Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/minimap2/minimap2_2.17+dfsg-12+b3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/minimap2-2.17+dfsg-12+b387f35k3k/minimap2_2.17+dfsg-12+b3_amd64.buildinfo Get source package info: minimap2=2.17+dfsg-12 Source URL: http://snapshot.notset.fr/mr/package/minimap2/2.17+dfsg-12/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 adwaita-icon-theme=3.38.0-1 aglfn=1.7+git20191031.4036a9c-2 apt=2.1.18 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-6 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 cython3=0.29.21-3+b1 d-shlibs=0.98 dash=0.5.11+git20200708+dd9ef66-5 dbus=1.12.20-1 dbus-user-session=1.12.20-1 dconf-gsettings-backend=0.38.0-1 dconf-service=0.38.0-1 debconf=1.5.74 debhelper=13.3.1 debian-archive-keyring=2019.1 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.10.0-1 diffutils=1:3.7-5 dmsetup=2:1.02.175-2 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210118-1 file=1:5.39-3 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 fonts-gfs-baskerville=1.1-6 fonts-gfs-porson=1.1-7 fonts-lmodern=2.004.5-6.1 fonts-urw-base35=20200910-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-3 gettext-base=0.21-3 ghostscript=9.53.3~dfsg-6 glib-networking=2.66.0-2 glib-networking-common=2.66.0-2 glib-networking-services=2.66.0-2 gnuplot=5.4.1+dfsg1-1 gnuplot-data=5.4.1+dfsg1-1 gnuplot-qt=5.4.1+dfsg1-1 gpgv=2.2.20-1 grep=3.6-1 groff-base=1.22.4-5 gsettings-desktop-schemas=3.38.0-2 gtk-update-icon-cache=3.24.24-1 gzip=1.10-2 hicolor-icon-theme=0.17-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libapache-pom-java=18-1 libapparmor1=2.13.6-7 libapt-pkg6.0=2.1.18 libarchive-zip-perl=1.68-1 libargon2-1=0~20171227-0.2 libasan6=10.2.1-6 libatk-bridge2.0-0=2.38.0-1 libatk1.0-0=2.36.0-2 libatk1.0-data=2.36.0-2 libatomic1=10.2.1-6 libatspi2.0-0=2.38.0-2 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libavahi-client3=0.8-3 libavahi-common-data=0.8-3 libavahi-common3=0.8-3 libbinutils=2.35.1-7 libblkid1=2.36.1-6 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo-gobject2=1.16.0-5 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=10.2.1-6 libcolord2=1.4.5-3 libcom-err2=1.45.6-1 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libcryptsetup12=2:2.3.4-2 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libcups2=2.3.3op1-7 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.20-1 libdconf1=0.38.0-1 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdeflate0=1.7-1 libdevmapper1.02.1=2:1.02.175-2 libdouble-conversion3=3.1.5-6.1 libdpkg-perl=1.20.7.1 libdrm-amdgpu1=2.4.103-2 libdrm-common=2.4.103-2 libdrm-intel1=2.4.103-2 libdrm-nouveau2=2.4.103-2 libdrm-radeon1=2.4.103-2 libdrm2=2.4.103-2 libedit2=3.1-20191231-2+b1 libegl-mesa0=20.3.3-1 libegl1=1.3.2-1 libelf1=0.182-3 libepoxy0=1.5.4-1 libevdev2=1.10.1+dfsg-1 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.10.0-1 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgbm1=20.3.3-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgd3=2.3.0-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgdk-pixbuf-2.0-0=2.42.2+dfsg-1 libgdk-pixbuf-xlib-2.0-0=2.40.2-2 libgdk-pixbuf2.0-0=2.40.2-2 libgdk-pixbuf2.0-common=2.42.2+dfsg-1 libgl1=1.3.2-1 libgl1-mesa-dri=20.3.3-1 libglapi-mesa=20.3.3-1 libglib2.0-0=2.66.4-1 libglvnd0=1.3.2-1 libglx-mesa0=20.3.3-1 libglx0=1.3.2-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgs9=9.53.3~dfsg-6 libgs9-common=9.53.3~dfsg-6 libgssapi-krb5-2=1.18.3-4 libgtk-3-0=3.24.24-1 libgtk-3-common=3.24.24-1 libgudev-1.0-0=234-1 libharfbuzz0b=2.7.4-1 libhogweed6=3.6-2 libice6=2:1.0.10-1 libicu67=67.1-6 libidn11=1.33-3 libidn2-0=2.3.0-5 libijs-0.35=0.35-15 libinput-bin=1.16.4-3 libinput10=1.16.4-3 libip4tc2=1.8.7-1 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjbig2dec0=0.19-1 libjpeg62-turbo=1:2.0.5-2 libjson-c5=0.15-1 libjson-glib-1.0-0=1.6.0-2 libjson-glib-1.0-common=1.6.0-2 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkmod2=28-1 libkpathsea6=2020.20200327.54578-6 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblcms2-2=2.12~rc1-2 libllvm11=1:11.0.1-2 liblsan0=10.2.1-6 liblua5.4-0=5.4.2-2 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd4c0=0.4.7-1 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpdec3=2.5.1~rc1-2 libmpfr6=4.1.0-3 libmtdev1=1.1.6-1 libncursesw6=6.2+20201114-2 libnettle8=3.6-2 libnotify4=0.7.9-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenjp2-7=2.3.1-1 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam-systemd=247.2-5 libpam0g=1.4.0-2 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpciaccess0=0.16-1 libpcre2-16-0=10.36-2 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libpdfbox-java=1:1.8.16-2 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libproxy1v5=0.4.17-1 libpsl5=0.21.0-1.1 libptexenc1=2020.20200327.54578-6 libpython3-all-dev=3.9.1-1 libpython3-dev=3.9.1-1 libpython3-stdlib=3.9.1-1 libpython3.9=3.9.1-3 libpython3.9-dev=3.9.1-3 libpython3.9-minimal=3.9.1-3 libpython3.9-stdlib=3.9.1-3 libqt5core5a=5.15.2+dfsg-3 libqt5dbus5=5.15.2+dfsg-3 libqt5gui5=5.15.2+dfsg-3 libqt5network5=5.15.2+dfsg-3 libqt5printsupport5=5.15.2+dfsg-3 libqt5svg5=5.15.2-2 libqt5widgets5=5.15.2+dfsg-3 libquadmath0=10.2.1-6 libreadline8=8.1-1 librest-0.7-0=0.8.1-1.1 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsensors-config=1:3.6.0-6 libsensors5=1:3.6.0-6 libsepol1=3.1-1 libsigsegv2=2.12-3 libsimde-dev=0.7.2-3 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-6 libsoup-gnome2.4-1=2.72.0-2 libsoup2.4-1=2.72.0-2 libsqlite3-0=3.34.1-1 libssl1.1=1.1.1i-2 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsynctex2=2020.20200327.54578-6 libsystemd0=247.2-5 libtasn1-6=4.16.0-2 libteckit0=2.5.10+ds1-3 libtexlua53=2020.20200327.54578-6 libtexluajit2=2020.20200327.54578-6 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-5 libunistring2=0.9.10-4 libuuid1=2.36.1-6 libvulkan1=1.2.162.0-1 libwacom-common=1.7-1 libwacom2=1.7-1 libwayland-client0=1.18.0-2~exp1.1 libwayland-cursor0=1.18.0-2~exp1.1 libwayland-egl1=1.18.0-2~exp1.1 libwayland-server0=1.18.0-2~exp1.1 libwebp6=0.6.1-2+b1 libwxbase3.0-0v5=3.0.5.1+dfsg-2 libwxgtk3.0-gtk3-0v5=3.0.5.1+dfsg-2 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx11-xcb1=2:1.7.0-2 libxau6=1:1.0.8-1+b2 libxaw7=2:1.0.13-1.1 libxcb-dri2-0=1.14-2.1 libxcb-dri3-0=1.14-2.1 libxcb-glx0=1.14-2.1 libxcb-icccm4=0.4.1-1.1 libxcb-image0=0.4.0-1+b3 libxcb-keysyms1=0.4.0-1+b2 libxcb-present0=1.14-2.1 libxcb-randr0=1.14-2.1 libxcb-render-util0=0.3.9-1+b1 libxcb-render0=1.14-2.1 libxcb-shape0=1.14-2.1 libxcb-shm0=1.14-2.1 libxcb-sync1=1.14-2.1 libxcb-util1=0.4.0-1+b1 libxcb-xfixes0=1.14-2.1 libxcb-xinerama0=1.14-2.1 libxcb-xinput0=1.14-2.1 libxcb-xkb1=1.14-2.1 libxcb1=1.14-2.1 libxcomposite1=1:0.4.5-1 libxcursor1=1:1.2.0-2 libxdamage1=1:1.1.5-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxfixes3=1:5.0.3-2 libxi6=2:1.7.10-1 libxinerama1=2:1.1.4-2 libxkbcommon-x11-0=1.0.3-2 libxkbcommon0=1.0.3-2 libxml2=2.9.10+dfsg-6.3+b1 libxmu6=2:1.1.2-2+b3 libxpm4=1:3.5.12-1 libxrandr2=2:1.5.1-1 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxt6=1:1.2.0-1 libxxf86vm1=1:1.1.4-1+b2 libxxhash0=0.8.0-2 libz3-4=4.8.9-1 libzstd1=1.4.8+dfsg-1 libzzip-0-13=0.13.62-3.2 linux-libc-dev=5.10.9-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 mount=2.36.1-6 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 poppler-data=0.4.10-1 preview-latex-style=12.2-1 python3=3.9.1-1 python3-all=3.9.1-1 python3-all-dev=3.9.1-1 python3-dev=3.9.1-1 python3-distutils=3.9.1-2 python3-lib2to3=3.9.1-2 python3-minimal=3.9.1-1 python3.9=3.9.1-3 python3.9-dev=3.9.1-3 python3.9-minimal=3.9.1-3 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 shared-mime-info=2.0-1 systemd=247.2-5 systemd-sysv=247.2-5 systemd-timesyncd=247.2-5 sysvinit-utils=2.96-5 t1utils=1.41-4 tar=1.32+dfsg-1 tex-common=6.15 texlive-base=2020.20210113-1 texlive-binaries=2020.20200327.54578-6 texlive-font-utils=2020.20210113-1 texlive-fonts-recommended=2020.20210113-1 texlive-lang-greek=2020.20210113-1 texlive-latex-base=2020.20210113-1 texlive-latex-extra=2020.20210113-1 texlive-latex-recommended=2020.20210113-1 texlive-pictures=2020.20210113-1 texlive-science=2020.20210113-1 tzdata=2020f-1 ucf=3.0043 util-linux=2.36.1-6 x11-common=1:7.7+21 xdg-utils=1.1.3-4 xkb-data=2.29-2 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210130T024253Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210124T203726Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d minimap2=2.17+dfsg-12 && mkdir -p /build/minimap2-7P2TXG && dpkg-source --no-check -x /*.dsc /build/minimap2-7P2TXG/minimap2-2.17+dfsg && cd /build/minimap2-7P2TXG/minimap2-2.17+dfsg && { printf '%s' 'minimap2 (2.17+dfsg-12+b3) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild using libsimde-dev 0.7.2-3 -- all / amd64 / i386 Build Daemon (x86-conova-01) Wed, 27 Jan 2021 09:48:57 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/minimap2-7P2TXG" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/minimap2-7P2TXG/minimap2-2.17+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611740937" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/minimap2-7P2TXG /tmp/minimap2-2.17+dfsg-12+b387f35k3k bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.8Okn3lYkiW as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.8Okn3lYkiW Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-6). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (932 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4661 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210130T024253Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210124T203726Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.8Okn3lYkiW Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210130T024253Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210124T203726Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210130T024253Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210130T024253Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210130T024253Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210130T024253Z unstable/main amd64 Packages [11.7 MB] Fetched 34.4 MB in 29s (1185 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.8Okn3lYkiW I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d minimap2=2.17+dfsg-12 && mkdir -p /build/minimap2-7P2TXG && dpkg-source --no-check -x /*.dsc /build/minimap2-7P2TXG/minimap2-2.17+dfsg && cd /build/minimap2-7P2TXG/minimap2-2.17+dfsg && { printf '%s' 'minimap2 (2.17+dfsg-12+b3) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild using libsimde-dev 0.7.2-3 -- all / amd64 / i386 Build Daemon (x86-conova-01) Wed, 27 Jan 2021 09:48:57 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/minimap2-7P2TXG"' exec /tmp/mmdebstrap.8Okn3lYkiW Reading package lists... NOTICE: 'minimap2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimap2.git Please use: git clone https://salsa.debian.org/med-team/minimap2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 183 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main minimap2 2.17+dfsg-12 (dsc) [2268 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main minimap2 2.17+dfsg-12 (tar) [170 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main minimap2 2.17+dfsg-12 (diff) [10.7 kB] Fetched 183 kB in 0s (1052 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'minimap2_2.17+dfsg-12.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting minimap2 in /build/minimap2-7P2TXG/minimap2-2.17+dfsg dpkg-source: info: unpacking minimap2_2.17+dfsg.orig.tar.xz dpkg-source: info: unpacking minimap2_2.17+dfsg-12.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 simde dpkg-source: info: applying ar.patch dpkg-source: info: applying link_mappy_to_libminimap.patch dpkg-source: info: applying python-sse4-arch.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/minimap2-7P2TXG/minimap2-2.17+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611740937" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.8Okn3lYkiW dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.17+dfsg-12+b3 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_auto_clean make -j4 clean make[2]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+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/minimap2-7P2TXG/minimap2-2.17+dfsg' rm -f MT-human.mmi rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf rm -f libminimap2.a make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' dh_clean debian/rules binary-arch debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_auto_build -- amd64=1 make -j4 "INSTALL=install --strip-program=true" amd64=1 make[2]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC main.c -o main.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kthread.c -o kthread.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC misc.c -o misc.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC bseq.c -o bseq.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sketch.c -o sketch.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sdust.c -o sdust.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC options.c -o options.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC index.c -o index.o index.c: In function ‘mm_idx_load’: index.c:495:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 495 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:498:4: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 498 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:501:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 501 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:510:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 510 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:512:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 512 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:513:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 513 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:520:4: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 520 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:528:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 528 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC chain.c -o chain.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC align.c -o align.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC hit.c -o hit.o hit.c: In function ‘mm_gen_regs’: hit.c:74:18: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 74 | r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hit.c:2: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC map.c -o map.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC format.c -o format.o format.c: In function ‘mm_write_sam3’: format.c:391:36: warning: variable ‘this_rev’ set but not used [-Wunused-but-set-variable] 391 | int this_rid = -1, this_pos = -1, this_rev = 0; | ^~~~~~~~ cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC pe.c -o pe.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC esterr.c -o esterr.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC splitidx.c -o splitidx.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC ksw2_extz2_sse.c -o ksw2_extz2_sse.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC ksw2_extd2_sse.c -o ksw2_extd2_sse.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC ksw2_exts2_sse.c -o ksw2_exts2_sse.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o rm -f libminimap2.a ar csrD libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o cc -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' cd tex && make make[2]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg/tex' gnuplot roc.gp epstopdf --outfile roc-color.pdf roc-color.eps pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2; This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-01-09> xparse <2020-03-03> (./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 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This is BibTeX, Version 0.99d (TeX Live 2020/Debian) The top-level auxiliary file: minimap2.aux The style file: apalike.bst Database file #1: minimap2.bib This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-01-09> xparse <2020-03-03> (./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/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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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 Underfull \hbox (badness 1642) in paragraph at lines 20--24 []\OT1/ptm/m/n/9 Berlin, K. et al. (2015). Assembling large genomes with 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 2635) in paragraph at lines 32--36 []\OT1/ptm/m/n/9 Chaisson, M. J. and Tesler, G. (2012). Mapping single Underfull \hbox (badness 10000) in paragraph at lines 55--59 \OT1/ptm/m/n/9 searches six times over other SIMD implementations. Underfull \hbox (badness 5578) in paragraph at lines 90--95 \OT1/ptm/m/n/9 of a human genome with ultra-long reads. \OT1/ptm/m/it/9 bioRxi v\OT1/ptm/m/n/9 . 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] 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){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on minimap2.pdf (6 pages, 249712 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-01-09> xparse <2020-03-03> (./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/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Font Warning: Font shape `OML/cmm/m/it' in size <6.5> not available (Font) size <6> substituted on input line 58. LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <6.5> not available (Font) size <6> substituted on input line 58. Underfull \hbox (badness 1478) in paragraph at lines 71--80 \OT1/ptm/m/n/9 minor modifications could enable the base algorithm to map Underfull \hbox (badness 1019) in paragraph at lines 71--80 \OT1/ptm/m/n/9 mRNAs as well. Minimap2 becomes a first RNA-seq aligner [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 204. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (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 1642) in paragraph at lines 20--24 []\OT1/ptm/m/n/9 Berlin, K. et al. (2015). Assembling large genomes with Underfull \hbox (badness 2635) in paragraph at lines 32--36 []\OT1/ptm/m/n/9 Chaisson, M. J. and Tesler, G. (2012). Mapping single Underfull \hbox (badness 10000) in paragraph at lines 55--59 \OT1/ptm/m/n/9 searches six times over other SIMD implementations. Underfull \hbox (badness 5578) in paragraph at lines 90--95 \OT1/ptm/m/n/9 of a human genome with ultra-long reads. \OT1/ptm/m/it/9 bioRxi v\OT1/ptm/m/n/9 . 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){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on minimap2.pdf (6 pages, 253333 bytes). Transcript written on minimap2.log. make[2]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg/tex' dh_auto_build --buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_ext cythoning python/mappy.pyx to python/mappy.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/minimap2-7P2TXG/minimap2-2.17+dfsg/python/mappy.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'mappy' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/python x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c align.c -o build/temp.linux-x86_64-3.9/align.o -DHAVE_KALLOC -msse4.1 align.c: In function ‘mm_get_hplen_back’: align.c:346:29: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 346 | if (mm_seq4_get(mi->S, i) != c) break; | ^~ align.c: In function ‘mm_seed_ext_score’: align.c:533:49: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 533 | 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:620:45: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 620 | re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len; | ^~~~~~ align.c:672:44: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 672 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re; | ^ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c bseq.c -o build/temp.linux-x86_64-3.9/bseq.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c chain.c -o build/temp.linux-x86_64-3.9/chain.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c esterr.c -o build/temp.linux-x86_64-3.9/esterr.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c format.c -o build/temp.linux-x86_64-3.9/format.o -DHAVE_KALLOC -msse4.1 format.c: In function ‘mm_event_identity’: format.c:268:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 268 | for (i = 0; i < r->p->n_cigar; ++i) { | ^ format.c: In function ‘mm_write_sam3’: format.c:391:36: warning: variable ‘this_rev’ set but not used [-Wunused-but-set-variable] 391 | int this_rid = -1, this_pos = -1, this_rev = 0; | ^~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c hit.c -o build/temp.linux-x86_64-3.9/hit.o -DHAVE_KALLOC -msse4.1 hit.c: In function ‘mm_hit_sort’: hit.c:171:48: warning: variable ‘no_cigar’ set but not used [-Wunused-but-set-variable] 171 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~ hit.c:171:33: warning: variable ‘has_cigar’ set but not used [-Wunused-but-set-variable] 171 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~~ hit.c: In function ‘mm_join_long’: hit.c:324:40: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 324 | max_gap = a0e->x + max_gap > a1s->x? max_gap : a1s->x - a0e->x; | ^~~~~~~ hit.c:325:40: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 325 | min_gap = a0e->x + min_gap < a1s->x? min_gap : a1s->x - a0e->x; | ^~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c index.c -o build/temp.linux-x86_64-3.9/index.o -DHAVE_KALLOC -msse4.1 index.c: In function ‘mm_idx_name2id’: index.c:149:25: 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:358:63: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 358 | 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:458:16: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 458 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function ‘mm_idx_load’: index.c:505:16: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 505 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function ‘mm_idx_bed_read’: index.c:698:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 698 | for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals | ^ index.c: In function ‘mm_idx_bed_junc’: index.c:708:35: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 708 | if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1; | ^~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c kalloc.c -o build/temp.linux-x86_64-3.9/kalloc.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_extd2_sse.c -o build/temp.linux-x86_64-3.9/ksw2_extd2_sse.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_exts2_sse.c -o build/temp.linux-x86_64-3.9/ksw2_exts2_sse.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_extz2_sse.c -o build/temp.linux-x86_64-3.9/ksw2_extz2_sse.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_ll_sse.c -o build/temp.linux-x86_64-3.9/ksw2_ll_sse.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c kthread.c -o build/temp.linux-x86_64-3.9/kthread.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c map.c -o build/temp.linux-x86_64-3.9/map.o -DHAVE_KALLOC -msse4.1 map.c: In function ‘mm_dust_minier’: map.c:52:42: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘const long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 52 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32; | ^ map.c:53:36: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 53 | int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v]; | ^ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c misc.c -o build/temp.linux-x86_64-3.9/misc.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c options.c -o build/temp.linux-x86_64-3.9/options.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c pe.c -o build/temp.linux-x86_64-3.9/pe.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c python/mappy.c -o build/temp.linux-x86_64-3.9/python/mappy.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c sdust.c -o build/temp.linux-x86_64-3.9/sdust.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c sketch.c -o build/temp.linux-x86_64-3.9/sketch.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c splitidx.c -o build/temp.linux-x86_64-3.9/splitidx.o -DHAVE_KALLOC -msse4.1 x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/minimap2-7P2TXG/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/align.o build/temp.linux-x86_64-3.9/bseq.o build/temp.linux-x86_64-3.9/chain.o build/temp.linux-x86_64-3.9/esterr.o build/temp.linux-x86_64-3.9/format.o build/temp.linux-x86_64-3.9/hit.o build/temp.linux-x86_64-3.9/index.o build/temp.linux-x86_64-3.9/kalloc.o build/temp.linux-x86_64-3.9/ksw2_extd2_sse.o build/temp.linux-x86_64-3.9/ksw2_exts2_sse.o build/temp.linux-x86_64-3.9/ksw2_extz2_sse.o build/temp.linux-x86_64-3.9/ksw2_ll_sse.o build/temp.linux-x86_64-3.9/kthread.o build/temp.linux-x86_64-3.9/map.o build/temp.linux-x86_64-3.9/misc.o build/temp.linux-x86_64-3.9/options.o build/temp.linux-x86_64-3.9/pe.o build/temp.linux-x86_64-3.9/python/mappy.o build/temp.linux-x86_64-3.9/sdust.o build/temp.linux-x86_64-3.9/sketch.o build/temp.linux-x86_64-3.9/splitidx.o -lz -lm -lpthread -o /build/minimap2-7P2TXG/minimap2-2.17+dfsg/.pybuild/cpython3_3.9/build/mappy.cpython-39-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.9 copying and adjusting python/minimap2.py -> build/scripts-3.9 changing mode of build/scripts-3.9/minimap2.py from 644 to 755 make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' debian/test_script [M::mm_idx_gen::0.013*0.40] collected minimizers [M::mm_idx_gen::0.017*0.46] sorted minimizers [M::main::0.017*0.46] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.018*0.48] mid_occ = 2 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.018*0.48] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 [M::worker_pipeline::0.052*0.78] mapped 1 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa [M::main] Real time: 0.053 sec; CPU: 0.041 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.003*1.50] collected minimizers [M::mm_idx_gen::0.004*1.85] sorted minimizers [M::main::0.007*1.44] 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::0.007*1.42] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa [M::main] Real time: 0.008 sec; CPU: 0.011 sec; Peak RSS: 0.004 GB [M::main::0.004*1.19] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.004*1.18] mid_occ = 2 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.005*1.17] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 [M::worker_pipeline::0.057*0.71] mapped 1 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa [M::main] Real time: 0.059 sec; CPU: 0.042 sec; Peak RSS: 0.006 GB rm test.sam make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_auto_install dh_auto_install --buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp running install running build running build_ext skipping 'python/mappy.c' Cython extension (up-to-date) running build_scripts running install_lib creating /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr creating /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/lib creating /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/lib/python3.9 creating /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/lib/python3.9/dist-packages copying /build/minimap2-7P2TXG/minimap2-2.17+dfsg/.pybuild/cpython3_3.9/build/mappy.cpython-39-x86_64-linux-gnu.so -> /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/lib/python3.9/dist-packages running install_scripts creating /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/bin copying build/scripts-3.9/minimap2.py -> /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/bin changing mode of /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/bin/minimap2.py to 755 running install_egg_info Writing /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/mappy-2.17.egg-info make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_installman --language=C make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' dh_python3 -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' dh_fixperms -a dh_missing -a dh_dwz -a -a debian/rules override_dh_strip make[1]: Entering directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_strip ranlib /build/minimap2-7P2TXG/minimap2-2.17+dfsg/debian/libminimap2-dev/usr/lib/libminimap2.a make[1]: Leaving directory '/build/minimap2-7P2TXG/minimap2-2.17+dfsg' dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libminimap2-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-mappy: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-mappy: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-mappy: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-mappy: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.17+dfsg-12+b3_amd64.deb'. dpkg-deb: building package 'minimap2' in '../minimap2_2.17+dfsg-12+b3_amd64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.17+dfsg-12+b3_amd64.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.17+dfsg-12+b3_amd64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.17+dfsg-12+b3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../minimap2_2.17+dfsg-12+b3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/minimap2-7P2TXG /tmp/minimap2-2.17+dfsg-12+b387f35k3k I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.8Okn3lYkiW... I: success in 898.1297 seconds md5: libminimap2-dev_2.17+dfsg-12+b3_amd64.deb: OK md5: minimap2-dbgsym_2.17+dfsg-12+b3_amd64.deb: OK md5: minimap2_2.17+dfsg-12+b3_amd64.deb: OK md5: python3-mappy-dbgsym_2.17+dfsg-12+b3_amd64.deb: OK md5: python3-mappy_2.17+dfsg-12+b3_amd64.deb: OK sha1: libminimap2-dev_2.17+dfsg-12+b3_amd64.deb: OK sha1: minimap2-dbgsym_2.17+dfsg-12+b3_amd64.deb: OK sha1: minimap2_2.17+dfsg-12+b3_amd64.deb: OK sha1: python3-mappy-dbgsym_2.17+dfsg-12+b3_amd64.deb: OK sha1: python3-mappy_2.17+dfsg-12+b3_amd64.deb: OK sha256: libminimap2-dev_2.17+dfsg-12+b3_amd64.deb: OK sha256: minimap2-dbgsym_2.17+dfsg-12+b3_amd64.deb: OK sha256: minimap2_2.17+dfsg-12+b3_amd64.deb: OK sha256: python3-mappy-dbgsym_2.17+dfsg-12+b3_amd64.deb: OK sha256: python3-mappy_2.17+dfsg-12+b3_amd64.deb: OK Checksums: OK