystem=pybuild
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_4.3.7-2_i386.deb'.
dpkg-deb: building package 'sortmerna' in '../sortmerna_4.3.7-2_i386.deb'.
dpkg-genbuildinfo --build=binary -O../sortmerna_4.3.7-2_i386.buildinfo
dpkg-genchanges --build=binary -O../sortmerna_4.3.7-2_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/10443/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/10443 and its subdirectories
I: Current time: Tue Apr 14 08:23:48 +14 2026
I: pbuilder-time-stamp: 1776104628