I: pbuilder: network access will be disabled during build I: Current time: Wed May 17 04:35:13 -12 2023 I: pbuilder-time-stamp: 1684341313 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [uncalled_2.2+ds1-1.dsc] I: copying [./uncalled_2.2+ds1.orig.tar.xz] I: copying [./uncalled_2.2+ds1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 16 02:54:22 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./uncalled_2.2+ds1-1.dsc: no acceptable signature found dpkg-source: info: extracting uncalled in uncalled-2.2+ds1 dpkg-source: info: unpacking uncalled_2.2+ds1.orig.tar.xz dpkg-source: info: unpacking uncalled_2.2+ds1-1.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 fix_debug dpkg-source: info: applying skip_read_until dpkg-source: info: applying debian_pdqsort dpkg-source: info: applying 32bit 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/12929/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='578315f437b043f0ae9849df1372f7fe' 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='12929' 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.pCkvsTtB/pbuilderrc_CEiD --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pCkvsTtB/b1 --logfile b1/build.log uncalled_2.2+ds1-1.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 virt64b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/12929/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 ... 19329 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} 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} 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} readline-common{a} sensible-utils{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, 98 newly installed, 0 to remove and 0 not upgraded. Need to get 47.2 MB of archives. After unpacking 175 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-3 [131 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf dh-python all 5.20230130 [104 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf hdf5-helpers armhf 1.10.8+repack1-1 [27.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libaec0 armhf 1.0.6-1+b1 [19.8 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libsz2 armhf 1.0.6-1+b1 [7864 B] Get: 48 http://deb.debian.org/debian bookworm/main armhf libaec-dev armhf 1.0.6-1+b1 [18.1 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libbwa-dev armhf 0.7.17-7+b2 [148 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libcurl4-openssl-dev armhf 7.88.1-9 [453 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libexpat1-dev armhf 2.5.0-1 [134 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libhdf5-103-1 armhf 1.10.8+repack1-1 [1183 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libhdf5-fortran-102 armhf 1.10.8+repack1-1 [82.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-100 armhf 1.10.8+repack1-1 [65.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-fortran-100 armhf 1.10.8+repack1-1 [38.8 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libhdf5-cpp-103-1 armhf 1.10.8+repack1-1 [119 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-cpp-100 armhf 1.10.8+repack1-1 [25.2 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [260 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libssl-dev armhf 3.0.8-1 [2132 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libhdf5-dev armhf 1.10.8+repack1-1 [2573 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libfast5-dev all 0.6.5-7 [50.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libpython3.11 armhf 3.11.2-6 [1710 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libpython3.11-dev armhf 3.11.2-6 [3518 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf libpython3-dev armhf 3.11.2-1+b1 [9556 B] Get: 84 http://deb.debian.org/debian bookworm/main armhf libpython3-all-dev armhf 3.11.2-1+b1 [1068 B] Get: 85 http://deb.debian.org/debian bookworm/main armhf libtoml11-dev all 3.7.1-3 [58.7 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf pdqsort-dev all 0.0.0+git20180419-2.1 [9988 B] Get: 87 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf pybind11-dev all 2.10.3-1 [186 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf python3-all armhf 3.11.2-1+b1 [1060 B] Get: 92 http://deb.debian.org/debian bookworm/main armhf python3.11-dev armhf 3.11.2-6 [615 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf python3-dev armhf 3.11.2-1+b1 [26.2 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf python3-all-dev armhf 3.11.2-1+b1 [1076 B] Get: 95 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB] Get: 96 http://deb.debian.org/debian bookworm/main armhf python3-numpy armhf 1:1.24.2-1 [4165 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf python3-pybind11 all 2.10.3-1 [199 kB] Get: 98 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB] Fetched 47.2 MB in 5s (8999 kB/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 ... 19329 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19645 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20079 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_armhf.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../45-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../46-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../47-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../48-libcurl4_7.88.1-9_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-9) ... Selecting previously unselected package libcurl4-openssl-dev:armhf. Preparing to unpack .../49-libcurl4-openssl-dev_7.88.1-9_armhf.deb ... Unpacking libcurl4-openssl-dev:armhf (7.88.1-9) ... Selecting previously unselected package libexpat1-dev:armhf. 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Selecting previously unselected package libjs-underscore. Preparing to unpack .../66-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 .../67-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../68-liblapack3_3.11.0-2_armhf.deb ... Unpacking liblapack3:armhf (3.11.0-2) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../69-libpkgconf3_1.8.1-1_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-1) ... Selecting previously unselected package libpython3.11:armhf. Preparing to unpack .../70-libpython3.11_3.11.2-6_armhf.deb ... Unpacking libpython3.11:armhf (3.11.2-6) ... Selecting previously unselected package libpython3.11-dev:armhf. Preparing to unpack .../71-libpython3.11-dev_3.11.2-6_armhf.deb ... Unpacking libpython3.11-dev:armhf (3.11.2-6) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../72-libpython3-dev_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-dev:armhf (3.11.2-1+b1) ... Selecting previously unselected package libpython3-all-dev:armhf. Preparing to unpack .../73-libpython3-all-dev_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-all-dev:armhf (3.11.2-1+b1) ... Selecting previously unselected package libtoml11-dev. Preparing to unpack .../74-libtoml11-dev_3.7.1-3_all.deb ... Unpacking libtoml11-dev (3.7.1-3) ... Selecting previously unselected package pdqsort-dev. Preparing to unpack .../75-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 .../76-pkgconf-bin_1.8.1-1_armhf.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:armhf. 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Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libtoml11-dev (3.7.1-3) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up pybind11-dev (2.10.3-1) ... Setting up libaec0:armhf (1.0.6-1+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... 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) ... Setting up libexpat1-dev:armhf (2.5.0-1) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-2) ... 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 (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7+b2) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libsz2:armhf (1.0.6-1+b1) ... 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 liblapack3:armhf (3.11.0-2) ... 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 (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:armhf (8.2-1.3) ... Setting up libaec-dev:armhf (1.0.6-1+b1) ... Setting up libjpeg-dev:armhf (1:2.1.5-2) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up pkgconf:armhf (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... 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Setting up python3-pybind11 (2.10.3-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up libpython3-dev:armhf (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-all (3.11.2-1+b1) ... Setting up libpython3-all-dev:armhf (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... 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 (1:1.24.2-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libfast5-dev (0.6.5-7) ... Processing triggers for libc-bin (2.36-9) ... 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/uncalled-2.2+ds1/ && 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_2.2+ds1-1_source.changes dpkg-buildpackage: info: source package uncalled dpkg-buildpackage: info: source version 2.2+ds1-1 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/uncalled-2.2+ds1' 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:240: python3.11 setup.py clean running clean removing '/build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it make[1]: Leaving directory '/build/uncalled-2.2+ds1' 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:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/index.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/sim_utils.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/pafstats.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/debug.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/args.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/__init__.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/minknow_client.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_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 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:202: SetuptoolsDeprecationWarning: Installing 'uncalled.conf' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'uncalled.conf' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'uncalled.conf' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) creating /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/defaults.toml -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers.txt -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers_threshs.txt -> /build/uncalled-2.2+ds1/.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 creating build/temp.linux-armhf-cpython-311 creating build/temp.linux-armhf-cpython-311/src arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/chunk.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/client_sim.o -std=c++11 -O3 In file included from /usr/include/c++/12/vector:70, 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++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 439 | 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++/12/bits/stl_vector.h:1294:21, inlined from ‘std::vector > ClientSim::get_read_chunks()’ at src/client_sim.cpp:266:26: /usr/include/c++/12/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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/map_pool.o -std=c++11 -O3 In file included from /usr/include/c++/12/vector:70, from src/map_pool.hpp:28, from src/map_pool.cpp:26: /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: 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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/mapper.o -std=c++11 -O3 src/mapper.cpp: In member function ‘void Mapper::update_seeds(PathBuffer&, bool)’: src/mapper.cpp:673:13: warning: unused variable ‘sa_start’ [-Wunused-variable] 673 | u64 sa_start = sa_end - ref_len + 1; | ^~~~~~~~ src/mapper.cpp:676:14: warning: variable ‘clust’ set but not used [-Wunused-but-set-variable] 676 | auto clust = seed_tracker_.add_seed( | ^~~~~ src/mapper.cpp: In copy constructor ‘Mapper::PathBuffer::PathBuffer(const Mapper::PathBuffer&)’: src/mapper.cpp:736:16: 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] 736 | 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++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /usr/include/pdqsort.h:26, from src/mapper.cpp:24: /usr/include/c++/12/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++/12/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:523:16: /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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/normalizer.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/pybinder.o -std=c++11 -O3 In file included from /usr/include/c++/12/vector:70, 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++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: 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:293:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _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:296:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _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:319:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _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:322:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: 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++/12/bits/stl_vector.h:1294:21, inlined from ‘std::vector, long long unsigned int> > BwaIndex::get_seqs() const [with KmerLen KLEN = k5]’ at src/bwa_index.hpp:224:27: /usr/include/c++/12/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:1514:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1287 | _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++/12/bits/stl_vector.h:1294:21, inlined from ‘toml::result, std::__cxx11::basic_string > toml::detail::parse_array(location&) [with Value = toml::basic_value]’ at /usr/include/toml/parser.hpp:1123:29: /usr/include/c++/12/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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/range.o -std=c++11 -O3 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/read_buffer.o -std=c++11 -O3 In file included from /usr/include/c++/12/vector:70, from src/read_buffer.hpp:28, from src/read_buffer.cpp:24: /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | 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++/12/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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/realtime_pool.o -std=c++11 -O3 In file included from /usr/include/c++/12/vector:70, from src/realtime_pool.hpp:28, from src/realtime_pool.cpp:28: /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 439 | 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++/12/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 -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/seed_tracker.o -std=c++11 -O3 In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from src/seed_tracker.hpp:30, from src/seed_tracker.cpp:26: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | 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++/12/bits/stl_algo.h:4853:18, inlined from ‘void SeedTracker::print(std::ostream&, u16)’ at src/seed_tracker.cpp:242:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __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++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = SeedTracker::print(std::ostream&, u16)::]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘void SeedTracker::print(std::ostream&, u16)’ at src/seed_tracker.cpp:242:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -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-armhf-cpython-311/src/self_align_ref.o -std=c++11 -O3 In file included from /usr/include/c++/12/vector:70, 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++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | 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++/12/bits/stl_vector.h:1294:21, inlined from ‘std::vector > self_align(const std::string&, u32)’ at src/self_align_ref.cpp:78:37: /usr/include/c++/12/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++/12/bits/stl_vector.h:1294:21, inlined from ‘std::vector > self_align(const std::string&, u32)’ at src/self_align_ref.cpp:83:37: /usr/include/c++/12/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/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/src/chunk.o build/temp.linux-armhf-cpython-311/src/client_sim.o build/temp.linux-armhf-cpython-311/src/event_detector.o build/temp.linux-armhf-cpython-311/src/event_profiler.o build/temp.linux-armhf-cpython-311/src/fast5_reader.o build/temp.linux-armhf-cpython-311/src/map_pool.o build/temp.linux-armhf-cpython-311/src/mapper.o build/temp.linux-armhf-cpython-311/src/normalizer.o build/temp.linux-armhf-cpython-311/src/pybinder.o build/temp.linux-armhf-cpython-311/src/range.o build/temp.linux-armhf-cpython-311/src/read_buffer.o build/temp.linux-armhf-cpython-311/src/realtime_pool.o build/temp.linux-armhf-cpython-311/src/seed_tracker.o build/temp.linux-armhf-cpython-311/src/self_align_ref.o -L./submods/bwa -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lbwa -lhdf5 -lz -ldl -lm -o /build/uncalled-2.2+ds1/.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:240: cd /build/uncalled-2.2+ds1/.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:240: /usr/bin/python3 setup.py install --root /build/uncalled-2.2+ds1/debian/uncalled running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( 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 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:202: SetuptoolsDeprecationWarning: Installing 'uncalled.conf' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'uncalled.conf' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'uncalled.conf' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext All submodules present Found libbwa.a Found libhdf5.a running build_scripts running install_lib creating /build/uncalled-2.2+ds1/debian/uncalled/usr creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11 creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/_uncalled.cpython-311-arm-linux-gnueabihf.so -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/index.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/sim_utils.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/pafstats.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/r94_5mers_threshs.txt -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/r94_5mers.txt -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/defaults.toml -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/debug.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/args.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__init__.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/minknow_client.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/sim_utils.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/pafstats.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/debug.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/args.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/__init__.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/index.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/index.py to index.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/sim_utils.py to sim_utils.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/pafstats.py to pafstats.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/debug.py to debug.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/args.py to args.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__init__.py to __init__.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/minknow_client.py to minknow_client.cpython-311.pyc running install_egg_info Copying uncalled.egg-info to /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled-2.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/uncalled-2.2+ds1/debian/uncalled/usr/bin copying build/scripts-3.11/uncalled -> /build/uncalled-2.2+ds1/debian/uncalled/usr/bin changing mode of /build/uncalled-2.2+ds1/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 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' in '../uncalled_2.2+ds1-1_armhf.deb'. dpkg-deb: building package 'uncalled-dbgsym' in '../uncalled-dbgsym_2.2+ds1-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../uncalled_2.2+ds1-1_armhf.buildinfo dpkg-genchanges --build=binary -O../uncalled_2.2+ds1-1_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/12929 and its subdirectories I: Current time: Wed May 17 04:44:50 -12 2023 I: pbuilder-time-stamp: 1684341890