Fri Mar 29 19:00:17 UTC 2024 I: starting to build minimap2/trixie/i386 on jenkins on '2024-03-29 19:00' Fri Mar 29 19:00:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/16451/console.log Fri Mar 29 19:00:17 UTC 2024 I: Downloading source for trixie/minimap2=2.27+dfsg-1 --2024-03-29 19:00:17-- http://deb.debian.org/debian/pool/main/m/minimap2/minimap2_2.27%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2315 (2.3K) [text/prs.lines.tag] Saving to: ‘minimap2_2.27+dfsg-1.dsc’ 0K .. 100% 312M=0s 2024-03-29 19:00:17 (312 MB/s) - ‘minimap2_2.27+dfsg-1.dsc’ saved [2315/2315] Fri Mar 29 19:00:17 UTC 2024 I: minimap2_2.27+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimap2 Binary: minimap2, libminimap2-dev, python3-mappy Architecture: any Version: 2.27+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/lh3/minimap2 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimap2 Vcs-Git: https://salsa.debian.org/med-team/minimap2.git Testsuite: autopkgtest Testsuite-Triggers: python3-all Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-dev Package-List: libminimap2-dev deb libdevel optional arch=any minimap2 deb science optional arch=any python3-mappy deb python optional arch=any Checksums-Sha1: 5b1fc195a089c03049c1da7e1130fbeea929c3b3 200448 minimap2_2.27+dfsg.orig.tar.xz a7aa130e9464843d8736dc295f5628441895c4e7 11544 minimap2_2.27+dfsg-1.debian.tar.xz Checksums-Sha256: 3ee11256b940a750072baa0f70e32187f61613f83d3936eb0a5eaedff1cf16df 200448 minimap2_2.27+dfsg.orig.tar.xz 45d509d32766d87c4ca3c8ed7310e2758794418e0c53918fda09f45f8cac5826 11544 minimap2_2.27+dfsg-1.debian.tar.xz Files: 2f98c85235a8086e03367622ae70aef0 200448 minimap2_2.27+dfsg.orig.tar.xz 2b0538bcbffb92d0d127c6a47728340b 11544 minimap2_2.27+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmX4beEACgkQPCZ2P2xn 5uIp7g/+L/NnH0UhRPs5Y1qnjFBKgw65y0MB8QyW2WoSqf9qETpmdf83ZiFUfvFD rksJOsodwd4eOVLTInCh50i5bVO0uumldzPSpvM0hcw1eDYv/cjwMMxlZ8NGcWp7 X0PXQ3Xh6j+iwXf6WVOthAYc4ZPVXninEMyk+Lq031bq8fQ3gc3e9UlAgxPjobXu lH4yCYFiv4DNr9+eysuumVsuNWpN5JizJB1h1oE9f5RVtefMW1npnWsIIDs8JnXi ecN57AKNinVHB0OB3ECcyPODBK6Y9nvHVua05WjaD8PMXhjVHX0frINIVU/0x6z5 1N+3oj4hMjJLF3Q8lix+cWIymFBkAUJv6Q/mpp64U2PJopE5auVnvj//URNogy4i 9mwuktMMh7/atf75McmLZzf/lNz4x3B09EeGIucA6sMDU30fdaG8RSnigqpHgYBE S5fmEN98NoTXPY1rgZ3DyKM1wJvRZkk/ql5mRKSEECN9CkChnKPmKHqAIg5VkupX fG904wehRHFfUlZmvrAyc+6xoMzPFXyZVoGd4YrJifFFLmdD+Pc6xYhNoR/EU0r5 PNfV5Q2E1tEUJgVuk/2744D/8i1aSkhI6GmsCP+ir0dtxT8cxszrB4pecw6kxCT8 7RGdqGTqs9gENRB03xH3WzFPy4y4IAqR6cu0r0u+jqESlXNpGzA= =dJxC -----END PGP SIGNATURE----- Fri Mar 29 19:00:17 UTC 2024 I: Checking whether the package is not for us Fri Mar 29 19:00:17 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Fri Mar 29 19:00:17 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Fri Mar 29 19:03:50 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 1 13:23:21 -12 2025 I: pbuilder-time-stamp: 1746149001 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: using eatmydata during job I: Copying source file I: copying [minimap2_2.27+dfsg-1.dsc] I: copying [./minimap2_2.27+dfsg.orig.tar.xz] I: copying [./minimap2_2.27+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 18 16:37:53 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./minimap2_2.27+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting minimap2 in minimap2-2.27+dfsg dpkg-source: info: unpacking minimap2_2.27+dfsg.orig.tar.xz dpkg-source: info: unpacking minimap2_2.27+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying do_not_use_natbib.bst.patch dpkg-source: info: applying ar.patch dpkg-source: info: applying link_mappy_to_libminimap.patch dpkg-source: info: applying python-sse4-arch.patch dpkg-source: info: applying simde dpkg-source: info: applying reenable-simde.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/91328/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='50a9c6af65d14016b96c2e7795c278af' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='91328' 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.keXOitia/pbuilderrc_0I4w --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.keXOitia/b1 --logfile b1/build.log minimap2_2.27+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 28 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/91328/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team 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-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-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 ... 19876 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-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-science; however: Package texlive-science is not installed. pbuilder-satisfydepends-dummy depends on texlive-font-utils; however: Package texlive-font-utils is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on gnuplot-nox | gnuplot; however: Package gnuplot-nox is not installed. Package gnuplot is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-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: aglfn{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cython3{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-gfs-baskerville{a} fonts-gfs-porson{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} ghostscript{a} gnuplot-data{a} gnuplot-nox{a} groff-base{a} intltool-debian{a} libabsl20220623{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libkpathsea6{a} liblcms2-2{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpotrace0{a} libptexenc1{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} librav1e0{a} libreadline8{a} libsharpyuv0{a} libsimde-dev{a} libsm6{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libyuv0{a} libzzip-0-13{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} poppler-data{a} preview-latex-style{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{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} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-font-utils{a} texlive-fonts-recommended{a} texlive-lang-greek{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-science{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation groff javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx ps2eps ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 185 newly installed, 0 to remove and 0 not upgraded. Need to get 276 MB of archives. After unpacking 787 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 14 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.2-1 [807 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.2-1 [2244 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 cython3 i386 3.0.8-1 [6323 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 d-shlibs all 0.106 [10.9 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.14.1 [85.6 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 debhelper all 13.14.1 [890 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.11.5-1 [131 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240310 [106 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libpng16-16 i386 1.6.43-1 [285 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b1 [449 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 66 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1 [462 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libgs-common all 10.02.1~dfsg-3 [147 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libgs10-common all 10.02.1~dfsg-3 [474 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libavahi-common-data i386 0.8-13+b1 [111 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libavahi-common3 i386 0.8-13+b1 [45.3 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libdbus-1-3 i386 1.14.10-4 [216 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libavahi-client3 i386 0.8-13+b1 [49.2 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libcups2 i386 2.4.7-1+b1 [263 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libidn12 i386 1.42-2 [81.3 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libijs-0.35 i386 0.35-15.1+b1 [15.7 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libjbig2dec0 i386 0.20-1+b1 [66.5 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b2 [197 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4 [107 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4 [314 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libgs10 i386 10.02.1~dfsg-3 [2639 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 ghostscript i386 10.02.1~dfsg-3 [49.9 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 gnuplot-data all 6.0.0+dfsg1-1 [72.1 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.0-1+b1 [587 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20230828-1 [97.5 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libaom3 i386 3.8.2-2 [1910 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libdav1d7 i386 1.4.1-1 [330 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libabsl20220623 i386 20220623.1-3 [447 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libgav1-1 i386 0.18.0-1+b1 [307 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 librav1e0 i386 0.7.1-2 [650 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libyuv0 i386 0.0~git202401110.af6ac82-1 [108 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libavif16 i386 1.0.4-1 [112 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libheif-plugin-dav1d i386 1.17.6-1 [9936 B] Get: 119 http://deb.debian.org/debian trixie/main i386 libde265-0 i386 1.0.15-1 [195 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libheif-plugin-libde265 i386 1.17.6-1 [13.4 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libheif1 i386 1.17.6-1 [299 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libxpm4 i386 1:3.5.17-1 [57.5 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libgd3 i386 2.3.3-9+b1 [129 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libglib2.0-0 i386 2.78.4-1 [1520 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 liblua5.4-0 i386 5.4.6-3 [168 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2 [2234 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.52.0+ds-1 [224 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.52.0+ds-1 [51.0 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.52.0+ds-1 [35.9 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.3.2-0.4 [121 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 gnuplot-nox i386 6.0.0+dfsg1-1 [926 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libapache-pom-java all 29-2 [5276 B] Get: 138 http://deb.debian.org/debian trixie/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.5.0-2+b2 [159 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 libkpathsea6 i386 2023.20230311.66589-9 [157 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 147 http://deb.debian.org/debian trixie/main i386 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 libpotrace0 i386 1.16-2+b1 [24.2 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 libptexenc1 i386 2023.20230311.66589-9 [48.1 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 libpython3.11 i386 3.11.8-1 [2009 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 libpython3.11-dev i386 3.11.8-1 [4726 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.11.6-1 [9496 B] Get: 154 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.2-1 [1927 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 libpython3.12 i386 3.12.2-1 [2156 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.2-1 [5108 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 libpython3-all-dev i386 3.11.6-1 [1072 B] Get: 158 http://deb.debian.org/debian trixie/main i386 libsimde-dev all 0.8.0-1 [458 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 libsynctex2 i386 2023.20230311.66589-9 [64.6 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 libteckit0 i386 2.5.12+ds1-1 [284 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 libtexlua53-5 i386 2023.20230311.66589-9 [127 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 libxmu6 i386 2:1.1.3-3 [62.5 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 libxaw7 i386 2:1.0.14-1 [209 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 165 http://deb.debian.org/debian trixie/main i386 libzzip-0-13 i386 0.13.72+dfsg.1-1.1+b1 [58.1 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 tex-common all 6.18 [32.5 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 preview-latex-style all 13.2-1 [350 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.2-1 [653 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.11.6-1 [1060 B] Get: 170 http://deb.debian.org/debian trixie/main i386 python3.11-dev i386 3.11.8-1 [509 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.11.6-1 [26.1 kB] Get: 172 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.2-1 [507 kB] Get: 173 http://deb.debian.org/debian trixie/main i386 python3-all-dev i386 3.11.6-1 [1080 B] Get: 174 http://deb.debian.org/debian trixie/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 texlive-binaries i386 2023.20230311.66589-9 [8274 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 177 http://deb.debian.org/debian trixie/main i386 texlive-base all 2023.20240207-1 [22.0 MB] Get: 178 http://deb.debian.org/debian trixie/main i386 texlive-font-utils all 2023.20240207-1 [7046 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 180 http://deb.debian.org/debian trixie/main i386 texlive-lang-greek all 2023.20240207-1 [79.2 MB] Get: 181 http://deb.debian.org/debian trixie/main i386 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 182 http://deb.debian.org/debian trixie/main i386 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 184 http://deb.debian.org/debian trixie/main i386 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Get: 185 http://deb.debian.org/debian trixie/main i386 texlive-science all 2023.20240207-1 [3804 kB] Fetched 276 MB in 4s (77.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package poppler-data. (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 ... 19876 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.5.0-2+b2) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20727 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../5-libreadline8_8.2-3+b1_i386.deb ... Unpacking libreadline8:i386 (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_i386.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21715 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../001-libpython3.12-minimal_3.12.2-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.2-1_i386.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../005-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... 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Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up libgraphite2-3:i386 (1.3.14-2) ... Setting up libsimde-dev (0.8.0-1) ... Setting up liblcms2-2:i386 (2.14-2+b1) ... Setting up libpixman-1-0:i386 (0.42.2-1+b1) ... Setting up libsharpyuv0:i386 (1.3.2-0.4) ... Setting up libaom3:i386 (3.8.2-2) ... Setting up libabsl20220623:i386 (20220623.1-3) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up liblerc4:i386 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up fonts-gfs-porson (1.1-7) ... Setting up libdatrie1:i386 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.78.4-1) ... No schema files found: doing nothing. Setting up libijs-0.35:i386 (0.35-15.1+b1) ... Setting up libdebhelper-perl (13.14.1) ... Setting up libgs-common (10.02.1~dfsg-3) ... Setting up libbrotli1:i386 (1.1.0-2+b3) ... Setting up libfontbox-java (1:1.8.16-5) ... Setting up libpython3.12-minimal:i386 (3.12.2-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up libdeflate0:i386 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libzzip-0-13:i386 (0.13.72+dfsg.1-1.1+b1) ... Setting up file (1:5.45-2+b1) ... Setting up libjbig0:i386 (2.1-6.1+b1) ... Setting up librav1e0:i386 (0.7.1-2) ... Setting up poppler-data (0.4.12-1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 2 01:24:03 UTC 2025. Universal Time is now: Fri May 2 01:24:03 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:i386 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:i386 (2.5.0-2+b2) ... 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Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:i386 (2023.20230311.66589-9) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:i386 (1.16-2+b1) ... 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 gnuplot-data (6.0.0+dfsg1-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libavif16:i386 (1.0.4-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libedit2:i386 (3.1-20230828-1) ... 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Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libpython3.12-stdlib:i386 (3.12.2-1) ... Setting up libxpm4:i386 (1:3.5.17-1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up libpango-1.0-0:i386 (1.52.0+ds-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.0-1+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6:i386 (1:1.2.1-1.1) ... Setting up libcups2:i386 (2.4.7-1+b1) ... Setting up libpangoft2-1.0-0:i386 (1.52.0+ds-1) ... Setting up libpython3.12:i386 (3.12.2-1) ... Setting up libpangocairo-1.0-0:i386 (1.52.0+ds-1) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libxmu6:i386 (2:1.1.3-3) ... Setting up libpython3.11:i386 (3.11.8-1) ... Setting up libxi6:i386 (2:1.8.1-1) ... Setting up preview-latex-style (13.2-1) ... Setting up debhelper (13.14.1) ... Setting up python3 (3.11.6-1) ... Setting up libpython3.12-dev:i386 (3.12.2-1) ... Setting up libxaw7:i386 (2:1.0.14-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.11-dev:i386 (3.11.8-1) ... Setting up python3.12-dev (3.12.2-1) ... Setting up cython3 (3.0.8-1) ... Setting up texlive-binaries (2023.20230311.66589-9) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-lib2to3 (3.11.5-1) ... Setting up texlive-base (2023.20240207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 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 libgs10-common (10.02.1~dfsg-3) ... Setting up libpython3-dev:i386 (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 texlive-lang-greek (2023.20240207-1) ... Setting up texlive-font-utils (2023.20240207-1) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up libpython3-all-dev:i386 (3.11.6-1) ... Setting up python3-dev (3.11.6-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Setting up texlive-pictures (2023.20240207-1) ... Setting up texlive-fonts-recommended (2023.20240207-1) ... Setting up libgs10:i386 (10.02.1~dfsg-3) ... Setting up dh-python (6.20240310) ... Setting up python3-all-dev (3.11.6-1) ... Setting up texlive-science (2023.20240207-1) ... Setting up texlive-latex-extra (2023.20240207-1) ... Setting up ghostscript (10.02.1~dfsg-3) ... Setting up libheif-plugin-dav1d:i386 (1.17.6-1) ... Setting up libheif1:i386 (1.17.6-1) ... Setting up libgd3:i386 (2.3.3-9+b1) ... Setting up gnuplot-nox (6.0.0+dfsg1-1) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up libheif-plugin-libde265:i386 (1.17.6-1) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 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/minimap2-2.27+dfsg/ && 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 > ../minimap2_2.27+dfsg-1_source.changes dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.27+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_clean make -j22 clean make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' rm -fr gmon.out *.o a.out minimap2 sdust minimap2-lite *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_clean --buildsystem=pybuild 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/minimap2-2.27+dfsg/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-i686' 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/minimap2-2.27+dfsg/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it cd tex && make clean make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_build -- make -j22 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC main.c -o main.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kthread.c -o kthread.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC misc.c -o misc.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC bseq.c -o bseq.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sketch.c -o sketch.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sdust.c -o sdust.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC options.c -o options.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC index.c -o index.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC lchain.c -o lchain.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC align.c -o align.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC hit.c -o hit.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC seed.c -o seed.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC map.c -o map.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC format.c -o format.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC pe.c -o pe.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC esterr.c -o esterr.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC splitidx.c -o splitidx.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o kalloc.c: In function 'km_stat_print': kalloc.c:222:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:53: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:66: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:78: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:91: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~ | | | size_t {aka unsigned int} map.c: In function 'mm_map_frag': map.c:365:60: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d map.c:365:70: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d map.c:365:82: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d index.c: In function 'mm_idx_load': index.c:520:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o rm -f libminimap2.a ar csrD libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o cc -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' cd tex && make make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' gnuplot roc.gp epstopdf --outfile roc-color.pdf roc-color.eps Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2; This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) 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This is BibTeX, Version 0.99d (TeX Live 2023/Debian) The top-level auxiliary file: minimap2.aux The style file: apalike.bst Database file #1: minimap2.bib This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (./bioinfo.cls Document Class: bioinfo 2003/02/08 0.1 (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/crop/crop.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(./minimap2.aux Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. ) (see the transcript file for additional information) Output written on minimap2.pdf (6 pages, 265939 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (./bioinfo.cls Document Class: bioinfo 2003/02/08 0.1 (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/crop/crop.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Font Warning: Font shape `OML/cmm/m/it' in size <6.5> not available (Font) size <6> substituted on input line 58. LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <6.5> not available (Font) size <6> substituted on input line 58. Underfull \hbox (badness 1478) in paragraph at lines 71--80 \OT1/ptm/m/n/9 minor modifications could enable the base algorithm to map Underfull \hbox (badness 1019) in paragraph at lines 71--80 \OT1/ptm/m/n/9 mRNAs as well. Minimap2 becomes a first RNA-seq aligner [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 204. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 204. Underfull \vbox (badness 10000) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [2] Underfull \hbox (badness 1769) in paragraph at lines 382--386 \OT1/ptm/m/n/8 performs local alignment between the two subsequences involved i n Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [3] LaTeX Font Warning: Font shape `OT1/cmtt/m/n' in size <6.5> not available (Font) size <6> substituted on input line 492. Overfull \hbox (9.0pt too wide) in paragraph at lines 496--515 [][] Underfull \hbox (badness 1248) in paragraph at lines 518--535 []\OT1/ptm/m/n/9 2016[]), Kart (v2.2.5; []Lin and Hsu[], []2017[]), minialign ( v0.5.3; Overfull \hbox (3.90332pt too wide) in paragraph at lines 518--535 []\OT1/ptm/m/n/9 https://github.com/ocxtal/minialign[]) and NGMLR (v0.2.5; []Se dlazeck Underfull \hbox (badness 2189) in paragraph at lines 590--597 \OT1/ptm/m/n/9 GMAP (v2017-06-20; []Wu and Watanabe[], []2005[]), minimap2, Underfull \hbox (badness 1424) in paragraph at lines 590--597 \OT1/ptm/m/n/9 et al.[], []2013[]). In general, minimap2 is more consistent wit h Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [4 <./roc-color.pdf>] Underfull \hbox (badness 4634) in paragraph at lines 598--610 \OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2 Underfull \hbox (badness 2096) in paragraph at lines 647--659 \OT1/ptm/m/n/9 v3.5 ([]Depristo et al.[], []2011[]). This run was sequenced fro m Underfull \hbox (badness 1454) in paragraph at lines 662--671 \OT1/ptm/m/n/9 the paftools.js script from the minimap2 package, we called Underfull \hbox (badness 1137) in paragraph at lines 662--671 \OT1/ptm/m/n/9 regions. The transition-to-transversion ratio (ts/tv) is 2.01. I n Underfull \hbox (badness 2027) in paragraph at lines 687--700 []\OT1/ptm/m/n/9 The capability of minimap2 comes from a fast base-level Underfull \hbox (badness 1226) in paragraph at lines 714--719 \OT1/ptm/m/n/9 releasing their masterpiece and insightful notes before formal Package hyperref Warning: Difference (3) between bookmark levels is greater (hyperref) than one, level fixed on input line 720. (./minimap2.bbl Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [5] Underfull \hbox (badness 1953) in paragraph at lines 120--123 []\OT1/ptm/m/n/7 Li, H. et al. (2009). The Sequence Alignment/Map format and S AMtools. Underfull \vbox (badness 10000) has occurred while \output is active) Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [6] (./minimap2.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. ) (see the transcript file for additional information) Output written on minimap2.pdf (6 pages, 269463 bytes). Transcript written on minimap2.log. make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' dh_auto_build --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_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/minimap2-2.27+dfsg/python/mappy.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling python/mappy.pyx because it changed. [1/1] Cythonizing python/mappy.pyx building 'mappy' extension creating build creating build/temp.linux-i686-cpython-312 creating build/temp.linux-i686-cpython-312/python i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c align.c -o build/temp.linux-i686-cpython-312/align.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP align.c: In function 'mm_get_hplen_back': align.c:365:43: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 365 | if (mm_seq4_get(mi->S, i) != c) break; | ^~ align.c: In function 'mm_seed_ext_score': align.c:552:56: warning: operand of '?:' changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 552 | re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len; | ^~~~~~~~~~~~ align.c: In function 'mm_align1': align.c:646:59: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 646 | re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len; | ^~~~~~ align.c:698:65: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 698 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re; | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c bseq.c -o build/temp.linux-i686-cpython-312/bseq.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c esterr.c -o build/temp.linux-i686-cpython-312/esterr.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c format.c -o build/temp.linux-i686-cpython-312/format.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c hit.c -o build/temp.linux-i686-cpython-312/hit.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP hit.c: In function 'mm_hit_sort': hit.c:190:55: warning: variable 'no_cigar' set but not used [-Wunused-but-set-variable] 190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~ hit.c:190:40: warning: variable 'has_cigar' set but not used [-Wunused-but-set-variable] 190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c index.c -o build/temp.linux-i686-cpython-312/index.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP index.c: In function 'mm_idx_name2id': index.c:149:32: warning: operand of '?:' changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 149 | return k == kh_end(h)? -1 : kh_val(h, k); | ^~ index.c: In function 'mm_idx_gen': index.c:382:70: warning: operand of '?:' changes signedness from 'int' to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 382 | pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size; | ^~~~~~~~~~~~~~~ index.c: In function 'mm_idx_dump': index.c:483:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 483 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function 'mm_idx_load': index.c:531:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 531 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function 'mm_idx_bed_read': index.c:748:23: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 748 | for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals | ^ index.c: In function 'mm_idx_bed_junc': index.c:758:42: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 758 | if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1; | ^~ index.c: In function 'mm_idx_load': index.c:520:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c kalloc.c -o build/temp.linux-i686-cpython-312/kalloc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP kalloc.c: In function 'km_stat_print': kalloc.c:222:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:53: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:66: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:78: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:91: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~ | | | size_t {aka unsigned int} i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extd2_sse.c -o build/temp.linux-i686-cpython-312/ksw2_extd2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition ksw2_extd2_sse.c: In function 'ksw_extd2_sse': ksw2_extd2_sse.c:62:17: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 62 | zero_ = _mm_set1_epi8(0); | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_exts2_sse.c -o build/temp.linux-i686-cpython-312/ksw2_exts2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition ksw2_exts2_sse.c: In function 'ksw_exts2_sse': ksw2_exts2_sse.c:59:17: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 59 | zero_ = _mm_set1_epi8(0); | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extz2_sse.c -o build/temp.linux-i686-cpython-312/ksw2_extz2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition ksw2_extz2_sse.c: In function 'ksw_extz2_sse': ksw2_extz2_sse.c:49:17: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 49 | zero_ = _mm_set1_epi8(0); | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_ll_sse.c -o build/temp.linux-i686-cpython-312/ksw2_ll_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_ll_sse.c: In function 'ksw_ll_i16': ksw2_ll_sse.c:101:14: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 101 | zero = _mm_set1_epi32(0); | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c kthread.c -o build/temp.linux-i686-cpython-312/kthread.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c lchain.c -o build/temp.linux-i686-cpython-312/lchain.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP lchain.c: In function 'mg_chain_bk_end': lchain.c:18:37: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 18 | s = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function 'mg_chain_backtrack': lchain.c:51:46: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 51 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c:66:46: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 66 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function 'mg_lchain_dp': lchain.c:190:56: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare] 190 | if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) { | ^ lchain.c:204:57: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare] 204 | if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i])) | ^~ lchain.c: In function 'mg_lchain_rmq': lchain.c:295:117: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 295 | while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) { | ^ lchain.c:304:155: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 304 | while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) { | ^ lchain.c:356:34: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 356 | if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root); | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c map.c -o build/temp.linux-i686-cpython-312/map.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP map.c: In function 'mm_dust_minier': map.c:48:70: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 48 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32; | ^ map.c:49:64: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'unsigned int' due to unsignedness of other operand [-Wsign-compare] 49 | int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v]; | ^ map.c: In function 'mm_map_frag': map.c:365:60: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d map.c:365:70: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d map.c:365:82: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c misc.c -o build/temp.linux-i686-cpython-312/misc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c options.c -o build/temp.linux-i686-cpython-312/options.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c pe.c -o build/temp.linux-i686-cpython-312/pe.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c python/mappy.c -o build/temp.linux-i686-cpython-312/python/mappy.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP python/mappy.c: In function '__Pyx_PyInt_AndObjC': python/mappy.c:15226:36: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'long int' [-Wsign-compare] 15226 | if ((intval & PyLong_MASK) == intval) { | ^~ python/mappy.c:15228:71: warning: operand of '?:' changes signedness from 'long int' to 'long unsigned int' due to unsignedness of other operand [-Wsign-compare] 15228 | long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1)); | ^~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c sdust.c -o build/temp.linux-i686-cpython-312/sdust.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c seed.c -o build/temp.linux-i686-cpython-312/seed.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP seed.c: In function 'mm_seed_mz_flt': seed.c:9:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] 9 | if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return; | ^~ seed.c: In function 'mm_seed_select': seed.c:65:28: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 65 | if (a[i].n > max_occ) ++m; | ^ seed.c:68:38: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 68 | if (i == n || a[i].n <= max_occ) { | ^~ seed.c:71:54: warning: operand of '?:' changes signedness from 'int' to 'unsigned int' due to unsignedness of other operand [-Wsign-compare] 71 | int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1; | ^~~ seed.c:81:60: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 81 | if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap | ^ seed.c:90:52: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 90 | if (a[j].n > max_max_occ) | ^ seed.c: In function 'mm_collect_matches': seed.c:109:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 109 | for (i = 0; i < n_m0; ++i) | ^ seed.c:110:36: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 110 | if (m[i].n > max_occ) | ^ seed.c:113:56: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) { | ^ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c sketch.c -o build/temp.linux-i686-cpython-312/sketch.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c splitidx.c -o build/temp.linux-i686-cpython-312/splitidx.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/align.o build/temp.linux-i686-cpython-312/bseq.o build/temp.linux-i686-cpython-312/esterr.o build/temp.linux-i686-cpython-312/format.o build/temp.linux-i686-cpython-312/hit.o build/temp.linux-i686-cpython-312/index.o build/temp.linux-i686-cpython-312/kalloc.o build/temp.linux-i686-cpython-312/ksw2_extd2_sse.o build/temp.linux-i686-cpython-312/ksw2_exts2_sse.o build/temp.linux-i686-cpython-312/ksw2_extz2_sse.o build/temp.linux-i686-cpython-312/ksw2_ll_sse.o build/temp.linux-i686-cpython-312/kthread.o build/temp.linux-i686-cpython-312/lchain.o build/temp.linux-i686-cpython-312/map.o build/temp.linux-i686-cpython-312/misc.o build/temp.linux-i686-cpython-312/options.o build/temp.linux-i686-cpython-312/pe.o build/temp.linux-i686-cpython-312/python/mappy.o build/temp.linux-i686-cpython-312/sdust.o build/temp.linux-i686-cpython-312/seed.o build/temp.linux-i686-cpython-312/sketch.o build/temp.linux-i686-cpython-312/splitidx.o -L/usr/lib/i386-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.12/build/mappy.cpython-312-i386-linux-gnu.so running build_scripts creating build/scripts-3.12 copying and adjusting python/minimap2.py -> build/scripts-3.12 changing mode of build/scripts-3.12/minimap2.py 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_ext building 'mappy' extension creating build/temp.linux-i686-cpython-311 creating build/temp.linux-i686-cpython-311/python i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c align.c -o build/temp.linux-i686-cpython-311/align.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP align.c: In function 'mm_get_hplen_back': align.c:365:43: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 365 | if (mm_seq4_get(mi->S, i) != c) break; | ^~ align.c: In function 'mm_seed_ext_score': align.c:552:56: warning: operand of '?:' changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 552 | re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len; | ^~~~~~~~~~~~ align.c: In function 'mm_align1': align.c:646:59: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 646 | re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len; | ^~~~~~ align.c:698:65: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 698 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re; | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c bseq.c -o build/temp.linux-i686-cpython-311/bseq.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c esterr.c -o build/temp.linux-i686-cpython-311/esterr.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c format.c -o build/temp.linux-i686-cpython-311/format.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c hit.c -o build/temp.linux-i686-cpython-311/hit.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP hit.c: In function 'mm_hit_sort': hit.c:190:55: warning: variable 'no_cigar' set but not used [-Wunused-but-set-variable] 190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~ hit.c:190:40: warning: variable 'has_cigar' set but not used [-Wunused-but-set-variable] 190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~~ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c index.c -o build/temp.linux-i686-cpython-311/index.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP index.c: In function 'mm_idx_name2id': index.c:149:32: warning: operand of '?:' changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 149 | return k == kh_end(h)? -1 : kh_val(h, k); | ^~ index.c: In function 'mm_idx_gen': index.c:382:70: warning: operand of '?:' changes signedness from 'int' to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 382 | pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size; | ^~~~~~~~~~~~~~~ index.c: In function 'mm_idx_dump': index.c:483:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 483 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function 'mm_idx_load': index.c:531:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 531 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function 'mm_idx_bed_read': index.c:748:23: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 748 | for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals | ^ index.c: In function 'mm_idx_bed_junc': index.c:758:42: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 758 | if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1; | ^~ index.c: In function 'mm_idx_load': index.c:520:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c kalloc.c -o build/temp.linux-i686-cpython-311/kalloc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP kalloc.c: In function 'km_stat_print': kalloc.c:222:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:53: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:66: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:78: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~~ | | | size_t {aka unsigned int} kalloc.c:222:91: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", | ~~^ | | | long int | %d 223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores); | ~~~~~~~~~~ | | | size_t {aka unsigned int} i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_extd2_sse.c -o build/temp.linux-i686-cpython-311/ksw2_extd2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition ksw2_extd2_sse.c: In function 'ksw_extd2_sse': ksw2_extd2_sse.c:62:17: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 62 | zero_ = _mm_set1_epi8(0); | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_exts2_sse.c -o build/temp.linux-i686-cpython-311/ksw2_exts2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition ksw2_exts2_sse.c: In function 'ksw_exts2_sse': ksw2_exts2_sse.c:59:17: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 59 | zero_ = _mm_set1_epi8(0); | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_extz2_sse.c -o build/temp.linux-i686-cpython-311/ksw2_extz2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition ksw2_extz2_sse.c: In function 'ksw_extz2_sse': ksw2_extz2_sse.c:49:17: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 49 | zero_ = _mm_set1_epi8(0); | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_ll_sse.c -o build/temp.linux-i686-cpython-311/ksw2_ll_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_ll_sse.c: In function 'ksw_ll_i16': ksw2_ll_sse.c:101:14: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 101 | zero = _mm_set1_epi32(0); | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c kthread.c -o build/temp.linux-i686-cpython-311/kthread.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c lchain.c -o build/temp.linux-i686-cpython-311/lchain.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP lchain.c: In function 'mg_chain_bk_end': lchain.c:18:37: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 18 | s = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function 'mg_chain_backtrack': lchain.c:51:46: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 51 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c:66:46: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 66 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function 'mg_lchain_dp': lchain.c:190:56: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare] 190 | if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) { | ^ lchain.c:204:57: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long long unsigned int'} and 'long long int' [-Wsign-compare] 204 | if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i])) | ^~ lchain.c: In function 'mg_lchain_rmq': lchain.c:295:117: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 295 | while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) { | ^ lchain.c:304:155: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 304 | while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) { | ^ lchain.c:356:34: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 356 | if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root); | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c map.c -o build/temp.linux-i686-cpython-311/map.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP map.c: In function 'mm_dust_minier': map.c:48:70: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 48 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32; | ^ map.c:49:64: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'unsigned int' due to unsignedness of other operand [-Wsign-compare] 49 | int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v]; | ^ map.c: In function 'mm_map_frag': map.c:365:60: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d map.c:365:70: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d map.c:365:82: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); | ~~^ ~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c misc.c -o build/temp.linux-i686-cpython-311/misc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c options.c -o build/temp.linux-i686-cpython-311/options.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c pe.c -o build/temp.linux-i686-cpython-311/pe.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c python/mappy.c -o build/temp.linux-i686-cpython-311/python/mappy.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP python/mappy.c: In function '__Pyx_PyInt_AndObjC': python/mappy.c:15226:36: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'long int' [-Wsign-compare] 15226 | if ((intval & PyLong_MASK) == intval) { | ^~ python/mappy.c:15228:71: warning: operand of '?:' changes signedness from 'long int' to 'long unsigned int' due to unsignedness of other operand [-Wsign-compare] 15228 | long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1)); | ^~~~~~~~~~ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c sdust.c -o build/temp.linux-i686-cpython-311/sdust.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c seed.c -o build/temp.linux-i686-cpython-311/seed.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP seed.c: In function 'mm_seed_mz_flt': seed.c:9:19: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] 9 | if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return; | ^~ seed.c: In function 'mm_seed_select': seed.c:65:28: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 65 | if (a[i].n > max_occ) ++m; | ^ seed.c:68:38: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 68 | if (i == n || a[i].n <= max_occ) { | ^~ seed.c:71:54: warning: operand of '?:' changes signedness from 'int' to 'unsigned int' due to unsignedness of other operand [-Wsign-compare] 71 | int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1; | ^~~ seed.c:81:60: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 81 | if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap | ^ seed.c:90:52: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 90 | if (a[j].n > max_max_occ) | ^ seed.c: In function 'mm_collect_matches': seed.c:109:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 109 | for (i = 0; i < n_m0; ++i) | ^ seed.c:110:36: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 110 | if (m[i].n > max_occ) | ^ seed.c:113:56: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) { | ^ i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c sketch.c -o build/temp.linux-i686-cpython-311/sketch.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-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/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c splitidx.c -o build/temp.linux-i686-cpython-311/splitidx.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/align.o build/temp.linux-i686-cpython-311/bseq.o build/temp.linux-i686-cpython-311/esterr.o build/temp.linux-i686-cpython-311/format.o build/temp.linux-i686-cpython-311/hit.o build/temp.linux-i686-cpython-311/index.o build/temp.linux-i686-cpython-311/kalloc.o build/temp.linux-i686-cpython-311/ksw2_extd2_sse.o build/temp.linux-i686-cpython-311/ksw2_exts2_sse.o build/temp.linux-i686-cpython-311/ksw2_extz2_sse.o build/temp.linux-i686-cpython-311/ksw2_ll_sse.o build/temp.linux-i686-cpython-311/kthread.o build/temp.linux-i686-cpython-311/lchain.o build/temp.linux-i686-cpython-311/map.o build/temp.linux-i686-cpython-311/misc.o build/temp.linux-i686-cpython-311/options.o build/temp.linux-i686-cpython-311/pe.o build/temp.linux-i686-cpython-311/python/mappy.o build/temp.linux-i686-cpython-311/sdust.o build/temp.linux-i686-cpython-311/seed.o build/temp.linux-i686-cpython-311/sketch.o build/temp.linux-i686-cpython-311/splitidx.o -L/usr/lib/i386-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.11/build/mappy.cpython-311-i386-linux-gnu.so running build_scripts creating build/scripts-3.11 copying and adjusting python/minimap2.py -> build/scripts-3.11 changing mode of build/scripts-3.11/minimap2.py from 644 to 755 make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' debian/test_script [M::mm_idx_gen::0.003*1.38] collected minimizers [M::mm_idx_gen::0.004*1.75] sorted minimizers [M::main::0.004*1.74] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.004*1.70] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.004*1.67] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.013*1.22] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa [M::main] Real time: 0.013 sec; CPU: 0.016 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.002*1.53] collected minimizers [M::mm_idx_gen::0.003*1.93] sorted minimizers [M::main::0.005*1.54] loaded/built the index for 1 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.005*1.52] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa [M::main] Real time: 0.006 sec; CPU: 0.009 sec; Peak RSS: 0.004 GB [M::main::0.003*1.21] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.003*1.19] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.003*1.18] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.011*1.10] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa [M::main] Real time: 0.012 sec; CPU: 0.014 sec; Peak RSS: 0.006 GB rm test.sam make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_install dh_auto_install --buildsystem=pybuild I: pybuild base:305: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp /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_ext running build_scripts running install_lib creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.12 creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.12/dist-packages copying /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.12/build/mappy.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.12/dist-packages running install_egg_info running egg_info creating mappy.egg-info writing mappy.egg-info/PKG-INFO writing dependency_links to mappy.egg-info/dependency_links.txt writing top-level names to mappy.egg-info/top_level.txt writing manifest file 'mappy.egg-info/SOURCES.txt' reading manifest file 'mappy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'sse2neon/emmintrin.h' adding license file 'LICENSE.txt' writing manifest file 'mappy.egg-info/SOURCES.txt' Copying mappy.egg-info to /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/mappy-2.27.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin copying build/scripts-3.12/minimap2.py -> /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin changing mode of /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin/minimap2.py to 755 I: pybuild base:305: /usr/bin/python3 setup.py install --root /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp /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_ext running build_scripts running install_lib creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.11 creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.11/dist-packages copying /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.11/build/mappy.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.11/dist-packages running install_egg_info running egg_info writing mappy.egg-info/PKG-INFO writing dependency_links to mappy.egg-info/dependency_links.txt writing top-level names to mappy.egg-info/top_level.txt reading manifest file 'mappy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'sse2neon/emmintrin.h' adding license file 'LICENSE.txt' writing manifest file 'mappy.egg-info/SOURCES.txt' Copying mappy.egg-info to /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/mappy-2.27.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/minimap2.py -> /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin changing mode of /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin/minimap2.py to 755 make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_fixperms dh_missing dh_dwz -a debian/rules override_dh_strip make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_strip ranlib /build/reproducible-path/minimap2-2.27+dfsg/debian/libminimap2-dev/usr/lib/libminimap2.a make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libminimap2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_i386.deb'. dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_i386.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_i386.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_i386.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/91328 and its subdirectories I: Current time: Thu May 1 13:26:49 -12 2025 I: pbuilder-time-stamp: 1746149209 Fri Mar 29 19:03:50 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Fri Mar 29 19:03:50 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Fri Mar 29 19:09:19 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Fri Mar 29 19:09:19 UTC 2024 I: minimap2_2.27+dfsg-1_i386.changes: Format: 1.8 Date: Mon, 18 Mar 2024 17:12:17 +0100 Source: minimap2 Binary: libminimap2-dev minimap2 minimap2-dbgsym python3-mappy python3-mappy-dbgsym Architecture: i386 Version: 2.27+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libminimap2-dev - development headers for libminimap minimap2 - versatile pairwise aligner for genomic and spliced nucleotide seq python3-mappy - Python3 interface minimap2 Closes: 1046060 Changes: minimap2 (2.27+dfsg-1) unstable; urgency=medium . * Team upload. * d/rules, d/clean: simply cleanup code. * d/rules: clean using pybuild. Closes: #1046060 Checksums-Sha1: 492457e674bf24f69d6e5e9167824fbaff6da55b 138872 libminimap2-dev_2.27+dfsg-1_i386.deb 9fafecc7c36158b8928e7574c8c39a6dc64d11cb 245280 minimap2-dbgsym_2.27+dfsg-1_i386.deb cc650054b5127d8dad055f6701feb588fbb725ba 11553 minimap2_2.27+dfsg-1_i386.buildinfo a1b8931263d2a38b8babbe9f42b4b650a5141f34 395444 minimap2_2.27+dfsg-1_i386.deb b68789854092a410c48f4ff124f67d8b5ed769f7 1048132 python3-mappy-dbgsym_2.27+dfsg-1_i386.deb 5f9b7cf8342306607dd69c11b2250b24afdd3899 230440 python3-mappy_2.27+dfsg-1_i386.deb Checksums-Sha256: ce137b9ac37c76d061134754b1dda7b7aa3e811f81918397fb57754cf9c71467 138872 libminimap2-dev_2.27+dfsg-1_i386.deb 4907778b8227a6d95b100fcff0360e20e8754d2d3d9898310184f3865a14dd10 245280 minimap2-dbgsym_2.27+dfsg-1_i386.deb 519383a04f5354bf5a85660a5f42f77fce8c04486a15662e6d6ffb7fa0cc317b 11553 minimap2_2.27+dfsg-1_i386.buildinfo 9bb941d2fff0eebfb6578cbdfc6e7a1fb968d413d750475ad5a91f5d4ad5c7cf 395444 minimap2_2.27+dfsg-1_i386.deb cb5010f5d9b1d7e50bff64c52070d1aa5185529a665b09456d65d1693a9b7061 1048132 python3-mappy-dbgsym_2.27+dfsg-1_i386.deb a1a7cb05182b2a937d86c800772350a1bed7843362ff7d4b0ff5042a1778869f 230440 python3-mappy_2.27+dfsg-1_i386.deb Files: 0836a898f8d1d9ce8b29d9093aa358df 138872 libdevel optional libminimap2-dev_2.27+dfsg-1_i386.deb 99ecb509bf0912ae59fe883b969efd30 245280 debug optional minimap2-dbgsym_2.27+dfsg-1_i386.deb 394fbe306755c746c0f6cb0d39f381cf 11553 science optional minimap2_2.27+dfsg-1_i386.buildinfo a779595c35f9348f123022cb46dedf70 395444 science optional minimap2_2.27+dfsg-1_i386.deb bf944a126f72f786c8d50e6aaec65eb1 1048132 debug optional python3-mappy-dbgsym_2.27+dfsg-1_i386.deb c15c0aca4de50cafe512f6f8d7cbdcb6 230440 python optional python3-mappy_2.27+dfsg-1_i386.deb Fri Mar 29 19:09:20 UTC 2024 I: diffoscope 261 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_2-16451.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.keXOitia/minimap2_2.27+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.keXOitia/minimap2_2.27+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.keXOitia/minimap2_2.27+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.keXOitia/b1/minimap2_2.27+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.keXOitia/b2/minimap2_2.27+dfsg-1_i386.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: 0.404s) 0.404s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.047s) 0.047s 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: 721ms CPU time consumed: 720ms Fri Mar 29 19:09:21 UTC 2024 I: diffoscope 261 found no differences in the changes files, and a .buildinfo file also exists. Fri Mar 29 19:09:21 UTC 2024 I: minimap2 from trixie built successfully and reproducibly on i386. Fri Mar 29 19:09:23 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Mar 29 19:09:23 UTC 2024 I: Submitting 16K b1/minimap2_2.27+dfsg-1_i386.buildinfo.asc Fri Mar 29 19:09:23 UTC 2024 I: Submitting 16K b2/minimap2_2.27+dfsg-1_i386.buildinfo.asc Fri Mar 29 19:09:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Mar 29 19:09:24 UTC 2024 I: Done submitting .buildinfo files. Fri Mar 29 19:09:24 UTC 2024 I: Removing signed minimap2_2.27+dfsg-1_i386.buildinfo.asc files: removed './b1/minimap2_2.27+dfsg-1_i386.buildinfo.asc' removed './b2/minimap2_2.27+dfsg-1_i386.buildinfo.asc'