Mon Apr 1 10:32:39 UTC 2024 I: starting to build uncalled/trixie/armhf on jenkins on '2024-04-01 10:32' Mon Apr 1 10:32:39 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/1263/console.log Mon Apr 1 10:32:39 UTC 2024 I: Downloading source for trixie/uncalled=2.3+ds-1 --2024-04-01 10:32:40-- http://deb.debian.org/debian/pool/main/u/uncalled/uncalled_2.3%2bds-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2145 (2.1K) [text/prs.lines.tag] Saving to: ‘uncalled_2.3+ds-1.dsc’ 0K .. 100% 236M=0s 2024-04-01 10:32:40 (236 MB/s) - ‘uncalled_2.3+ds-1.dsc’ saved [2145/2145] Mon Apr 1 10:32:40 UTC 2024 I: uncalled_2.3+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: uncalled Binary: uncalled Architecture: any Version: 2.3+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/skovaka/UNCALLED Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/uncalled Vcs-Git: https://salsa.debian.org/med-team/uncalled.git Testsuite: autopkgtest Build-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 Package-List: uncalled deb science optional arch=any Checksums-Sha1: 1f70131d17758676a4dff853f0e0e3aab41a8f33 155052 uncalled_2.3+ds.orig.tar.xz def01daf1d68602f3c732cfbb851d3a881814df1 4880 uncalled_2.3+ds-1.debian.tar.xz Checksums-Sha256: b7ccb020555b2f547faba7a2c4e925ac28f7883c5fa3752179c59c3ab7d7b450 155052 uncalled_2.3+ds.orig.tar.xz dfa3befeea6bebc20145e05f3774fee4b18c809bdec01d264e3546f48c569713 4880 uncalled_2.3+ds-1.debian.tar.xz Files: e822e23ebeadea6b48257c626285603f 155052 uncalled_2.3+ds.orig.tar.xz 30d78045a74a7a2e4f1a719c10783e21 4880 uncalled_2.3+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmSw5HkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHzZA//WNciaPRzHMNc1w/l9eEPh0UU1gIyh1+N KP/ufD1K0HLG4TsXbMcAW74mFBsYAagAYp+U+F56viHNgxOF2csZZcmAcpYs3ofh 2WS36IxcVaY+ym4CPCUDup6fNB3AXosCEqHpc290S6QIjJ+Ggl3Q16eqnfFg3qII FF9IA4Le98j7cX5oWAHGyAE6ntGS/PIEOt5u/QZ/p7govBnhuZO5lICA7xOpk+Jo oXPswULKKC0w08RFC0i9ZvhLEkiLsIwiOKt/OsTueoIDlIKKhX013tu6Zvx1cdOc J4wZKewZLPvFQ7fXDS6KQTCBQhZqsJuPJIGvGdazzNsMAVBGYb8Fti46X4iej0q0 rITBuj1qYLj6VHG3ENahf62j1WnPQfIAqKpE24Le+UIiKDMsR9nXNsqKbdNqEyDv BEa2Dmq+zeW6XcjudFKr2x+A5HMJ+J+YECajE31Edz0H7jN3O+0sKGHU31feamIg 4S1gQ4tLTtNeZbM7MVW5RVziHQKvR/lPb5gkd2patL23kjf3oIxCVjh7dZ4K2rN6 Tl3IfOzvcV3oZ6uNlG8xQr72nATdSP4o9qDdyuYRHmyM6aH5bZZa10Q/OSdYAz8e m6isZHHvGGqZW2LDTp6OljLLomF/XqLGDsD+XeJE+OOIVIICKNTOQmniWRWqW46W Dyqpf+ZqMgc= =koVk -----END PGP SIGNATURE----- Mon Apr 1 10:32:40 UTC 2024 I: Checking whether the package is not for us Mon Apr 1 10:32:40 UTC 2024 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Mon Apr 1 10:32:40 UTC 2024 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Mon Apr 1 11:21:05 UTC 2024 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 31 22:32:50 -12 2024 I: pbuilder-time-stamp: 1711967570 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/10834/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='9a991f08e3b84c5e892040ae734a818e' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='10834' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/pbuilderrc_hSKr --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/b1 --logfile b1/build.log uncalled_2.3+ds-1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux wbq0 6.1.0-18-armmp #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 27 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/10834/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: armhf 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 ... 19637 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} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfast5-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssl-dev{a} libsub-override-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 libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 107 newly installed, 0 to remove and 0 not upgraded. Need to get 58.8 MB of archives. After unpacking 221 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.5.0-2+b2 [80.2 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.2-1 [793 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.2-1 [1845 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-1+b2 [33.4 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf python3-distutils all 3.11.5-1 [131 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20240310 [106 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf hdf5-helpers armhf 1.10.10+repack-3+b1 [23.5 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libaec0 armhf 1.1.3-1 [21.5 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libsz2 armhf 1.1.3-1 [7724 B] Get: 54 http://deb.debian.org/debian trixie/main armhf libaec-dev armhf 1.1.3-1 [18.8 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libbwa-dev armhf 0.7.17-7+b3 [147 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libcurl4 armhf 8.5.0-2 [383 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libcurl4-openssl-dev armhf 8.5.0-2 [495 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libexpat1-dev armhf 2.5.0-2+b2 [134 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libhdf5-103-1 armhf 1.10.10+repack-3+b1 [1190 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14-20240201-3 [263 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libhdf5-fortran-102 armhf 1.10.10+repack-3+b1 [78.5 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-100 armhf 1.10.10+repack-3+b1 [61.1 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-fortran-100 armhf 1.10.10+repack-3+b1 [34.7 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libhdf5-cpp-103-1 armhf 1.10.10+repack-3+b1 [121 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-cpp-100 armhf 1.10.10+repack-3+b1 [20.8 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2+b2 [260 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libjpeg-dev armhf 1:2.1.5-2+b2 [72.1 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.1.5-1 [2152 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libhdf5-dev armhf 1.10.10+repack-3+b1 [2611 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libfast5-dev all 0.6.5-7 [50.2 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libpython3.11 armhf 3.11.8-1 [1710 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libpython3.11-dev armhf 3.11.8-1 [3420 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libpython3-dev armhf 3.11.6-1 [9456 B] Get: 90 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.2-1 [1800 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libpython3.12 armhf 3.12.2-1 [1850 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libpython3.12-dev armhf 3.12.2-1 [3659 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libpython3-all-dev armhf 3.11.6-1 [1072 B] Get: 94 http://deb.debian.org/debian trixie/main armhf libtoml11-dev all 3.8.1-2 [61.0 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf pdqsort-dev all 0.0.0+git20180419-2.1 [9988 B] Get: 96 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf pybind11-dev all 2.11.1-2 [191 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.2-1 [653 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf python3-all armhf 3.11.6-1 [1060 B] Get: 102 http://deb.debian.org/debian trixie/main armhf python3.11-dev armhf 3.11.8-1 [509 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf python3-dev armhf 3.11.6-1 [26.1 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf python3.12-dev armhf 3.12.2-1 [507 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf python3-all-dev armhf 3.11.6-1 [1076 B] Get: 106 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.24.2-2 [4016 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf python3-pybind11 all 2.11.1-2 [201 kB] Fetched 58.8 MB in 5s (10.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19637 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-2+b2_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libhdf5-103-1:armhf (1.10.10+repack-3+b1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../56-libgfortran5_14-20240201-3_armhf.deb ... Unpacking libgfortran5:armhf (14-20240201-3) ... Selecting previously unselected package libhdf5-fortran-102:armhf. Preparing to unpack .../57-libhdf5-fortran-102_1.10.10+repack-3+b1_armhf.deb ... Unpacking libhdf5-fortran-102:armhf (1.10.10+repack-3+b1) ... Selecting previously unselected package libhdf5-hl-100:armhf. Preparing to unpack .../58-libhdf5-hl-100_1.10.10+repack-3+b1_armhf.deb ... Unpacking libhdf5-hl-100:armhf (1.10.10+repack-3+b1) ... Selecting previously unselected package libhdf5-hl-fortran-100:armhf. Preparing to unpack .../59-libhdf5-hl-fortran-100_1.10.10+repack-3+b1_armhf.deb ... Unpacking libhdf5-hl-fortran-100:armhf (1.10.10+repack-3+b1) ... Selecting previously unselected package libhdf5-cpp-103-1:armhf. 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Preparing to unpack .../65-libjpeg-dev_1%3a2.1.5-2+b2_armhf.deb ... Unpacking libjpeg-dev:armhf (1:2.1.5-2+b2) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../66-libssl-dev_3.1.5-1_armhf.deb ... Unpacking libssl-dev:armhf (3.1.5-1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../67-libhdf5-dev_1.10.10+repack-3+b1_armhf.deb ... Unpacking libhdf5-dev (1.10.10+repack-3+b1) ... Selecting previously unselected package libfast5-dev. Preparing to unpack .../68-libfast5-dev_0.6.5-7_all.deb ... Unpacking libfast5-dev (0.6.5-7) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../69-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../70-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../71-libjs-sphinxdoc_7.2.6-6_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-6) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../72-liblapack3_3.12.0-3_armhf.deb ... Unpacking liblapack3:armhf (3.12.0-3) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../73-libpkgconf3_1.8.1-1+b2_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-1+b2) ... Selecting previously unselected package libpython3.11:armhf. Preparing to unpack .../74-libpython3.11_3.11.8-1_armhf.deb ... Unpacking libpython3.11:armhf (3.11.8-1) ... Selecting previously unselected package libpython3.11-dev:armhf. Preparing to unpack .../75-libpython3.11-dev_3.11.8-1_armhf.deb ... Unpacking libpython3.11-dev:armhf (3.11.8-1) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../76-libpython3-dev_3.11.6-1_armhf.deb ... Unpacking libpython3-dev:armhf (3.11.6-1) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../77-libpython3.12-stdlib_3.12.2-1_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.2-1) ... Selecting previously unselected package libpython3.12:armhf. Preparing to unpack .../78-libpython3.12_3.12.2-1_armhf.deb ... Unpacking libpython3.12:armhf (3.12.2-1) ... Selecting previously unselected package libpython3.12-dev:armhf. Preparing to unpack .../79-libpython3.12-dev_3.12.2-1_armhf.deb ... Unpacking libpython3.12-dev:armhf (3.12.2-1) ... Selecting previously unselected package libpython3-all-dev:armhf. Preparing to unpack .../80-libpython3-all-dev_3.11.6-1_armhf.deb ... Unpacking libpython3-all-dev:armhf (3.11.6-1) ... Selecting previously unselected package libtoml11-dev. Preparing to unpack .../81-libtoml11-dev_3.8.1-2_all.deb ... Unpacking libtoml11-dev (3.8.1-2) ... Selecting previously unselected package pdqsort-dev. Preparing to unpack .../82-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 .../83-pkgconf-bin_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../84-pkgconf_1.8.1-1+b2_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-1+b2) ... Selecting previously unselected package pkg-config:armhf. Preparing to unpack .../85-pkg-config_1.8.1-1+b2_armhf.deb ... Unpacking pkg-config:armhf (1.8.1-1+b2) ... Selecting previously unselected package pybind11-dev. Preparing to unpack .../86-pybind11-dev_2.11.1-2_all.deb ... Unpacking pybind11-dev (2.11.1-2) ... Selecting previously unselected package python3.12. Preparing to unpack .../87-python3.12_3.12.2-1_armhf.deb ... Unpacking python3.12 (3.12.2-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../88-python3-all_3.11.6-1_armhf.deb ... Unpacking python3-all (3.11.6-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../89-python3.11-dev_3.11.8-1_armhf.deb ... Unpacking python3.11-dev (3.11.8-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../90-python3-dev_3.11.6-1_armhf.deb ... Unpacking python3-dev (3.11.6-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../91-python3.12-dev_3.12.2-1_armhf.deb ... Unpacking python3.12-dev (3.12.2-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../92-python3-all-dev_3.11.6-1_armhf.deb ... Unpacking python3-all-dev (3.11.6-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../93-python3-numpy_1%3a1.24.2-2_armhf.deb ... Unpacking python3-numpy (1:1.24.2-2) ... Selecting previously unselected package python3-pybind11. Preparing to unpack .../94-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:armhf (1.5.7-1+b2) ... Setting up libpsl5:armhf (0.21.2-1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up hdf5-helpers (1.10.10+repack-3+b1) ... Setting up libtoml11-dev (3.8.1-2) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libpython3.12-minimal:armhf (3.12.2-1) ... Setting up libnghttp2-14:armhf (1.59.0-1) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libaec0:armhf (1.1.3-1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 1 10:34:56 UTC 2024. Universal Time is now: Mon Apr 1 10:34:56 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libpkgconf3:armhf (1.8.1-1+b2) ... Setting up libexpat1-dev:armhf (2.5.0-2+b2) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-2+b2) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-2+b2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up pdqsort-dev (0.0.0+git20180419-2.1) ... Setting up libssl-dev:armhf (3.1.5-1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:armhf (14-20240201-3) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7+b3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:armhf (1.11.0-4) ... Setting up netbase (6.4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up libsz2:armhf (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 libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.2-1) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:armhf (8.2-3+b1) ... Setting up libaec-dev:armhf (1.1.3-1) ... Setting up libjpeg-dev:armhf (1:2.1.5-2+b2) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1+b2) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libcurl4:armhf (8.5.0-2) ... Setting up libpython3.12-stdlib:armhf (3.12.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcurl4-openssl-dev:armhf (8.5.0-2) ... Setting up libhdf5-103-1:armhf (1.10.10+repack-3+b1) ... Setting up libhdf5-cpp-103-1:armhf (1.10.10+repack-3+b1) ... Setting up libpython3.12:armhf (3.12.2-1) ... Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up libhdf5-hl-100:armhf (1.10.10+repack-3+b1) ... Setting up python3.11 (3.11.8-1) ... Setting up libpython3.11:armhf (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up libpython3.12-dev:armhf (3.12.2-1) ... Setting up libhdf5-hl-cpp-100:armhf (1.10.10+repack-3+b1) ... Setting up libpython3.11-dev:armhf (3.11.8-1) ... Setting up libhdf5-fortran-102:armhf (1.10.10+repack-3+b1) ... Setting up python3.12-dev (3.12.2-1) ... Setting up libhdf5-hl-fortran-100:armhf (1.10.10+repack-3+b1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up libpython3-dev:armhf (3.11.6-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3.11-dev (3.11.8-1) ... Setting up python3-all (3.11.6-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up libpython3-all-dev:armhf (3.11.6-1) ... Setting up python3-dev (3.11.6-1) ... Setting up libhdf5-dev (1.10.10+repack-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20240310) ... Setting up python3-all-dev (3.11.6-1) ... Setting up libfast5-dev (0.6.5-7) ... Processing triggers for libc-bin (2.37-15) ... 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: Running cd /build/reproducible-path/uncalled-2.3+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 armhf 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:305: 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-armv7l' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:305: 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-armv7l' 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:305: 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:305: 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:305: /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/pafstats.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/sim_utils.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/index.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/args.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-armv7l-cpython-312 creating build/temp.linux-armv7l-cpython-312/src arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/chunk.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/client_sim.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../detail/common.h:314, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../attr.h:13, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/class.h:12, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13, from src/util.hpp:34, from src/client_sim.hpp:29, from src/client_sim.cpp:24: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector > ClientSim::get_read_chunks()’ at src/client_sim.cpp:266:26: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/event_detector.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/event_profiler.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/fast5_reader.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/map_pool.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from src/map_pool.hpp:28, from src/map_pool.cpp:26: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Paf&}; _Tp = Paf; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Paf; _Alloc = std::allocator]’, inlined from ‘std::vector MapPool::update()’ at src/map_pool.cpp:52:26: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/mapper.o -std=c++11 -O3 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 { | ^~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /usr/include/pdqsort.h:26, from src/mapper.cpp:24: /usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Mapper::PathBuffer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/pdqsort.h: In function ‘void pdqsort_detail::pdqsort_loop(Iter, Iter, Compare, int, bool) [with Iter = __gnu_cxx::__normal_iterator >; Compare = std::less; bool Branchless = false]’: /usr/include/pdqsort.h:412:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 412 | inline void pdqsort_loop(Iter begin, Iter end, Compare comp, int bad_allowed, bool leftmost = true) { | ^~~~~~~~~~~~ /usr/include/pdqsort.h:412:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/pdqsort.h:499:52: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 499 | pdqsort_loop(begin, pivot_pos, comp, bad_allowed, leftmost); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void pdqsort(Iter, Iter, Compare) [with Iter = __gnu_cxx::__normal_iterator >; Compare = std::less]’, inlined from ‘void pdqsort(Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >]’ at /usr/include/pdqsort.h:525:12, inlined from ‘bool Mapper::map_next()’ at src/mapper.cpp:531:16: /usr/include/pdqsort.h:514:84: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 512 | pdqsort_detail::pdqsort_loop::type>::value && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::is_arithmetic::value_type>::value>( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 515 | begin, end, comp, pdqsort_detail::log2(end - begin)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/pdqsort.h:514:84: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/normalizer.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/pybinder.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../detail/common.h:314, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../attr.h:13, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/class.h:12, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13, from src/pybinder.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:297:26: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:300:30: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:323:26: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:326:30: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const toml::basic_value&}; _Tp = toml::basic_value; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {toml::basic_value}; _Tp = toml::basic_value; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, long long unsigned int>}; _Tp = std::pair, long long unsigned int>; _Alloc = std::allocator, long long unsigned int> >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector, long long unsigned int> >::iterator’ changed in GCC 7.1 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::allocator >, long long unsigned int>}; _Tp = std::pair, long long unsigned int>; _Alloc = std::allocator, long long unsigned int> >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair, long long unsigned int>; _Alloc = std::allocator, long long unsigned int> >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector, long long unsigned int> > BwaIndex::get_seqs() const [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:228:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, long long unsigned int>*, std::vector, long long unsigned int> > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = toml::basic_value; _Alloc = std::allocator >]’, inlined from ‘toml::result > toml::detail::insert_nested_key(typename Value::table_type&, const Value&, InputIterator, InputIterator, region, bool) [with Value = toml::basic_value; InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >]’ at /usr/include/toml/parser.hpp:1625:32: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {toml::basic_value}; _Tp = toml::basic_value; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = toml::basic_value; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘toml::result, std::__cxx11::basic_string > toml::detail::parse_array(location&, std::size_t) [with Value = toml::basic_value]’ at /usr/include/toml/parser.hpp:1217:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/range.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/read_buffer.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from src/read_buffer.hpp:28, from src/read_buffer.cpp:24: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, short unsigned int, const unsigned int&, float, const std::vector >&, unsigned int&, short unsigned int&}; _Tp = Chunk; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, short unsigned int, const unsigned int&, float, const std::vector >&, unsigned int&, short unsigned int&}; _Tp = Chunk; _Alloc = std::allocator]’, inlined from ‘u32 ReadBuffer::get_chunks(std::vector&, bool, u32) const’ at src/read_buffer.cpp:326:33: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/realtime_pool.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from src/realtime_pool.hpp:28, from src/realtime_pool.cpp:28: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {short unsigned int, unsigned int&, Paf&}; _Tp = std::tuple; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {short unsigned int, unsigned int&, Paf&}; _Tp = std::tuple; _Alloc = std::allocator >]’, inlined from ‘std::vector > RealtimePool::update()’ at src/realtime_pool.cpp:163:33: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/seed_tracker.o -std=c++11 -O3 In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from src/seed_tracker.hpp:30, from src/seed_tracker.cpp:26: /usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SeedCluster; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]’: /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = SeedTracker::print(std::ostream&, u16)::]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from ‘void SeedTracker::print(std::ostream&, u16)’ at src/seed_tracker.cpp:242:14: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = SeedTracker::print(std::ostream&, u16)::]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from ‘void SeedTracker::print(std::ostream&, u16)’ at src/seed_tracker.cpp:242:14: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-312/src/self_align_ref.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../detail/common.h:314, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../attr.h:13, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/class.h:12, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13, from src/util.hpp:34, from src/range.hpp:28, from src/self_align_ref.cpp:28: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector > self_align(const std::string&, u32)’ at src/self_align_ref.cpp:78:37: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector > self_align(const std::string&, u32)’ at src/self_align_ref.cpp:83:37: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/src/chunk.o build/temp.linux-armv7l-cpython-312/src/client_sim.o build/temp.linux-armv7l-cpython-312/src/event_detector.o build/temp.linux-armv7l-cpython-312/src/event_profiler.o build/temp.linux-armv7l-cpython-312/src/fast5_reader.o build/temp.linux-armv7l-cpython-312/src/map_pool.o build/temp.linux-armv7l-cpython-312/src/mapper.o build/temp.linux-armv7l-cpython-312/src/normalizer.o build/temp.linux-armv7l-cpython-312/src/pybinder.o build/temp.linux-armv7l-cpython-312/src/range.o build/temp.linux-armv7l-cpython-312/src/read_buffer.o build/temp.linux-armv7l-cpython-312/src/realtime_pool.o build/temp.linux-armv7l-cpython-312/src/seed_tracker.o build/temp.linux-armv7l-cpython-312/src/self_align_ref.o -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lbwa -lhdf5 -lz -ldl -lm -o /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/_uncalled.cpython-312-arm-linux-gnueabihf.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:305: /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/pafstats.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/sim_utils.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/index.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/args.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-armv7l-cpython-311 creating build/temp.linux-armv7l-cpython-311/src arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/chunk.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/client_sim.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../detail/common.h:314, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../attr.h:13, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/class.h:12, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13, from src/util.hpp:34, from src/client_sim.hpp:29, from src/client_sim.cpp:24: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector > ClientSim::get_read_chunks()’ at src/client_sim.cpp:266:26: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/event_detector.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/event_profiler.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/fast5_reader.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/map_pool.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from src/map_pool.hpp:28, from src/map_pool.cpp:26: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Paf&}; _Tp = Paf; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Paf; _Alloc = std::allocator]’, inlined from ‘std::vector MapPool::update()’ at src/map_pool.cpp:52:26: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/mapper.o -std=c++11 -O3 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 { | ^~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /usr/include/pdqsort.h:26, from src/mapper.cpp:24: /usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Mapper::PathBuffer; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/pdqsort.h: In function ‘void pdqsort_detail::pdqsort_loop(Iter, Iter, Compare, int, bool) [with Iter = __gnu_cxx::__normal_iterator >; Compare = std::less; bool Branchless = false]’: /usr/include/pdqsort.h:412:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 412 | inline void pdqsort_loop(Iter begin, Iter end, Compare comp, int bad_allowed, bool leftmost = true) { | ^~~~~~~~~~~~ /usr/include/pdqsort.h:412:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/pdqsort.h:499:52: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 499 | pdqsort_loop(begin, pivot_pos, comp, bad_allowed, leftmost); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void pdqsort(Iter, Iter, Compare) [with Iter = __gnu_cxx::__normal_iterator >; Compare = std::less]’, inlined from ‘void pdqsort(Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >]’ at /usr/include/pdqsort.h:525:12, inlined from ‘bool Mapper::map_next()’ at src/mapper.cpp:531:16: /usr/include/pdqsort.h:514:84: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 512 | pdqsort_detail::pdqsort_loop::type>::value && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::is_arithmetic::value_type>::value>( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 515 | begin, end, comp, pdqsort_detail::log2(end - begin)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/pdqsort.h:514:84: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/normalizer.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/pybinder.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../detail/common.h:314, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../attr.h:13, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/class.h:12, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13, from src/pybinder.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:297:26: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:300:30: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:323:26: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘BwaIndex::FwdRevCoords BwaIndex::range_to_fms(std::string, u64, u64) [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:326:30: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const toml::basic_value&}; _Tp = toml::basic_value; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {toml::basic_value}; _Tp = toml::basic_value; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, long long unsigned int>}; _Tp = std::pair, long long unsigned int>; _Alloc = std::allocator, long long unsigned int> >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector, long long unsigned int> >::iterator’ changed in GCC 7.1 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::allocator >, long long unsigned int>}; _Tp = std::pair, long long unsigned int>; _Alloc = std::allocator, long long unsigned int> >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair, long long unsigned int>; _Alloc = std::allocator, long long unsigned int> >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector, long long unsigned int> > BwaIndex::get_seqs() const [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:228:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, long long unsigned int>*, std::vector, long long unsigned int> > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = toml::basic_value; _Alloc = std::allocator >]’, inlined from ‘toml::result > toml::detail::insert_nested_key(typename Value::table_type&, const Value&, InputIterator, InputIterator, region, bool) [with Value = toml::basic_value; InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >]’ at /usr/include/toml/parser.hpp:1625:32: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {toml::basic_value}; _Tp = toml::basic_value; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = toml::basic_value; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘toml::result, std::__cxx11::basic_string > toml::detail::parse_array(location&, std::size_t) [with Value = toml::basic_value]’ at /usr/include/toml/parser.hpp:1217:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/range.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/read_buffer.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from src/read_buffer.hpp:28, from src/read_buffer.cpp:24: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, short unsigned int, const unsigned int&, float, const std::vector >&, unsigned int&, short unsigned int&}; _Tp = Chunk; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, short unsigned int, const unsigned int&, float, const std::vector >&, unsigned int&, short unsigned int&}; _Tp = Chunk; _Alloc = std::allocator]’, inlined from ‘u32 ReadBuffer::get_chunks(std::vector&, bool, u32) const’ at src/read_buffer.cpp:326:33: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/realtime_pool.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from src/realtime_pool.hpp:28, from src/realtime_pool.cpp:28: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {short unsigned int, unsigned int&, Paf&}; _Tp = std::tuple; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {short unsigned int, unsigned int&, Paf&}; _Tp = std::tuple; _Alloc = std::allocator >]’, inlined from ‘std::vector > RealtimePool::update()’ at src/realtime_pool.cpp:163:33: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/seed_tracker.o -std=c++11 -O3 In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from src/seed_tracker.hpp:30, from src/seed_tracker.cpp:26: /usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SeedCluster; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]’: /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = SeedTracker::print(std::ostream&, u16)::]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from ‘void SeedTracker::print(std::ostream&, u16)’ at src/seed_tracker.cpp:242:14: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = SeedTracker::print(std::ostream&, u16)::]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from ‘void SeedTracker::print(std::ostream&, u16)’ at src/seed_tracker.cpp:242:14: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-armv7l-cpython-311/src/self_align_ref.o -std=c++11 -O3 In file included from /usr/include/c++/13/vector:72, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../detail/common.h:314, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/../attr.h:13, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/detail/class.h:12, from /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:13, from src/util.hpp:34, from src/range.hpp:28, from src/self_align_ref.cpp:28: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector > self_align(const std::string&, u32)’ at src/self_align_ref.cpp:78:37: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector > self_align(const std::string&, u32)’ at src/self_align_ref.cpp:83:37: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/src/chunk.o build/temp.linux-armv7l-cpython-311/src/client_sim.o build/temp.linux-armv7l-cpython-311/src/event_detector.o build/temp.linux-armv7l-cpython-311/src/event_profiler.o build/temp.linux-armv7l-cpython-311/src/fast5_reader.o build/temp.linux-armv7l-cpython-311/src/map_pool.o build/temp.linux-armv7l-cpython-311/src/mapper.o build/temp.linux-armv7l-cpython-311/src/normalizer.o build/temp.linux-armv7l-cpython-311/src/pybinder.o build/temp.linux-armv7l-cpython-311/src/range.o build/temp.linux-armv7l-cpython-311/src/read_buffer.o build/temp.linux-armv7l-cpython-311/src/realtime_pool.o build/temp.linux-armv7l-cpython-311/src/seed_tracker.o build/temp.linux-armv7l-cpython-311/src/self_align_ref.o -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lbwa -lhdf5 -lz -ldl -lm -o /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.11_uncalled/build/_uncalled.cpython-311-arm-linux-gnueabihf.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:305: 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:305: 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:305: /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-arm-linux-gnueabihf.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/pafstats.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/debug.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/__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/index.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 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__/minknow_client.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__/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__/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__/__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__/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__/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/args.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled 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/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/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/__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/index.py to index.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/args.py to args.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:305: /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/pafstats.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/debug.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/__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/index.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 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__/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/__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__/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__/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__/__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__/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/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.cpython-311-arm-linux-gnueabihf.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/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/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/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/__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/index.py to index.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/args.py to args.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_armhf.deb'. dpkg-deb: building package 'uncalled' in '../uncalled_2.3+ds-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../uncalled_2.3+ds-1_armhf.buildinfo dpkg-genchanges --build=binary -O../uncalled_2.3+ds-1_armhf.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: 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/10834 and its subdirectories I: Current time: Sun Mar 31 23:20:41 -12 2024 I: pbuilder-time-stamp: 1711970441 Mon Apr 1 11:21:08 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Mon Apr 1 11:21:08 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Mon Apr 1 11:44:22 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Mon Apr 1 11:44:25 UTC 2024 I: uncalled_2.3+ds-1_armhf.changes: Format: 1.8 Date: Fri, 14 Jul 2023 07:55:11 +0200 Source: uncalled Binary: uncalled uncalled-dbgsym Architecture: armhf Version: 2.3+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: uncalled - Utility for Nanopore Current Alignment to Large Expanses of DNA Changes: uncalled (2.3+ds-1) unstable; urgency=medium . [ Andreas Tille ] * Team upload. * New upstream version (Refreshed patches) * Standards-Version: 4.6.2 (routine-update) * Set upstream metadata fields: Bug-Submit. . [ Nilesh Patra ] * Update patch to link to hdf5 lib on system + The upstream way to summon extra_objects for it is not relevant to us (downstream). Checksums-Sha1: 2bebf93dc48d5c1baf58640341dc402c64ab5d62 12788500 uncalled-dbgsym_2.3+ds-1_armhf.deb cf49e6e8aee5b181c52775439ef4ad3bd475de76 8001 uncalled_2.3+ds-1_armhf.buildinfo f16ce17358fe3abd7ef811bc4cba140dfbf7cb08 685768 uncalled_2.3+ds-1_armhf.deb Checksums-Sha256: 7d211860be1811c97c7d959979b925448cab2d8d4faa9ab912ab0cd573032dd0 12788500 uncalled-dbgsym_2.3+ds-1_armhf.deb 1e4bf72a1bba7b22d15e38be9bff7353080a7b3325a6cf0e03a7a217d931ce20 8001 uncalled_2.3+ds-1_armhf.buildinfo 8ed5364f5ceafd305b51c39623f53657040c02ef5921aca210896a03c66ab3d3 685768 uncalled_2.3+ds-1_armhf.deb Files: fa01fb52556faa892faa1ee6c4287950 12788500 debug optional uncalled-dbgsym_2.3+ds-1_armhf.deb 96ce8316fcd85ee81b1dfb29d0ac85f9 8001 science optional uncalled_2.3+ds-1_armhf.buildinfo e0d8702b5f1c262beb83529b3e8ac195 685768 science optional uncalled_2.3+ds-1_armhf.deb Mon Apr 1 11:44:26 UTC 2024 I: diffoscope 261 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_10-1263.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/uncalled_2.3+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/uncalled_2.3+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/uncalled_2.3+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/b1/uncalled_2.3+ds-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.2n9jeeD3/b2/uncalled_2.3+ds-1_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.465s) 0.465s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.155s) 0.155s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 770ms CPU time consumed: 768ms Mon Apr 1 11:44:27 UTC 2024 I: diffoscope 261 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 1 11:44:27 UTC 2024 I: uncalled from trixie built successfully and reproducibly on armhf. Mon Apr 1 11:44:28 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Apr 1 11:44:28 UTC 2024 I: Submitting 12K b1/uncalled_2.3+ds-1_armhf.buildinfo.asc Mon Apr 1 11:44:29 UTC 2024 I: Submitting 12K b2/uncalled_2.3+ds-1_armhf.buildinfo.asc Mon Apr 1 11:44:30 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 1 11:44:30 UTC 2024 I: Done submitting .buildinfo files. Mon Apr 1 11:44:30 UTC 2024 I: Removing signed uncalled_2.3+ds-1_armhf.buildinfo.asc files: removed './b1/uncalled_2.3+ds-1_armhf.buildinfo.asc' removed './b2/uncalled_2.3+ds-1_armhf.buildinfo.asc'