I: pbuilder: network access will be disabled during build I: Current time: Thu May 16 16:43:43 +14 2024 I: pbuilder-time-stamp: 1715827423 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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/2405037/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 16 02:43 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2405037/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2405037/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8a6ea247850f4efb923a8a36822b6332 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2405037 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qhemZOFQ/pbuilderrc_xmKO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qhemZOFQ/b2 --logfile b2/build.log minimap2_2.27+dfsg-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 15 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2405037/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: arm64 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 ... 19744 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} libabsl20230802{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} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{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} libglib2.0-0t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{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} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{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} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} librav1e0{a} libreadline8t64{a} libsharpyuv0{a} libsimde-dev{a} libsm6{a} libsub-override-perl{a} libsvtav1enc1d1{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} libxt6t64{a} libyuv0{a} libzzip-0-13t64{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 krb5-locales 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, 192 newly installed, 0 to remove and 0 not upgraded. Need to get 269 MB of archives. After unpacking 806 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 cython3 arm64 3.0.10+dfsg-5 [3120 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.106 [10.9 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 66 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgs-common all 10.03.0~dfsg-1 [148 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libgs10-common all 10.03.0~dfsg-1 [474 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-13+b2 [112 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-13+b2 [42.4 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.14.10-4+b1 [195 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-13+b2 [45.7 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 82 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libcups2t64 arm64 2.4.7-1.2+b1 [230 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libidn12 arm64 1.42-2 [79.2 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libijs-0.35 arm64 0.35-15.1+b1 [14.9 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libjbig2dec0 arm64 0.20-1+b2 [59.6 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libgs10 arm64 10.03.0~dfsg-1 [2294 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 ghostscript arm64 10.03.0~dfsg-1 [50.3 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 gnuplot-data all 6.0.0+dfsg1-3 [72.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libaom3 arm64 3.8.2-2 [1528 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libdav1d7 arm64 1.4.1-1 [251 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libgav1-1 arm64 0.19.0-2+b1 [481 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 librav1e0 arm64 0.7.1-2 [630 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libsvtav1enc1d1 arm64 1.7.0+dfsg-2+b1 [1083 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libyuv0 arm64 0.0~git202401110.af6ac82-1 [123 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libavif16 arm64 1.0.4-3 [99.4 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-dav1d arm64 1.17.6-1+b2 [9888 B] Get: 126 http://deb.debian.org/debian trixie/main arm64 libde265-0 arm64 1.0.15-1+b1 [151 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-libde265 arm64 1.17.6-1+b2 [13.0 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libheif1 arm64 1.17.6-1+b2 [247 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libxpm4 arm64 1:3.5.17-1+b1 [52.9 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libgd3 arm64 2.3.3-9+b3 [114 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.80.2-1 [1393 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 liblua5.4-0 arm64 5.4.6-3+b1 [135 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.52.2+ds-1 [206 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.52.2+ds-1 [45.5 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.52.2+ds-1 [33.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 gnuplot-nox arm64 6.0.0+dfsg1-3 [837 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 145 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libkpathsea6 arm64 2023.20230311.66589-9+b2 [151 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 154 http://deb.debian.org/debian trixie/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libpotrace0 arm64 1.16-2+b1 [23.1 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libptexenc1 arm64 2023.20230311.66589-9+b2 [46.3 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libpython3.11t64 arm64 3.11.9-1 [1814 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libpython3.11-dev arm64 3.11.9-1 [4358 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.11.8-1 [9564 B] Get: 161 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.3-1 [1948 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.3-1 [4745 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.11.8-1 [1072 B] Get: 165 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libsynctex2 arm64 2023.20230311.66589-9+b2 [59.8 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libteckit0 arm64 2.5.12+ds1-1 [300 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libtexlua53-5 arm64 2023.20230311.66589-9+b2 [105 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libxmu6 arm64 2:1.1.3-3+b2 [55.5 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libxaw7 arm64 2:1.0.14-1+b2 [182 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.1-1 [77.5 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2+b1 [56.7 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 tex-common all 6.18 [32.5 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3.11-dev arm64 3.11.9-1 [501 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.3-1 [499 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.11.8-1 [1072 B] Get: 181 http://deb.debian.org/debian trixie/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 texlive-binaries arm64 2023.20230311.66589-9+b2 [7353 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 185 http://deb.debian.org/debian trixie/main arm64 texlive-font-utils all 2023.20240207-1 [7046 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 texlive-lang-greek all 2023.20240207-1 [79.2 MB] Get: 188 http://deb.debian.org/debian trixie/main arm64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 191 http://deb.debian.org/debian trixie/main arm64 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Get: 192 http://deb.debian.org/debian trixie/main arm64 texlive-science all 2023.20240207-1 [3804 kB] Fetched 269 MB in 2s (156 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 ... 19744 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:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20594 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... 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-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21586 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... 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%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package ucf. 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Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up libsimde-dev (0.8.2-1) ... Setting up liblcms2-2:arm64 (2.14-2+b1) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... Setting up libaom3:arm64 (3.8.2-2) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up fonts-gfs-porson (1.1-7) ... Setting up libdatrie1:arm64 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libijs-0.35:arm64 (0.35-15.1+b1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libgs-common (10.03.0~dfsg-1) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libfontbox-java (1:1.8.16-5) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... 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Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libyuv0:arm64 (0.0~git202401110.af6ac82-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... 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:arm64 (2023.20230311.66589-9+b2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (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 (3.12.3-1) ... Setting up gnuplot-data (6.0.0+dfsg1-3) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libpdfbox-java (1:1.8.16-5) ... 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Setting up libpython3.12t64:arm64 (3.12.3-1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libpython3.11-dev:arm64 (3.11.9-1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libpangoft2-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libcups2t64:arm64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxmu6:arm64 (2:1.1.3-3+b2) ... Setting up libpython3-dev:arm64 (3.11.8-1) ... Setting up libxi6:arm64 (2:1.8.1-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up preview-latex-style (13.2-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:arm64 (3.12.3-1) ... Setting up libxaw7:arm64 (2:1.0.14-1+b2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-all-dev:arm64 (3.11.8-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up cython3 (3.0.10+dfsg-5) ... Setting up texlive-binaries (2023.20230311.66589-9+b2) ... 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 (3.12.3-1) ... 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 (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up libgs10-common (10.03.0~dfsg-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-all (3.11.8-1) ... 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 python3-dev (3.11.8-1) ... 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:arm64 (10.03.0~dfsg-1) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up texlive-science (2023.20240207-1) ... Setting up texlive-latex-extra (2023.20240207-1) ... Setting up ghostscript (10.03.0~dfsg-1) ... Setting up libheif-plugin-dav1d:arm64 (1.17.6-1+b2) ... Setting up libheif1:arm64 (1.17.6-1+b2) ... Setting up libgd3:arm64 (2.3.3-9+b3) ... Setting up gnuplot-nox (6.0.0+dfsg1-3) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up libheif-plugin-libde265:arm64 (1.17.6-1+b2) ... Processing triggers for libc-bin (2.38-10) ... 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: user script /srv/workspace/pbuilder/2405037/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2405037/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/minimap2-2.27+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 arm64 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 -j12 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:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running clean removing '/build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running clean removing '/build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-aarch64' 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 -- -f Makefile.simde make -j12 "INSTALL=install --strip-program=true" -f Makefile.simde make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 main.c -o main.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 kthread.c -o kthread.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 kalloc.c -o kalloc.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 misc.c -o misc.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 bseq.c -o bseq.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 sketch.c -o sketch.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 sdust.c -o sdust.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 options.c -o options.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 index.c -o index.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 lchain.c -o lchain.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 align.c -o align.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 hit.c -o hit.o 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 seed.c -o seed.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 map.c -o map.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 format.c -o format.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 pe.c -o pe.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 esterr.c -o esterr.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 splitidx.c -o splitidx.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o 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_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_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 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.o ksw2_extd2.o ksw2_exts2.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES 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) 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) 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Package natbib Warning: Citation `Dobin:2013kx' on page 4 undefined on input li ne 592. Underfull \hbox (badness 4634) in paragraph at lines 598--610 \OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2 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>] Package natbib Warning: Citation `Langmead:2012fk' on page 5 undefined on input line 637. Package natbib Warning: Citation `Zaharia:2011aa' on page 5 undefined on input line 638. Package natbib Warning: Citation `Depristo:2011vn' on page 5 undefined on input line 649. Package natbib Warning: Citation `Li223297' on page 5 undefined on input line 6 53. Package natbib Warning: Citation `Marcais:2018aa' on page 5 undefined on input line 664. 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. ) 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] Package natbib Warning: There were undefined citations. (./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. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/sttools/flushend.sty) (/usr/share/texlive/texmf-dist/tex/latex/sttools/stfloats.sty) (/usr/share/texlive/texmf-dist/tex/latex/amscls/amsthm.sty) (/usr/share/texlive/texmf-dist/tex/latex/changepage/chngpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/algorithm2e/algorithm2e.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/relsize/relsize.sty)) (./natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./minimap2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./minimap2.out) (./minimap2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1phv.fd) Underfull \hbox (badness 10000) detected at line 27 [] (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) Underfull \hbox (badness 1014) in paragraph at lines 36--47 \OT1/phv/b/n/8 Results: \OT1/phv/m/n/8 Minimap2 is a general-purpose alignment program to LaTeX Font Warning: Font shape `OT1/cmr/m/n' in size <6.5> not available (Font) size <6> substituted on input line 58. 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:311: /usr/bin/python3.12 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running build running build_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-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/python aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c align.c -o build/temp.linux-aarch64-cpython-312/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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; | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c bseq.c -o build/temp.linux-aarch64-cpython-312/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c esterr.c -o build/temp.linux-aarch64-cpython-312/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c format.c -o build/temp.linux-aarch64-cpython-312/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c hit.c -o build/temp.linux-aarch64-cpython-312/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c index.c -o build/temp.linux-aarch64-cpython-312/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c kalloc.c -o build/temp.linux-aarch64-cpython-312/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extd2_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_exts2_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extz2_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_ll_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c kthread.c -o build/temp.linux-aarch64-cpython-312/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c lchain.c -o build/temp.linux-aarch64-cpython-312/lchain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 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 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 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 unsigned int'} and '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 unsigned int'} and '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); | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c map.c -o build/temp.linux-aarch64-cpython-312/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 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:367:84: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int64_t' {aka 'long int'} [-Wsign-compare] 367 | if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) { | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c misc.c -o build/temp.linux-aarch64-cpython-312/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c options.c -o build/temp.linux-aarch64-cpython-312/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c pe.c -o build/temp.linux-aarch64-cpython-312/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c python/mappy.c -o build/temp.linux-aarch64-cpython-312/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c sdust.c -o build/temp.linux-aarch64-cpython-312/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c seed.c -o build/temp.linux-aarch64-cpython-312/seed.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 'long 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 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] 113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) { | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c sketch.c -o build/temp.linux-aarch64-cpython-312/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c splitidx.c -o build/temp.linux-aarch64-cpython-312/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/align.o build/temp.linux-aarch64-cpython-312/bseq.o build/temp.linux-aarch64-cpython-312/esterr.o build/temp.linux-aarch64-cpython-312/format.o build/temp.linux-aarch64-cpython-312/hit.o build/temp.linux-aarch64-cpython-312/index.o build/temp.linux-aarch64-cpython-312/kalloc.o build/temp.linux-aarch64-cpython-312/ksw2_extd2_sse.o build/temp.linux-aarch64-cpython-312/ksw2_exts2_sse.o build/temp.linux-aarch64-cpython-312/ksw2_extz2_sse.o build/temp.linux-aarch64-cpython-312/ksw2_ll_sse.o build/temp.linux-aarch64-cpython-312/kthread.o build/temp.linux-aarch64-cpython-312/lchain.o build/temp.linux-aarch64-cpython-312/map.o build/temp.linux-aarch64-cpython-312/misc.o build/temp.linux-aarch64-cpython-312/options.o build/temp.linux-aarch64-cpython-312/pe.o build/temp.linux-aarch64-cpython-312/python/mappy.o build/temp.linux-aarch64-cpython-312/sdust.o build/temp.linux-aarch64-cpython-312/seed.o build/temp.linux-aarch64-cpython-312/sketch.o build/temp.linux-aarch64-cpython-312/splitidx.o -L/usr/lib/aarch64-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.12/build/mappy.cpython-312-aarch64-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:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running build running build_ext building 'mappy' extension creating build/temp.linux-aarch64-cpython-311 creating build/temp.linux-aarch64-cpython-311/python aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c align.c -o build/temp.linux-aarch64-cpython-311/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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; | ^ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c bseq.c -o build/temp.linux-aarch64-cpython-311/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c esterr.c -o build/temp.linux-aarch64-cpython-311/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c format.c -o build/temp.linux-aarch64-cpython-311/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c hit.c -o build/temp.linux-aarch64-cpython-311/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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; | ^~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c index.c -o build/temp.linux-aarch64-cpython-311/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c kalloc.c -o build/temp.linux-aarch64-cpython-311/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_extd2_sse.c -o build/temp.linux-aarch64-cpython-311/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_exts2_sse.c -o build/temp.linux-aarch64-cpython-311/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_extz2_sse.c -o build/temp.linux-aarch64-cpython-311/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_ll_sse.c -o build/temp.linux-aarch64-cpython-311/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c kthread.c -o build/temp.linux-aarch64-cpython-311/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c lchain.c -o build/temp.linux-aarch64-cpython-311/lchain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 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 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 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 unsigned int'} and '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 unsigned int'} and '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); | ^ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c map.c -o build/temp.linux-aarch64-cpython-311/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 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:367:84: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int64_t' {aka 'long int'} [-Wsign-compare] 367 | if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) { | ^ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c misc.c -o build/temp.linux-aarch64-cpython-311/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c options.c -o build/temp.linux-aarch64-cpython-311/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c pe.c -o build/temp.linux-aarch64-cpython-311/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c python/mappy.c -o build/temp.linux-aarch64-cpython-311/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c sdust.c -o build/temp.linux-aarch64-cpython-311/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c seed.c -o build/temp.linux-aarch64-cpython-311/seed.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -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 'long 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 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] 113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) { | ^ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c sketch.c -o build/temp.linux-aarch64-cpython-311/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c splitidx.c -o build/temp.linux-aarch64-cpython-311/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/align.o build/temp.linux-aarch64-cpython-311/bseq.o build/temp.linux-aarch64-cpython-311/esterr.o build/temp.linux-aarch64-cpython-311/format.o build/temp.linux-aarch64-cpython-311/hit.o build/temp.linux-aarch64-cpython-311/index.o build/temp.linux-aarch64-cpython-311/kalloc.o build/temp.linux-aarch64-cpython-311/ksw2_extd2_sse.o build/temp.linux-aarch64-cpython-311/ksw2_exts2_sse.o build/temp.linux-aarch64-cpython-311/ksw2_extz2_sse.o build/temp.linux-aarch64-cpython-311/ksw2_ll_sse.o build/temp.linux-aarch64-cpython-311/kthread.o build/temp.linux-aarch64-cpython-311/lchain.o build/temp.linux-aarch64-cpython-311/map.o build/temp.linux-aarch64-cpython-311/misc.o build/temp.linux-aarch64-cpython-311/options.o build/temp.linux-aarch64-cpython-311/pe.o build/temp.linux-aarch64-cpython-311/python/mappy.o build/temp.linux-aarch64-cpython-311/sdust.o build/temp.linux-aarch64-cpython-311/seed.o build/temp.linux-aarch64-cpython-311/sketch.o build/temp.linux-aarch64-cpython-311/splitidx.o -L/usr/lib/aarch64-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.11/build/mappy.cpython-311-aarch64-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::0.002*2.32] collected minimizers [M::mm_idx_gen::0.004*2.55] sorted minimizers [M::main::0.004*2.53] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.005*2.41] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.005*2.32] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.023*1.32] 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: 0.025 sec; CPU: 0.033 sec; Peak RSS: 0.005 GB [M::mm_idx_gen::0.003*1.70] collected minimizers [M::mm_idx_gen::0.005*2.06] sorted minimizers [M::main::0.008*1.66] 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::0.008*1.63] 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: 0.010 sec; CPU: 0.015 sec; Peak RSS: 0.003 GB [M::main::0.005*1.31] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.005*1.28] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.006*1.26] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.024*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: 0.026 sec; CPU: 0.028 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:311: /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-aarch64-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:311: /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-aarch64-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' in '../minimap2_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2405037/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2405037/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2405037 and its subdirectories I: Current time: Thu May 16 16:46:54 +14 2024 I: pbuilder-time-stamp: 1715827614