I: pbuilder: network access will be disabled during build
I: Current time: Wed Apr 8 23:59:18 -12 2026
I: pbuilder-time-stamp: 1775735958
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: Copying source file
I: copying [metabat_2.15-4.dsc]
I: copying [./metabat_2.15.orig.tar.gz]
I: copying [./metabat_2.15-4.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./metabat_2.15-4.dsc: unsupported subcommand
dpkg-source: info: extracting metabat in metabat-2.15
dpkg-source: info: unpacking metabat_2.15.orig.tar.gz
dpkg-source: info: unpacking metabat_2.15-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1481034/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='48ef1f419feb4210a3308f3e31135a98'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='1481034'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.nnGYDtBi/pbuilderrc_g5QG --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nnGYDtBi/b1 --logfile b1/build.log metabat_2.15-4.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
I: uname -a
Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) 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/1481034/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), cmake, libboost-graph-dev, libboost-system-dev, libboost-filesystem-dev, libboost-serialization-dev, libboost-program-options-dev, libboost-iostreams-dev, zlib1g-dev, libhts-dev, pkg-config, python3
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19783 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 cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however:
Package libboost-graph-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-system-dev; however:
Package libboost-system-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however:
Package libboost-filesystem-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-serialization-dev; however:
Package libboost-serialization-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on pkg-config; however:
Package pkg-config is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 142 newly installed, 0 to remove and 0 not upgraded.
Need to get 89.7 MB of archives. After unpacking 490 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.6-1 [2268 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.6-1 [12.0 MB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.1+b1 [10.6 MB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.1+b1 [234 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.1+b1 [236 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.1+b1 [282 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-4.1+b1 [231 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-4.1+b1 [232 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-4.1+b1 [298 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-4.1+b1 [359 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.1+b1 [330 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.1+b1 [347 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.1+b1 [334 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.1+b1 [373 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-4.1+b1 [471 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-4.1+b1 [541 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-4.1+b1 [383 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.1+b1 [261 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1+b1 [347 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.1+b1 [376 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB]
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Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/metabat-2.15/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../metabat_2.15-4_source.changes
dpkg-buildpackage: info: source package metabat
dpkg-buildpackage: info: source version 2.15-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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/x86_64-linux-gnu ..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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
-- 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
Installing None MetaBAT into /usr
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1")
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
-- Checking for module 'htslib'
-- Found htslib, version 1.21
CMake Warning (dev) at src/CMakeLists.txt:4 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/include (found suitable version "1.83.0", minimum required is "1.55.0") found components: program_options filesystem system graph serialization iostreams regex
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
Using OpenMP
Boost cmake dir:
Boost include: /usr/include
Boost libraries:/usr/lib/x86_64-linux-gnu/libboost_program_options.a/usr/lib/x86_64-linux-gnu/libboost_filesystem.a/usr/lib/x86_64-linux-gnu/libboost_system.a/usr/lib/x86_64-linux-gnu/libboost_graph.a/usr/lib/x86_64-linux-gnu/libboost_serialization.a/usr/lib/x86_64-linux-gnu/libboost_iostreams.a/usr/lib/x86_64-linux-gnu/libboost_regex.a
Boost lib ver:1_83
Boost lib dir:/usr/lib/x86_64-linux-gnu
-- Configuring done (2.8s)
-- 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
-- Build files have been written to: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu
dh_auto_build
cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1
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cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o -MF CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o.d -o CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o -c /build/reproducible-path/metabat-2.15/src/jgi_summarize_bam_contig_depths.cpp
[ 25%] Building CXX object src/CMakeFiles/metabat1.dir/metabat1.cpp.o
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cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/metabat1.dir/metabat1.cpp.o -MF CMakeFiles/metabat1.dir/metabat1.cpp.o.d -o CMakeFiles/metabat1.dir/metabat1.cpp.o -c /build/reproducible-path/metabat-2.15/src/metabat1.cpp
cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/metabat2.dir/metabat2.cpp.o -MF CMakeFiles/metabat2.dir/metabat2.cpp.o.d -o CMakeFiles/metabat2.dir/metabat2.cpp.o -c /build/reproducible-path/metabat-2.15/src/metabat2.cpp
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cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -MF CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o.d -o CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -c /build/reproducible-path/metabat-2.15/src/contigOverlaps.cpp
In file included from /usr/include/boost/math/policies/error_handling.hpp:11,
from /usr/include/boost/math/distributions/detail/common_error_handling.hpp:12,
from /usr/include/boost/math/distributions/arcsine.hpp:35,
from /usr/include/boost/math/distributions.hpp:15,
from /build/reproducible-path/metabat-2.15/src/metabat1.h:40,
from /build/reproducible-path/metabat-2.15/src/metabat1.cpp:1:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
In file included from /usr/include/boost/math/policies/error_handling.hpp:11,
from /usr/include/boost/math/distributions/detail/common_error_handling.hpp:12,
from /usr/include/boost/math/distributions/arcsine.hpp:35,
from /usr/include/boost/math/distributions.hpp:15,
from /build/reproducible-path/metabat-2.15/src/metabat2.h:45,
from /build/reproducible-path/metabat-2.15/src/metabat2.cpp:1:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
In file included from /build/reproducible-path/metabat-2.15/src/jgi_summarize_bam_contig_depths.h:35,
from /build/reproducible-path/metabat-2.15/src/jgi_summarize_bam_contig_depths.cpp:5:
/build/reproducible-path/metabat-2.15/src/BamUtils.h: In member function ‘bam1_t* BamCache::getBam(const bam1_t*)’:
/build/reproducible-path/metabat-2.15/src/BamUtils.h:98:34: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
98 | bam_copy1(bam, copy);
| ~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/metabat-2.15/src/BamUtils.h: In member function ‘NameBamMap::iterator NameBamMap::insert(std::string, const bam1_t*, bool)’:
/build/reproducible-path/metabat-2.15/src/BamUtils.h:271:42: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
271 | bam_copy1(existing->second, bam);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/metabat-2.15/src/BamUtils.h: In static member function ‘static int BamUtils::_findPairInFile(const bam1_t*, void*)’:
/build/reproducible-path/metabat-2.15/src/BamUtils.h:582:34: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
582 | bam_copy1(data->mate, orphan);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/metabat-2.15/src/metabat1.h:207:55: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
207 | template<class T, class S> struct pair_equal_to: std::binary_function<T, std::pair<T, S>, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/metabat-2.15/src/metabat1.h:4:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/metabat-2.15/src/metabat1.cpp: In function ‘void pam_loop(int, ContigVector&, std::vector<double>&, ContigSet&, ClassMap&)’:
/build/reproducible-path/metabat-2.15/src/metabat1.cpp:1463:85: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = pair_equal_to<int, double>; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
1463 | medoid_vals[i] = std::find_if(rABD.begin(), rABD.end(), std::bind1st(pair_equal_to<int,double>(),medoid_ids[i]))->second;
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_function.h:1435:
/usr/include/c++/14/backward/binders.h:136:5: note: declared here
136 | bind1st(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
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[100%] Built target metabat1
make[2]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/metabat-2.15'
cp -a test/contigs_depth.txt obj-x86_64-linux-gnu
dh_auto_test
cd obj-x86_64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12
make[2]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j12
UpdateCTestConfiguration from :/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/DartConfiguration.tcl
UpdateCTestConfiguration from :/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/DartConfiguration.tcl
Test project /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
Connected to MAKE jobserver
test 1
Start 1: test_depths
1: Test command: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src/jgi_summarize_bam_contig_depths "--referenceFasta" "/build/reproducible-path/metabat-2.15/test/contigs.fa" "--outputDepth" "/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt" "/build/reproducible-path/metabat-2.15/test/contigs-1000.fastq.bam"
1: Working Directory: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/test
1: Test timeout computed to be: 10000000
test 2
Start 2: test_metabat1
2: Test command: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src/metabat1 "--inFile" "/build/reproducible-path/metabat-2.15/test/contigs.fa" "--abdFile" "/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt" "--outFile" "/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_bins" "-v"
2: Working Directory: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/test
2: Test timeout computed to be: 10000000
test 3
Start 3: test_metabat2
3: Test command: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src/metabat2 "--inFile" "/build/reproducible-path/metabat-2.15/test/contigs.fa" "--abdFile" "/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt" "--outFile" "/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_bins" "-v"
3: Working Directory: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/test
3: Test timeout computed to be: 10000000
1: Reference fasta file /build/reproducible-path/metabat-2.15/test/contigs.fa
1: Output depth matrix to /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt
1: jgi_summarize_bam_contig_depths nosha
1: Output matrix to /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt
1: Reading reference fasta file: /build/reproducible-path/metabat-2.15/test/contigs.fa
1: ... 1 sequences
1: 0: Opening bam: /build/reproducible-path/metabat-2.15/test/contigs-1000.fastq.bam
2: MetaBAT 1 (nosha) using p1 90.0%, p2 90.0%, p3 95.0%, minProb 80.0%, minBinned 40%, minCV 1.0, minContig 2500, minContigByCorr 1000, minCorr 92%, paired 0, and 20 bootstrapping
2: [00:00:00] Finished reading 1 contigs. Number of target contigs >= 2500 are 1, and [1000 and 2500) are 0
2: [00:00:00] Finished reading 1 contigs (using 1 including 0 short contigs) and 1 coverages from /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt
2: [Info] Correlation binning won't be applied since the number of samples (1) < minSamples (10)
3: MetaBAT 2 (nosha) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1775736151
3: [00:00:00] Executing with 12 threads
3: [00:00:00] Parsing abundance file
3: [00:00:00] Parsing assembly file
3: [00:00:00] Number of large contigs >= 2500 are 1.
3: [00:00:00] Reading abundance file
3: [00:00:00] Finished reading 1 contigs and 1 coverages from /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt
3: [00:00:00] Number of target contigs: 1 of large (>= 2500) and 0 of small ones (>=1000 & <2500).
3: [00:00:00] Start TNF calculation. nobs = 1
2: [00:00:00] Finished TNF calculation.
1: Processing bam files
1: Thread 0 finished: contigs-1000.fastq.bam with 1000 reads and 1000 readsWellMapped
1: Creating depth matrix file: /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt
2: [00:00:00] Finished building a probabilistic graph. (1 vertices and 0 edges)
3: [00:00:00] Finished TNF calculation.
1: Closing most bam files
1: Closing last bam file
1: Finished
1/3 Test #1: test_depths ...................... Passed 0.29 sec
2: [00:00:00] Bootstrapping 1/20 [-16.8Gb / 23.5Gb]
[00:00:00] Bootstrapping 2/20 [-16.8Gb / 23.5Gb]
[00:00:00] Bootstrapping 3/20 [-16.8Gb / 23.5Gb]
[00:00:00] Bootstrapping 4/20 [-16.8Gb / 23.5Gb]
[00:00:00] Bootstrapping 5/20 [-17.1Gb / 23.5Gb]
[00:00:00] Bootstrapping 6/20 [-17.4Gb / 23.5Gb]
[00:00:00] Bootstrapping 7/20 [-17.6Gb / 23.5Gb]
[00:00:00] Bootstrapping 8/20 [-17.6Gb / 23.5Gb]
[00:00:00] Bootstrapping 9/20 [-17.6Gb / 23.5Gb]
[00:00:00] Bootstrapping 10/20 [-17.6Gb / 23.5Gb]
[00:00:00] Bootstrapping 11/20 [-17.5Gb / 23.5Gb]
[00:00:00] Bootstrapping 12/20 [-17.5Gb / 23.5Gb]
[00:00:00] Bootstrapping 13/20 [-17.5Gb / 23.5Gb]
[00:00:00] Bootstrapping 14/20 [-17.4Gb / 23.5Gb]
[00:00:01] Bootstrapping 15/20 [-17.4Gb / 23.5Gb]
[00:00:01] Bootstrapping 16/20 [-17.4Gb / 23.5Gb]
[00:00:01] Bootstrapping 17/20 [-17.4Gb / 23.5Gb]
[00:00:01] Bootstrapping 18/20 [-17.3Gb / 23.5Gb]
[00:00:01] Bootstrapping 19/20 [-17.3Gb / 23.5Gb]
[00:00:01] Bootstrapping 20/20 [-17.3Gb / 23.5Gb]
[00:00:01] Bootstrapping 20/20 [-17.3Gb / 23.5Gb]
2: [00:00:01] Saved bootstrap intermediate file (boot.6018994539096241237) for reuse in case of failure
2: [00:00:01] Building Ensemble Graph 0.0% (0 of 1), ETA -2562047788015215:-30:-8 [-17.3Gb / 23.5Gb]
[00:00:01] Finished Ensemble Graph (1 vertices and 0 edges) [-17.3Gb / 23.5Gb]
2: [00:00:01] Starting Ensemble Binning [-17.3Gb / 23.5Gb]
2: [00:00:01] Running Ensemble Binning [-17.3Gb / 23.5Gb]
[00:00:01] Running Ensemble Binning 1 [-17.3Gb / 23.5Gb]
[00:00:01] Running Ensemble Binning 1 [-17.3Gb / 23.5Gb]
2: [00:00:01] Finished Ensemble Binning [-17.3Gb / 23.5Gb]
2: [00:00:01] Cleaned up intermediate files
2: [00:00:01] 0.00% (0 out of 5404 bases) was binned.
2: Number of clusters formed: 0
2/3 Test #2: test_metabat1 .................... Passed 1.43 sec
3: [00:00:00] Preparing TNF Graph Building [pTNF = 99.9; 0 / 1 (P = 0.00%) round 1]
[00:00:00] Preparing TNF Graph Building [pTNF = 99.8; 0 / 1 (P = 0.00%) round 2]
[00:00:00] Preparing TNF Graph Building [pTNF = 99.7; 0 / 1 (P = 0.00%) round 3]
[00:00:00] Preparing TNF Graph Building [pTNF = 99.4; 0 / 1 (P = 0.00%) round 4]
[00:00:00] Preparing TNF Graph Building [pTNF = 99.3; 0 / 1 (P = 0.00%) round 5]
[00:00:00] Preparing TNF Graph Building [pTNF = 99.1; 0 / 1 (P = 0.00%) round 6]
[00:00:00] Preparing TNF Graph Building [pTNF = 98.8; 0 / 1 (P = 0.00%) round 7]
[00:00:00] Preparing TNF Graph Building [pTNF = 98.5; 0 / 1 (P = 0.00%) round 8]
[00:00:00] Preparing TNF Graph Building [pTNF = 98.0; 0 / 1 (P = 0.00%) round 9]
[00:00:00] Preparing TNF Graph Building [pTNF = 97.7; 0 / 1 (P = 0.00%) round 10]
[00:00:00] Preparing TNF Graph Building [pTNF = 97.4; 0 / 1 (P = 0.00%) round 11]
[00:00:00] Preparing TNF Graph Building [pTNF = 97.0; 0 / 1 (P = 0.00%) round 12]
[00:00:00] Preparing TNF Graph Building [pTNF = 96.6; 0 / 1 (P = 0.00%) round 13]
[00:00:00] Preparing TNF Graph Building [pTNF = 96.1; 0 / 1 (P = 0.00%) round 14]
[00:00:00] Preparing TNF Graph Building [pTNF = 95.7; 0 / 1 (P = 0.00%) round 15]
[00:00:00] Preparing TNF Graph Building [pTNF = 95.2; 0 / 1 (P = 0.00%) round 16]
[00:00:00] Preparing TNF Graph Building [pTNF = 94.8; 0 / 1 (P = 0.00%) round 17]
[00:00:00] Preparing TNF Graph Building [pTNF = 94.3; 0 / 1 (P = 0.00%) round 18]
[00:00:00] Preparing TNF Graph Building [pTNF = 94.0; 0 / 1 (P = 0.00%) round 19]
[00:00:00] Preparing TNF Graph Building [pTNF = 93.6; 0 / 1 (P = 0.00%) round 20]
[00:00:01] Preparing TNF Graph Building [pTNF = 93.2; 0 / 1 (P = 0.00%) round 21]
[00:00:01] Preparing TNF Graph Building [pTNF = 92.8; 0 / 1 (P = 0.00%) round 22]
[00:00:01] Preparing TNF Graph Building [pTNF = 92.5; 0 / 1 (P = 0.00%) round 23]
[00:00:01] Preparing TNF Graph Building [pTNF = 92.2; 0 / 1 (P = 0.00%) round 24]
[00:00:01] Preparing TNF Graph Building [pTNF = 91.8; 0 / 1 (P = 0.00%) round 25]
[00:00:01] Preparing TNF Graph Building [pTNF = 91.5; 0 / 1 (P = 0.00%) round 26]
[00:00:01] Preparing TNF Graph Building [pTNF = 91.1; 0 / 1 (P = 0.00%) round 27]
[00:00:01] Preparing TNF Graph Building [pTNF = 90.8; 0 / 1 (P = 0.00%) round 28]
[00:00:01] Preparing TNF Graph Building [pTNF = 90.4; 0 / 1 (P = 0.00%) round 29]
[00:00:01] Preparing TNF Graph Building [pTNF = 89.9; 0 / 1 (P = 0.00%) round 30]
[00:00:01] Preparing TNF Graph Building [pTNF = 88.9; 0 / 1 (P = 0.00%) round 31]
[00:00:01] Preparing TNF Graph Building [pTNF = 88.0; 0 / 1 (P = 0.00%) round 32]
[00:00:01] Preparing TNF Graph Building [pTNF = 86.9; 0 / 1 (P = 0.00%) round 33]
[00:00:01] Preparing TNF Graph Building [pTNF = 85.8; 0 / 1 (P = 0.00%) round 34]
[00:00:01] Preparing TNF Graph Building [pTNF = 84.9; 0 / 1 (P = 0.00%) round 35]
[00:00:01] Preparing TNF Graph Building [pTNF = 83.9; 0 / 1 (P = 0.00%) round 36]
[00:00:01] Preparing TNF Graph Building [pTNF = 82.9; 0 / 1 (P = 0.00%) round 37]
[00:00:01] Preparing TNF Graph Building [pTNF = 82.0; 0 / 1 (P = 0.00%) round 38]
[00:00:01] Preparing TNF Graph Building [pTNF = 81.0; 0 / 1 (P = 0.00%) round 39]
[00:00:01] Preparing TNF Graph Building [pTNF = 80.0; 0 / 1 (P = 0.00%) round 40]
[00:00:01] Preparing TNF Graph Building [pTNF = 78.9; 0 / 1 (P = 0.00%) round 41]
[00:00:01] Preparing TNF Graph Building [pTNF = 77.8; 0 / 1 (P = 0.00%) round 42]
[00:00:01] Preparing TNF Graph Building [pTNF = 76.7; 0 / 1 (P = 0.00%) round 43]
[00:00:01] Preparing TNF Graph Building [pTNF = 75.8; 0 / 1 (P = 0.00%) round 44]
[00:00:01] Preparing TNF Graph Building [pTNF = 74.8; 0 / 1 (P = 0.00%) round 45]
[00:00:01] Preparing TNF Graph Building [pTNF = 73.9; 0 / 1 (P = 0.00%) round 46]
[00:00:01] Preparing TNF Graph Building [pTNF = 72.8; 0 / 1 (P = 0.00%) round 47]
[00:00:01] Preparing TNF Graph Building [pTNF = 71.9; 0 / 1 (P = 0.00%) round 48]
[00:00:01] Preparing TNF Graph Building [pTNF = 71.0; 0 / 1 (P = 0.00%) round 49]
[00:00:01] Finished Preparing TNF Graph Building [pTNF = 69.90]
3: [00:00:01] Finished Building TNF Graph (0 edges) [-16.9Gb / 23.5Gb]
3: No edges were formed by TNF.
3: [00:00:01] Rescuing singleton large contigs
3: [00:00:01] There are 0 bins already
3: [00:00:01] Outputting bins
3: [00:00:02] -nan% (0 bases) of large (>=2500) and 0.00% (0 bases) of small (<2500) contigs were binned.
3: 0 bins (0 bases in total) formed.
3: [00:00:02] Finished
3/3 Test #3: test_metabat2 .................... Passed 2.03 sec
100% tests passed, 0 tests failed out of 3
Total Test time (real) = 2.05 sec
make[2]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
make[1]: Leaving directory '/build/reproducible-path/metabat-2.15'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/metabat/
cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/metabat-2.15/debian/metabat AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/metabat-2.15 -B/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/runMetaBat.sh
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/merge_depths.pl
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/aggregateBinDepths.pl
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/aggregateContigOverlapsByBin.pl
CMake Error: failed to create symbolic link '/usr/bin/metabat': Permission denied
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/metabat1
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/metabat2
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/jgi_summarize_bam_contig_depths
-- Installing: /build/reproducible-path/metabat-2.15/debian/metabat/usr/bin/contigOverlaps
make[1]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/metabat-2.15'
dh_install
for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \
sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \
done
make[1]: Leaving directory '/build/reproducible-path/metabat-2.15'
dh_installdocs
dh_installchangelogs
dh_installexamples
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/metabat-2.15'
dh_installman --language=C
make[1]: Leaving directory '/build/reproducible-path/metabat-2.15'
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package metabat: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package metabat: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'metabat' in '../metabat_2.15-4_amd64.deb'.
dpkg-deb: building package 'metabat-dbgsym' in '../metabat-dbgsym_2.15-4_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../metabat_2.15-4_amd64.buildinfo
dpkg-genchanges --build=binary -O../metabat_2.15-4_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1481034 and its subdirectories
I: Current time: Thu Apr 9 00:02:46 -12 2026
I: pbuilder-time-stamp: 1775736166