I: pbuilder: network access will be disabled during build I: Current time: Wed May 22 20:39:47 +14 2024 I: pbuilder-time-stamp: 1716359987 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 [uncalled_2.3+ds-1.dsc] I: copying [./uncalled_2.3+ds.orig.tar.xz] I: copying [./uncalled_2.3+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 14 06:00:25 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting uncalled in uncalled-2.3+ds dpkg-source: info: unpacking uncalled_2.3+ds.orig.tar.xz dpkg-source: info: unpacking uncalled_2.3+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian_hdf5 dpkg-source: info: applying debian_bwa dpkg-source: info: applying debian_fast5 dpkg-source: info: applying debian_pybind11 dpkg-source: info: applying skip_read_until dpkg-source: info: applying debian_pdqsort dpkg-source: info: applying debian_toml11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3113015/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 22 06:39 /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/3113015/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3113015/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=8a3c333ffcb54a05b4924e8db1a351d8 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3113015 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.44T7zOuG/pbuilderrc_DqfX --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.44T7zOuG/b2 --logfile b2/build.log uncalled_2.3+ds-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 20 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3113015/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 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), python3-all, python3-all-dev, python3-setuptools, python3-pybind11, python3-numpy, pdqsort-dev, dh-python, libbwa-dev, libhdf5-dev, pkg-config, libfast5-dev, libtoml11-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 ... 19718 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 python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on pdqsort-dev; however: Package pdqsort-dev is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libfast5-dev; however: Package libfast5-dev is not installed. pbuilder-satisfydepends-dummy depends on libtoml11-dev; however: Package libtoml11-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} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbwa-dev{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdata-optlist-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfast5-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libparams-util-perl{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl-dev{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libsz2{a} libtoml11-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pdqsort-dev{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} pybind11-dev{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-pybind11{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 118 newly installed, 0 to remove and 0 not upgraded. Need to get 67.6 MB of archives. After unpacking 299 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 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 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsub-prototype-perl amd64 0.03-2+b2 [9744 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.10.10+repack-3.3 [23.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 59 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libbwa-dev amd64 0.7.17-7+b3 [156 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 67 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.7.1-5 [547 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.3 [89.3 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.3 [40.4 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.3 [21.3 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libfast5-dev all 0.6.5-7 [50.2 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 101 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.3-1 [2107 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.3-1 [5069 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.11.8-1 [1072 B] Get: 105 http://deb.debian.org/debian unstable/main amd64 libtoml11-dev all 3.8.1-2 [61.0 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 pdqsort-dev all 0.0.0+git20180419-2.1 [9988 B] Get: 107 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 2.11.1-2 [191 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.3-1 [499 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.11.8-1 [1072 B] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.11.1-2 [201 kB] Fetched 67.6 MB in 1s (112 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19718 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21026 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. 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Unpacking libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.3) ... Selecting previously unselected package libhdf5-cpp-103-1t64:amd64. Preparing to unpack .../071-libhdf5-cpp-103-1t64_1.10.10+repack-3.3_amd64.deb ... Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Selecting previously unselected package libhdf5-hl-cpp-100t64:amd64. Preparing to unpack .../072-libhdf5-hl-cpp-100t64_1.10.10+repack-3.3_amd64.deb ... Unpacking libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../073-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../074-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) ... Selecting previously unselected package libjpeg62-turbo-dev:amd64. 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Unpacking libpython3.11-dev:amd64 (3.11.9-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../087-libpython3-dev_3.11.8-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.8-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../088-libpython3.12-stdlib_3.12.3-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.3-1) ... Selecting previously unselected package libpython3.12t64:amd64. Preparing to unpack .../089-libpython3.12t64_3.12.3-1_amd64.deb ... Unpacking libpython3.12t64:amd64 (3.12.3-1) ... Selecting previously unselected package libpython3.12-dev:amd64. Preparing to unpack .../090-libpython3.12-dev_3.12.3-1_amd64.deb ... Unpacking libpython3.12-dev:amd64 (3.12.3-1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../091-libpython3-all-dev_3.11.8-1_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.11.8-1) ... Selecting previously unselected package libtoml11-dev. Preparing to unpack .../092-libtoml11-dev_3.8.1-2_all.deb ... Unpacking libtoml11-dev (3.8.1-2) ... Selecting previously unselected package pdqsort-dev. Preparing to unpack .../093-pdqsort-dev_0.0.0+git20180419-2.1_all.deb ... Unpacking pdqsort-dev (0.0.0+git20180419-2.1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../094-pkgconf-bin_1.8.1-1+b2_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../095-pkgconf_1.8.1-1+b2_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1+b2) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../096-pkg-config_1.8.1-1+b2_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1+b2) ... Selecting previously unselected package pybind11-dev. Preparing to unpack .../097-pybind11-dev_2.11.1-2_all.deb ... Unpacking pybind11-dev (2.11.1-2) ... Selecting previously unselected package python3.12. Preparing to unpack .../098-python3.12_3.12.3-1_amd64.deb ... Unpacking python3.12 (3.12.3-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../099-python3-all_3.11.8-1_amd64.deb ... Unpacking python3-all (3.11.8-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../100-python3.11-dev_3.11.9-1_amd64.deb ... Unpacking python3.11-dev (3.11.9-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../101-python3-dev_3.11.8-1_amd64.deb ... Unpacking python3-dev (3.11.8-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../102-python3.12-dev_3.12.3-1_amd64.deb ... Unpacking python3.12-dev (3.12.3-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../103-python3-all-dev_3.11.8-1_amd64.deb ... Unpacking python3-all-dev (3.11.8-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../104-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-10) ... Selecting previously unselected package python3-pybind11. Preparing to unpack .../105-python3-pybind11_2.11.1-2_all.deb ... Unpacking python3-pybind11 (2.11.1-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-1) ... Setting up hdf5-helpers (1.10.10+repack-3.3) ... Setting up libtoml11-dev (3.8.1-2) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed May 22 06:40:32 UTC 2024. Universal Time is now: Wed May 22 06:40:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up pdqsort-dev (0.0.0+git20180419-2.1) ... Setting up libssl-dev:amd64 (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libparams-util-perl (1.102-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14.1.0-1) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7+b3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.12-minimal (3.12.3-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libaec-dev:amd64 (1.1.3-1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up pkgconf:amd64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up pkg-config:amd64 (1.8.1-1+b2) ... Setting up libjs-sphinxdoc (7.2.6-7) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up groff-base (1.23.0-4) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:amd64 (3.12.3-1) ... Setting up libcurl4-openssl-dev:amd64 (8.7.1-5) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up libsub-override-perl (0.11-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:amd64 (3.12.3-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up libpython3-all-dev:amd64 (3.11.8-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-all (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3-dev (3.11.8-1) ... Setting up libhdf5-dev (1.10.10+repack-3.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-numpy (1:1.26.4+ds-10) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up libfast5-dev (0.6.5-7) ... Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3113015/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3113015/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/uncalled-2.3+ds/ && 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 > ../uncalled_2.3+ds-1_source.changes dpkg-buildpackage: info: source package uncalled dpkg-buildpackage: info: source version 2.3+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/uncalled-2.3+ds' if dpkg -s python3-pybind11 >/dev/null 2>/dev/null ; then \ dh_auto_clean ; \ else \ echo "skip dh_auto_clean since python3-pybind11 is not installed on your local machine" ; \ fi I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running clean removing '/build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running clean removing '/build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it make[1]: Leaving directory '/build/reproducible-path/uncalled-2.3+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running config I: pybuild base:311: python3.11 setup.py config /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running build running build_py creating /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled running egg_info creating uncalled.egg-info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing requirements to uncalled.egg-info/requires.txt writing top-level names to uncalled.egg-info/top_level.txt writing manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENCE' writing manifest file 'uncalled.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled.conf' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'uncalled.conf' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'uncalled.conf' to be distributed and are already explicitly excluding 'uncalled.conf' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf copying uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf running build_ext All submodules present Found libbwa.a Found libhdf5.a building '_uncalled' extension creating build creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/chunk.cpp -o build/temp.linux-x86_64-cpython-312/src/chunk.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/client_sim.cpp -o build/temp.linux-x86_64-cpython-312/src/client_sim.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/event_detector.cpp -o build/temp.linux-x86_64-cpython-312/src/event_detector.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/event_profiler.cpp -o build/temp.linux-x86_64-cpython-312/src/event_profiler.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/fast5_reader.cpp -o build/temp.linux-x86_64-cpython-312/src/fast5_reader.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/map_pool.cpp -o build/temp.linux-x86_64-cpython-312/src/map_pool.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/mapper.cpp -o build/temp.linux-x86_64-cpython-312/src/mapper.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ src/mapper.cpp: In member function ‘void Mapper::update_seeds(PathBuffer&, bool)’: src/mapper.cpp:681:13: warning: unused variable ‘sa_start’ [-Wunused-variable] 681 | u64 sa_start = sa_end - ref_len + 1; | ^~~~~~~~ src/mapper.cpp:684:14: warning: variable ‘clust’ set but not used [-Wunused-but-set-variable] 684 | auto clust = seed_tracker_.add_seed( | ^~~~~ src/mapper.cpp: In copy constructor ‘Mapper::PathBuffer::PathBuffer(const Mapper::PathBuffer&)’: src/mapper.cpp:744:16: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class Mapper::PathBuffer’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 744 | std::memcpy(this, &p, sizeof(PathBuffer)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/mapper.cpp:26: src/mapper.hpp:139:11: note: ‘class Mapper::PathBuffer’ declared here 139 | class PathBuffer { | ^~~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/normalizer.cpp -o build/temp.linux-x86_64-cpython-312/src/normalizer.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/pybinder.cpp -o build/temp.linux-x86_64-cpython-312/src/pybinder.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/range.cpp -o build/temp.linux-x86_64-cpython-312/src/range.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/read_buffer.cpp -o build/temp.linux-x86_64-cpython-312/src/read_buffer.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/realtime_pool.cpp -o build/temp.linux-x86_64-cpython-312/src/realtime_pool.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/seed_tracker.cpp -o build/temp.linux-x86_64-cpython-312/src/seed_tracker.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.12 -c src/self_align_ref.cpp -o build/temp.linux-x86_64-cpython-312/src/self_align_ref.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/src/chunk.o build/temp.linux-x86_64-cpython-312/src/client_sim.o build/temp.linux-x86_64-cpython-312/src/event_detector.o build/temp.linux-x86_64-cpython-312/src/event_profiler.o build/temp.linux-x86_64-cpython-312/src/fast5_reader.o build/temp.linux-x86_64-cpython-312/src/map_pool.o build/temp.linux-x86_64-cpython-312/src/mapper.o build/temp.linux-x86_64-cpython-312/src/normalizer.o build/temp.linux-x86_64-cpython-312/src/pybinder.o build/temp.linux-x86_64-cpython-312/src/range.o build/temp.linux-x86_64-cpython-312/src/read_buffer.o build/temp.linux-x86_64-cpython-312/src/realtime_pool.o build/temp.linux-x86_64-cpython-312/src/seed_tracker.o build/temp.linux-x86_64-cpython-312/src/self_align_ref.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib/x86_64-linux-gnu -lbwa -lhdf5 -lz -ldl -lm -o /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/_uncalled.cpython-312-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.12 copying and adjusting scripts/uncalled -> build/scripts-3.12 changing mode of build/scripts-3.12/uncalled from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running build running build_py creating /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled running egg_info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing requirements to uncalled.egg-info/requires.txt writing top-level names to uncalled.egg-info/top_level.txt reading manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENCE' writing manifest file 'uncalled.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled.conf' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'uncalled.conf' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'uncalled.conf' to be distributed and are already explicitly excluding 'uncalled.conf' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf running build_ext All submodules present Found libbwa.a Found libhdf5.a building '_uncalled' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/src x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/chunk.cpp -o build/temp.linux-x86_64-cpython-311/src/chunk.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/client_sim.cpp -o build/temp.linux-x86_64-cpython-311/src/client_sim.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/event_detector.cpp -o build/temp.linux-x86_64-cpython-311/src/event_detector.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/event_profiler.cpp -o build/temp.linux-x86_64-cpython-311/src/event_profiler.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/fast5_reader.cpp -o build/temp.linux-x86_64-cpython-311/src/fast5_reader.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/map_pool.cpp -o build/temp.linux-x86_64-cpython-311/src/map_pool.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/mapper.cpp -o build/temp.linux-x86_64-cpython-311/src/mapper.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ src/mapper.cpp: In member function ‘void Mapper::update_seeds(PathBuffer&, bool)’: src/mapper.cpp:681:13: warning: unused variable ‘sa_start’ [-Wunused-variable] 681 | u64 sa_start = sa_end - ref_len + 1; | ^~~~~~~~ src/mapper.cpp:684:14: warning: variable ‘clust’ set but not used [-Wunused-but-set-variable] 684 | auto clust = seed_tracker_.add_seed( | ^~~~~ src/mapper.cpp: In copy constructor ‘Mapper::PathBuffer::PathBuffer(const Mapper::PathBuffer&)’: src/mapper.cpp:744:16: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class Mapper::PathBuffer’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 744 | std::memcpy(this, &p, sizeof(PathBuffer)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/mapper.cpp:26: src/mapper.hpp:139:11: note: ‘class Mapper::PathBuffer’ declared here 139 | class PathBuffer { | ^~~~~~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/normalizer.cpp -o build/temp.linux-x86_64-cpython-311/src/normalizer.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/pybinder.cpp -o build/temp.linux-x86_64-cpython-311/src/pybinder.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/range.cpp -o build/temp.linux-x86_64-cpython-311/src/range.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/read_buffer.cpp -o build/temp.linux-x86_64-cpython-311/src/read_buffer.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/realtime_pool.cpp -o build/temp.linux-x86_64-cpython-311/src/realtime_pool.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/seed_tracker.cpp -o build/temp.linux-x86_64-cpython-311/src/seed_tracker.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/self_align_ref.cpp -o build/temp.linux-x86_64-cpython-311/src/self_align_ref.o -std=c++11 -O3 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/src/chunk.o build/temp.linux-x86_64-cpython-311/src/client_sim.o build/temp.linux-x86_64-cpython-311/src/event_detector.o build/temp.linux-x86_64-cpython-311/src/event_profiler.o build/temp.linux-x86_64-cpython-311/src/fast5_reader.o build/temp.linux-x86_64-cpython-311/src/map_pool.o build/temp.linux-x86_64-cpython-311/src/mapper.o build/temp.linux-x86_64-cpython-311/src/normalizer.o build/temp.linux-x86_64-cpython-311/src/pybinder.o build/temp.linux-x86_64-cpython-311/src/range.o build/temp.linux-x86_64-cpython-311/src/read_buffer.o build/temp.linux-x86_64-cpython-311/src/realtime_pool.o build/temp.linux-x86_64-cpython-311/src/seed_tracker.o build/temp.linux-x86_64-cpython-311/src/self_align_ref.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib/x86_64-linux-gnu -lbwa -lhdf5 -lz -ldl -lm -o /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/_uncalled.cpython-311-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.11 copying and adjusting scripts/uncalled -> build/scripts-3.11 changing mode of build/scripts-3.11/uncalled from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build; python3.12 -m unittest discover -v /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN I: pybuild base:311: cd /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/uncalled/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/uncalled-2.3+ds/debian/uncalled /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing requirements to uncalled.egg-info/requires.txt writing top-level names to uncalled.egg-info/top_level.txt reading manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENCE' writing manifest file 'uncalled.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled.conf' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'uncalled.conf' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'uncalled.conf' to be distributed and are already explicitly excluding 'uncalled.conf' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext All submodules present Found libbwa.a Found libhdf5.a running build_scripts running install_lib creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12 creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/_uncalled.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/debug.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/args.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/index.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/sim_utils.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/pafstats.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/minknow_client.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/args.py to args.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/sim_utils.py to sim_utils.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/debug.py to debug.cpython-312.pyc /usr/lib/python3.12/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/pafstats.py to pafstats.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/minknow_client.py to minknow_client.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/index.py to index.cpython-312.pyc running install_egg_info Copying uncalled.egg-info to /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled-2.3.0.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin copying build/scripts-3.12/uncalled -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin changing mode of /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin/uncalled to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/uncalled-2.3+ds/debian/uncalled /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing requirements to uncalled.egg-info/requires.txt writing top-level names to uncalled.egg-info/top_level.txt reading manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENCE' writing manifest file 'uncalled.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled.conf' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'uncalled.conf' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'uncalled.conf' to be distributed and are already explicitly excluding 'uncalled.conf' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext All submodules present Found libbwa.a Found libhdf5.a running build_scripts running install_lib creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11 creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/pafstats.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/args.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/sim_utils.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/minknow_client.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/index.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/debug.cpython-311.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/_uncalled.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/args.py to args.cpython-311.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/sim_utils.py to sim_utils.cpython-311.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/debug.py to debug.cpython-311.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/pafstats.py to pafstats.cpython-311.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/minknow_client.py to minknow_client.cpython-311.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/index.py to index.cpython-311.pyc running install_egg_info Copying uncalled.egg-info to /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled-2.3.0.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/uncalled -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin changing mode of /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin/uncalled to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 pydist:302: Cannot find package that provides minknow_api. Please add package that provides it to Build-Depends or add "minknow_api python3-minknow-api" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild 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 'uncalled-dbgsym' in '../uncalled-dbgsym_2.3+ds-1_amd64.deb'. dpkg-deb: building package 'uncalled' in '../uncalled_2.3+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../uncalled_2.3+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../uncalled_2.3+ds-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3113015/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3113015/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/3113015 and its subdirectories I: Current time: Wed May 22 20:46:40 +14 2024 I: pbuilder-time-stamp: 1716360400