minimap2 →
2.27+dfsg-1 →
armhf → 2024-06-11 12:47:35
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| minimap2 2.27+dfsg-1 (armhf) Tue, 11 Jun 2024 12:09:14 +0000 |
+==============================================================================+
Package: minimap2
Version: 2.27+dfsg-1
Source Version: 2.27+dfsg-1
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-faf43c28-5617-4494-97ab-bef7c03f6969' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/minimap2-fKUGH3/resolver-iaS7p6' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Ign:1 http://172.17.4.1/private trixie-staging InRelease
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.6 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.3 MB]
Ign:3 http://172.17.4.1/private trixie-staging/main armhf Packages
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.3 MB]
Ign:3 http://172.17.4.1/private trixie-staging/main armhf Packages
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.3 MB]
Fetched 24.2 MB in 3min 1s (134 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
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 214 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main minimap2 2.27+dfsg-1 (dsc) [2315 B]
Get:2 http://172.17.4.1/private trixie-staging/main minimap2 2.27+dfsg-1 (tar) [200 kB]
Get:3 http://172.17.4.1/private trixie-staging/main minimap2 2.27+dfsg-1 (diff) [11.5 kB]
Fetched 214 kB in 40s (5313 B/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/minimap2-fKUGH3/minimap2-2.27+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/minimap2-fKUGH3' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox, libsimde-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates cron cron-daemon-common dbus dbus-bin dbus-daemon
dbus-session-bus-common dbus-system-bus-common dmsetup
libalgorithm-diff-perl libalgorithm-merge-perl libapparmor1
libarchive-cpio-perl libcryptsetup12 libdevmapper1.02.1 libfdisk1
libfile-fcntllock-perl libjson-c5 libkmod2 libltdl-dev libltdl7
libmail-sendmail-perl libsys-hostname-long-perl libsystemd-shared openssl
systemd systemd-dev systemd-timesyncd util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
aglfn cython3 d-shlibs dh-python fontconfig fontconfig-config
fonts-dejavu-core fonts-dejavu-mono fonts-gfs-baskerville fonts-gfs-porson
fonts-lmodern fonts-urw-base35 ghostscript gnuplot-data gnuplot-nox
libabsl20230802 libaom3 libapache-pom-java libavahi-client3
libavahi-common-data libavahi-common3 libavif16 libbrotli1 libbsd0 libcairo2
libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1
libdav1d7 libde265-0 libdeflate0 libedit2 libexpat1-dev libfontbox-java
libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgd3
libglib2.0-0t64 libgraphite2-3 libgs-common libgs10 libgs10-common
libgssapi-krb5-2 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265
libheif1 libice6 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo
libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkpathsea6
libkrb5-3 liblcms2-2 liblerc4 liblua5.4-0 libnsl2 libopenjp2-7
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpdfbox-java libpixman-1-0 libpng16-16t64 libpotrace0
libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
libpython3.11t64 libpython3.12-dev libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 librav1e0 libsharpyuv0 libsimde-dev
libsm6 libsvtav1enc1d1 libsynctex2 libteckit0 libtexlua53-5 libthai-data
libthai0 libtiff6 libtirpc3t64 libwebp7 libwebpmux3 libx11-6 libx11-data
libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6
libxmu6 libxpm4 libxrender1 libxt6t64 libyuv0 libzzip-0-13t64 media-types
poppler-data preview-latex-style python3 python3-all python3-all-dev
python3-dev python3-distutils python3-lib2to3 python3-minimal
python3-pkg-resources python3-setuptools python3.11 python3.11-dev
python3.11-minimal python3.12 python3.12-dev python3.12-minimal t1utils
tex-common texlive-base texlive-binaries texlive-font-utils
texlive-fonts-recommended texlive-lang-greek texlive-latex-base
texlive-latex-extra texlive-latex-recommended texlive-pictures
texlive-science ucf x11-common xdg-utils xfonts-encodings xfonts-utils
zlib1g-dev
Suggested packages:
cython-doc flit python3-build python3-installer python3-wheel
fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gnuplot-doc
libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java
cups-common libgd-tools low-memory-monitor krb5-doc krb5-user
libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc
libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e
libheif-plugin-svtenc liblcms2-utils poppler-utils fonts-japanese-mincho
| fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic
fonts-arphic-ukai fonts-arphic-uming fonts-nanum python3-doc python3-tk
python3-venv python-setuptools-doc python3.11-venv python3.11-doc
binfmt-support python3.12-venv python3.12-doc perl-tk xpdf | pdf-viewer
xzdec texlive-binaries-sse2 hintview lcdf-typetools psutils
texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex
python3-pygments icc-profiles libfile-which-perl texlive-latex-extra-doc
texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex
texlive-pictures-doc vprerex texlive-science-doc
Recommended packages:
fonts-liberation groff libglib2.0-data shared-mime-info xdg-user-dirs
fonts-droid-fallback libheif-plugin-aomenc libheif-plugin-x265
javascript-common krb5-locales lmodern dvisvgm ps2eps tex-gyre tipa
default-jre libspreadsheet-parseexcel-perl texlive-plain-generic ruby tk
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
aglfn cython3 d-shlibs dh-python fontconfig fontconfig-config
fonts-dejavu-core fonts-dejavu-mono fonts-gfs-baskerville fonts-gfs-porson
fonts-lmodern fonts-urw-base35 ghostscript gnuplot-data gnuplot-nox
libabsl20230802 libaom3 libapache-pom-java libavahi-client3
libavahi-common-data libavahi-common3 libavif16 libbrotli1 libbsd0 libcairo2
libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1
libdav1d7 libde265-0 libdeflate0 libedit2 libexpat1-dev libfontbox-java
libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgav1-1 libgd3
libglib2.0-0t64 libgraphite2-3 libgs-common libgs10 libgs10-common
libgssapi-krb5-2 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265
libheif1 libice6 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo
libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkpathsea6
libkrb5-3 liblcms2-2 liblerc4 liblua5.4-0 libnsl2 libopenjp2-7
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpdfbox-java libpixman-1-0 libpng16-16t64 libpotrace0
libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
libpython3.11t64 libpython3.12-dev libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 librav1e0 libsharpyuv0 libsimde-dev
libsm6 libsvtav1enc1d1 libsynctex2 libteckit0 libtexlua53-5 libthai-data
libthai0 libtiff6 libtirpc3t64 libwebp7 libwebpmux3 libx11-6 libx11-data
libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6
libxmu6 libxpm4 libxrender1 libxt6t64 libyuv0 libzzip-0-13t64 media-types
poppler-data preview-latex-style python3 python3-all python3-all-dev
python3-dev python3-distutils python3-lib2to3 python3-minimal
python3-pkg-resources python3-setuptools python3.11 python3.11-dev
python3.11-minimal python3.12 python3.12-dev python3.12-minimal
sbuild-build-depends-main-dummy t1utils tex-common texlive-base
texlive-binaries texlive-font-utils texlive-fonts-recommended
texlive-lang-greek texlive-latex-base texlive-latex-extra
texlive-latex-recommended texlive-pictures texlive-science ucf x11-common
xdg-utils xfonts-encodings xfonts-utils zlib1g-dev
0 upgraded, 156 newly installed, 0 to remove and 23 not upgraded.
Need to get 243 MB/243 MB of archives.
After this operation, 682 MB of additional disk space will be used.
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Get:19 http://172.17.4.1/private trixie-staging/main armhf cython3 armhf 3.0.10+dfsg-5 [3154 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf d-shlibs all 0.106 [10.9 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
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Get:24 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20240422 [107 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
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Get:30 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libfontenc1 armhf 1:1.1.8-1 [20.8 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf xfonts-utils armhf 1:7.7+6 [82.5 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.15.0-1.1 [369 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf fontconfig armhf 2.15.0-1.1 [461 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf fonts-gfs-baskerville all 1.1-6 [43.7 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf fonts-gfs-porson all 1.1-7 [33.8 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf fonts-lmodern all 2.005-1 [4540 kB]
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Get:84 http://172.17.4.1/private trixie-staging/main armhf librav1e0 armhf 0.7.1-2 [553 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libsvtav1enc1d1 armhf 1.7.0+dfsg-2 [884 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libyuv0 armhf 0.0.1888.20240509-4 [83.2 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libavif16 armhf 1.0.4-3 [94.3 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-dav1d armhf 1.17.6-1+b1 [9568 B]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libde265-0 armhf 1.0.15-1+rpi1+b1 [140 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-libde265 armhf 1.17.6-1+b1 [12.5 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libheif1 armhf 1.17.6-1+b1 [237 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libxpm4 armhf 1:3.5.17-1+b1 [49.7 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libgd3 armhf 2.3.3-9+b3 [103 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0t64 armhf 2.80.2-2 [1287 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf liblua5.4-0 armhf 5.4.6-3+b1 [120 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libfribidi0 armhf 1.0.13-3+b1 [70.0 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libgraphite2-3 armhf 1.3.14-2 [62.8 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libharfbuzz0b armhf 8.3.0-2+b1 [2152 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libthai-data all 0.1.29-2 [168 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libdatrie1 armhf 0.2.13-3 [34.3 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libthai0 armhf 0.1.29-2 [46.1 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libpango-1.0-0 armhf 1.52.2+ds-1 [192 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libpangoft2-1.0-0 armhf 1.52.2+ds-1 [41.5 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libpangocairo-1.0-0 armhf 1.52.2+ds-1 [31.0 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf libwebpmux3 armhf 1.4.0-0.1 [120 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf gnuplot-nox armhf 6.0.0+dfsg1-3 [757 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libapache-pom-java all 29-2 [5276 B]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libcommons-parent-java all 56-1 [10.8 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libexpat1-dev armhf 2.6.2-1 [136 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libfontbox-java all 1:1.8.16-5 [211 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libjs-sphinxdoc all 7.2.6-8 [150 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libkpathsea6 armhf 2023.20230311.66589-9 [144 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libpaper-utils armhf 1.1.29 [8416 B]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libpdfbox-java all 1:1.8.16-5 [5527 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libpotrace0 armhf 1.16-2 [23.6 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libptexenc1 armhf 2023.20230311.66589-9 [42.9 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf libpython3.11t64 armhf 3.11.9-1+b1 [1639 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [903 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-dev armhf 3.11.9-1+b1 [2939 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libpython3-dev armhf 3.11.8-1 [9560 B]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libpython3.12-stdlib armhf 3.12.3-1+b1 [1791 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf libpython3.12t64 armhf 3.12.3-1+b1 [1766 kB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf libpython3.12-dev armhf 3.12.3-1+b1 [4216 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf libpython3-all-dev armhf 3.11.8-1 [1072 B]
Get:128 http://172.17.4.1/private trixie-staging/main armhf libsimde-dev all 0.8.2-1 [465 kB]
Get:129 http://172.17.4.1/private trixie-staging/main armhf libsynctex2 armhf 2023.20230311.66589-9 [48.4 kB]
Get:130 http://172.17.4.1/private trixie-staging/main armhf libteckit0 armhf 2.5.12+ds1-1 [259 kB]
Get:131 http://172.17.4.1/private trixie-staging/main armhf libtexlua53-5 armhf 2023.20230311.66589-9 [82.9 kB]
Get:132 http://172.17.4.1/private trixie-staging/main armhf libxmu6 armhf 2:1.1.3-3+b2 [50.7 kB]
Get:133 http://172.17.4.1/private trixie-staging/main armhf libxaw7 armhf 2:1.0.14-1+b2 [163 kB]
Get:134 http://172.17.4.1/private trixie-staging/main armhf libxi6 armhf 2:1.8.1-1 [73.4 kB]
Get:135 http://172.17.4.1/private trixie-staging/main armhf libzzip-0-13t64 armhf 0.13.72+dfsg.1-1.2 [52.7 kB]
Get:136 http://172.17.4.1/private trixie-staging/main armhf tex-common all 6.18 [32.5 kB]
Get:137 http://172.17.4.1/private trixie-staging/main armhf preview-latex-style all 13.2-1 [350 kB]
Get:138 http://172.17.4.1/private trixie-staging/main armhf python3.12 armhf 3.12.3-1+b1 [660 kB]
Get:139 http://172.17.4.1/private trixie-staging/main armhf python3-all armhf 3.11.8-1 [1056 B]
Get:140 http://172.17.4.1/private trixie-staging/main armhf python3.11-dev armhf 3.11.9-1+b1 [501 kB]
Get:141 http://172.17.4.1/private trixie-staging/main armhf python3-dev armhf 3.11.8-1 [26.1 kB]
Get:142 http://172.17.4.1/private trixie-staging/main armhf python3.12-dev armhf 3.12.3-1+b1 [499 kB]
Get:143 http://172.17.4.1/private trixie-staging/main armhf python3-all-dev armhf 3.11.8-1 [1072 B]
Get:144 http://172.17.4.1/private trixie-staging/main armhf t1utils armhf 1.41-4 [52.3 kB]
Get:145 http://172.17.4.1/private trixie-staging/main armhf texlive-binaries armhf 2023.20230311.66589-9 [5566 kB]
Get:146 http://172.17.4.1/private trixie-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:147 http://172.17.4.1/private trixie-staging/main armhf texlive-base all 2023.20240207-1 [22.0 MB]
Get:148 http://172.17.4.1/private trixie-staging/main armhf texlive-font-utils all 2023.20240207-1 [7046 kB]
Get:149 http://172.17.4.1/private trixie-staging/main armhf texlive-fonts-recommended all 2023.20240207-1 [4990 kB]
Get:150 http://172.17.4.1/private trixie-staging/main armhf texlive-lang-greek all 2023.20240207-1 [79.2 MB]
Get:151 http://172.17.4.1/private trixie-staging/main armhf texlive-latex-base all 2023.20240207-1 [1255 kB]
Get:152 http://172.17.4.1/private trixie-staging/main armhf texlive-latex-recommended all 2023.20240207-1 [8843 kB]
Get:153 http://172.17.4.1/private trixie-staging/main armhf texlive-pictures all 2023.20240207-1 [16.7 MB]
Get:154 http://172.17.4.1/private trixie-staging/main armhf texlive-latex-extra all 2023.20240207-1 [19.7 MB]
Get:155 http://172.17.4.1/private trixie-staging/main armhf texlive-science all 2023.20240207-1 [3804 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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invoke-rc.d: could not determine current runlevel
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Setting up libde265-0:armhf (1.0.15-1+rpi1+b1) ...
Setting up libwebpmux3:armhf (1.4.0-0.1) ...
Setting up libbsd0:armhf (0.12.2-1) ...
Setting up libyuv0:armhf (0.0.1888.20240509-4) ...
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:armhf (2023.20230311.66589-9) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up libpotrace0:armhf (1.16-2) ...
Setting up python3.12-minimal (3.12.3-1+b1) ...
Setting up gnuplot-data (6.0.0+dfsg1-3) ...
Setting up libpaper1:armhf (1.1.29) ...
Creating config file /etc/papersize with new version
Setting up libice6:armhf (2:1.0.10-1+b1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libxcb1:armhf (1.17.0-2) ...
Setting up libpdfbox-java (1:1.8.16-5) ...
Setting up libpython3.12-stdlib:armhf (3.12.3-1+b1) ...
Setting up libxcb-render0:armhf (1.17.0-2) ...
Setting up fontconfig-config (2.15.0-1.1) ...
Setting up python3.12 (3.12.3-1+b1) ...
Setting up libedit2:armhf (3.1-20240517-1) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:armhf (0.8-13+b2) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxcb-shm0:armhf (1.17.0-2) ...
Setting up libpaper-utils (1.1.29) ...
Setting up libpython3.12t64:armhf (3.12.3-1+b1) ...
Setting up tex-common (6.18) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libthai0:armhf (0.1.29-2) ...
Setting up libptexenc1:armhf (2023.20230311.66589-9) ...
Setting up libfreetype6:armhf (2.13.2+dfsg-1+b4) ...
Setting up libgssapi-krb5-2:armhf (1.20.1-6+b4) ...
Setting up libgav1-1:armhf (0.19.0-2+rpi1) ...
Setting up libjs-sphinxdoc (7.2.6-8) ...
Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libharfbuzz0b:armhf (8.3.0-2+b1) ...
Setting up libfontconfig1:armhf (2.15.0-1.1) ...
Setting up libsm6:armhf (2:1.2.3-1+b1) ...
Setting up libavahi-client3:armhf (0.8-13+b2) ...
Setting up fontconfig (2.15.0-1.1) ...
Regenerating fonts cache... done.
Setting up libavif16:armhf (1.0.4-3) ...
Setting up libxpm4:armhf (1:3.5.17-1+b1) ...
Setting up libxrender1:armhf (1:0.9.10-1.1+b1) ...
Setting up libtirpc3t64:armhf (1.3.4+ds-1.3) ...
Setting up preview-latex-style (13.2-1) ...
Setting up libpango-1.0-0:armhf (1.52.2+ds-1) ...
Setting up libxext6:armhf (2:1.3.4-1+b1) ...
Setting up libpython3.12-dev:armhf (3.12.3-1+b1) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up libcairo2:armhf (1.18.0-3+b1) ...
Setting up libxt6t64:armhf (1:1.2.1-1.2) ...
Setting up python3.12-dev (3.12.3-1+b1) ...
Setting up libnsl2:armhf (1.3.0-3+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.52.2+ds-1) ...
Setting up libcups2t64:armhf (2.4.7-1.2) ...
Setting up libpangocairo-1.0-0:armhf (1.52.2+ds-1) ...
Setting up libxmu6:armhf (2:1.1.3-3+b2) ...
Setting up libxi6:armhf (2:1.8.1-1) ...
Setting up libpython3.11-stdlib:armhf (3.11.9-1+b1) ...
Setting up libpython3.11t64:armhf (3.11.9-1+b1) ...
Setting up libxaw7:armhf (2:1.0.14-1+b2) ...
Setting up fonts-urw-base35 (20200910-8) ...
Setting up libpython3.11-dev:armhf (3.11.9-1+b1) ...
Setting up texlive-binaries (2023.20230311.66589-9) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up 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 libpython3-stdlib:armhf (3.11.8-1) ...
Setting up libgs10-common (10.03.1~dfsg-1) ...
Setting up python3.11 (3.11.9-1+b1) ...
Setting up libpython3-dev:armhf (3.11.8-1) ...
Setting up python3.11-dev (3.11.9-1+b1) ...
Setting up python3 (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 libpython3-all-dev:armhf (3.11.8-1) ...
Setting up texlive-latex-recommended (2023.20240207-1) ...
Setting up cython3 (3.0.10+dfsg-5) ...
Setting up texlive-pictures (2023.20240207-1) ...
Setting up texlive-fonts-recommended (2023.20240207-1) ...
Setting up python3-lib2to3 (3.12.3-3.1) ...
Setting up libgs10:armhf (10.03.1~dfsg-1) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up python3-distutils (3.12.3-3.1) ...
python3.12: can't get files for byte-compilation
Setting up python3-setuptools (68.1.2-2) ...
Setting up texlive-science (2023.20240207-1) ...
Setting up python3-all (3.11.8-1) ...
Setting up texlive-latex-extra (2023.20240207-1) ...
Setting up ghostscript (10.03.1~dfsg-1) ...
Setting up python3-dev (3.11.8-1) ...
Setting up dh-python (6.20240422) ...
Setting up python3-all-dev (3.11.8-1) ...
Setting up libheif-plugin-dav1d:armhf (1.17.6-1+b1) ...
Setting up libheif-plugin-libde265:armhf (1.17.6-1+b1) ...
Setting up libheif1:armhf (1.17.6-1+b1) ...
Setting up libgd3:armhf (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 sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.38-8+rpi1) ...
Processing triggers for systemd (255.3-1+rpi1+b1) ...
Processing triggers for man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
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.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.41-6+rpi1+b1 dpkg-dev_1.22.6+rpi1 g++-12_12.3.0-14+rpi1 g++-13_13.2.0-16.1+rpi1 gcc-12_12.3.0-14+rpi1 gcc-13_13.2.0-16.1+rpi1 libc6-dev_2.38-8+rpi1 libstdc++-12-dev_12.3.0-14+rpi1 libstdc++-13-dev_13.2.0-16.1+rpi1 libstdc++6_14-20240221-2.1+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 aglfn_1.7+git20191031.4036a9c-2 apt_2.9.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1+b1 binutils-arm-linux-gnueabihf_2.41-6+rpi1+b1 binutils-common_2.41-6+rpi1+b1 bsdextrautils_2.40.1-4+rpi1 bsdutils_1:2.40.1-4+rpi1 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3.1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-14+rpi1 cpp-13_13.2.0-16.1+rpi1 cpp-13-arm-linux-gnueabihf_13.2.0-16.1+rpi1 cron_3.0pl1-189 cron-daemon-common_3.0pl1-189 cython3_3.0.10+dfsg-5 d-shlibs_0.106 dash_0.5.12-8 dbus_1.14.10-4+b1 dbus-bin_1.14.10-4+b1 dbus-daemon_1.14.10-4+b1 dbus-session-bus-common_1.14.10-4 dbus-system-bus-common_1.14.10-4 debconf_1.5.86 debhelper_13.15.3 debianutils_5.17 dh-autoreconf_20 dh-python_6.20240422 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dmsetup_2:1.02.196-1 dpkg_1.22.6+rpi1 dpkg-dev_1.22.6+rpi1 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libpython3.11t64_3.11.9-1+b1 libpython3.12-dev_3.12.3-1+b1 libpython3.12-minimal_3.12.3-1+b1 libpython3.12-stdlib_3.12.3-1+b1 libpython3.12t64_3.12.3-1+b1 librav1e0_0.7.1-2 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+rpi1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b1 libsepol1_3.1-1 libsepol2_3.5-2+b1 libsframe1_2.41-6+rpi1+b1 libsharpyuv0_1.4.0-0.1 libsimde-dev_0.8.2-1 libsm6_2:1.2.3-1+b1 libsmartcols1_2.40.1-4+rpi1 libsqlite3-0_3.45.3-1 libss2_1.47.1-1 libssl1.1_1.1.1o-1 libssl3t64_3.2.1-3 libstdc++-12-dev_12.3.0-14+rpi1 libstdc++-13-dev_13.2.0-16.1+rpi1 libstdc++6_14-20240221-2.1+rpi1 libsvtav1enc1d1_1.7.0+dfsg-2 libsynctex2_2023.20230311.66589-9 libsys-hostname-long-perl_1.5-3 libsystemd-shared_255.3-1+rpi1+b1 libsystemd0_255.3-1+rpi1+b1 libtasn1-6_4.19.0-3+b2 libteckit0_2.5.12+ds1-1 libtexlua53-5_2023.20230311.66589-9 libthai-data_0.1.29-2 libthai0_0.1.29-2 libtiff6_4.5.1+git230720-4 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtool_2.4.7-7 libubsan1_14-20240221-2.1+rpi1 libuchardet0_0.0.8-1 libudev1_255.3-1+rpi1+b1 libunistring2_1.0-2 libunistring5_1.2-1 libuuid1_2.40.1-4+rpi1 libwebp7_1.4.0-0.1 libwebpmux3_1.4.0-0.1 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1+b2 libxcb-render0_1.17.0-2 libxcb-shm0_1.17.0-2 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1+b1 libxi6_2:1.8.1-1 libxml2_2.9.14+dfsg-1.3+b4 libxmu6_2:1.1.3-3+b2 libxpm4_1:3.5.17-1+b1 libxrender1_1:0.9.10-1.1+b1 libxt6t64_1:1.2.1-1.2 libxxhash0_0.8.2-2+b1 libyuv0_0.0.1888.20240509-4 libzstd1_1.5.5+dfsg2-2 libzzip-0-13t64_0.13.72+dfsg.1-1.2 linux-libc-dev_6.5.6-1+rpi1+b1 login_1:4.13+dfsg1-4 logsave_1.47.1-1 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 media-types_10.1.0 mount_2.40.1-4+rpi1 nano_8.0-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openssl_3.2.1-3 passwd_1:4.13+dfsg1-4 patch_2.7.6-7 perl_5.38.2-4 perl-base_5.38.2-4 perl-modules-5.38_5.38.2-4 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 poppler-data_0.4.12-1 preview-latex-style_13.2-1 python3_3.11.8-1 python3-all_3.11.8-1 python3-all-dev_3.11.8-1 python3-dev_3.11.8-1 python3-distutils_3.12.3-3.1 python3-lib2to3_3.12.3-3.1 python3-minimal_3.11.8-1 python3-pkg-resources_68.1.2-2 python3-setuptools_68.1.2-2 python3.11_3.11.9-1+b1 python3.11-dev_3.11.9-1+b1 python3.11-minimal_3.11.9-1+b1 python3.12_3.12.3-1+b1 python3.12-dev_3.12.3-1+b1 python3.12-minimal_3.12.3-1+b1 raspbian-archive-keyring_20120528.2 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.3-1+rpi1+b1 systemd-dev_255.3-1+rpi1 systemd-timesyncd_255.3-1+rpi1+b1 sysvinit-utils_3.09-1 t1utils_1.41-4 tar_1.35+dfsg-3 tex-common_6.18 texlive-base_2023.20240207-1 texlive-binaries_2023.20230311.66589-9 texlive-font-utils_2023.20240207-1 texlive-fonts-recommended_2023.20240207-1 texlive-lang-greek_2023.20240207-1 texlive-latex-base_2023.20240207-1 texlive-latex-extra_2023.20240207-1 texlive-latex-recommended_2023.20240207-1 texlive-pictures_2023.20240207-1 texlive-science_2023.20240207-1 tzdata_2024a-4 ucf_3.0043+nmu1 usr-is-merged_39 util-linux_2.40.1-4+rpi1 util-linux-extra_2.40.1-4+rpi1 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+6 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: minimap2
Binary: minimap2, libminimap2-dev, python3-mappy
Architecture: any
Version: 2.27+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/lh3/minimap2
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/minimap2
Vcs-Git: https://salsa.debian.org/med-team/minimap2.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-all
Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-dev
Package-List:
libminimap2-dev deb libdevel optional arch=any
minimap2 deb science optional arch=any
python3-mappy deb python optional arch=any
Checksums-Sha1:
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a7aa130e9464843d8736dc295f5628441895c4e7 11544 minimap2_2.27+dfsg-1.debian.tar.xz
Checksums-Sha256:
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45d509d32766d87c4ca3c8ed7310e2758794418e0c53918fda09f45f8cac5826 11544 minimap2_2.27+dfsg-1.debian.tar.xz
Files:
2f98c85235a8086e03367622ae70aef0 200448 minimap2_2.27+dfsg.orig.tar.xz
2b0538bcbffb92d0d127c6a47728340b 11544 minimap2_2.27+dfsg-1.debian.tar.xz
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gpgv: Signature made Mon Mar 18 16:37:53 2024 UTC
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 /<<PKGBUILDDIR>>
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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=4bea495dd1ba4e04a38aa376732db300
JOURNAL_STREAM=8:1357868
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-faf43c28-5617-4494-97ab-bef7c03f6969
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c48702
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package minimap2
dpkg-buildpackage: info: source version 2.27+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
I: pybuild base: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 '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
cd tex && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/tex'
rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf
make[2]: Leaving directory '/<<PKGBUILDDIR>>/tex'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- -f Makefile.simde
make -j4 "INSTALL=install --strip-program=true" -f Makefile.simde
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 main.c -o main.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kthread.c -o kthread.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kalloc.c -o kalloc.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 misc.c -o misc.o
kalloc.c: In function ‘km_stat_print’:
kalloc.c:222:42: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:53: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:66: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:78: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:91: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~
| |
| size_t {aka unsigned int}
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bseq.c -o bseq.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 sketch.c -o sketch.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 sdust.c -o sdust.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 options.c -o options.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 index.c -o index.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 lchain.c -o lchain.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 align.c -o align.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 seed.c -o seed.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 map.c -o map.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 format.c -o format.o
map.c: In function ‘mm_map_frag’:
map.c:365:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
map.c:365:70: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
map.c:365:82: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 pe.c -o pe.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 esterr.c -o esterr.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 splitidx.c -o splitidx.o
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.o
ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
5 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.o
ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
6 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o
ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
6 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: 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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 '/<<PKGBUILDDIR>>'
cd tex && make
make[2]: Entering directory '/<<PKGBUILDDIR>>/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;
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\OT1/ptm/m/n/9 mRNAs as well. Minimap2 becomes a first RNA-seq aligner
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\OT1/ptm/m/n/8 performs local alignment between the two subsequences involved i
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[]\OT1/ptm/m/n/9 2016[]), Kart (v2.2.5; []Lin and Hsu[], []2017[]), minialign (
v0.5.3;
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dlazeck
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\OT1/ptm/m/n/9 GMAP (v2017-06-20; []Wu and Watanabe[], []2005[]), minimap2,
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\OT1/ptm/m/n/9 et al.[], []2013[]). In general, minimap2 is more consistent wit
h
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\OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2
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\OT1/ptm/m/n/9 v3.5 ([]Depristo et al.[], []2011[]). This run was sequenced fro
m
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\OT1/ptm/m/n/9 the paftools.js script from the minimap2 package, we called
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[]\OT1/ptm/m/n/9 The capability of minimap2 comes from a fast base-level
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\OT1/ptm/m/n/9 releasing their masterpiece and insightful notes before formal
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[]\OT1/ptm/m/n/7 Li, H. et al. (2009). The Sequence Alignment/Map format and S
AMtools.
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(see the transcript file for additional information)</usr/share/texlive/texmf-d
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Output written on minimap2.pdf (6 pages, 269463 bytes).
Transcript written on minimap2.log.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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: /<<PKGBUILDDIR>>/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-armv7l-cpython-312
creating build/temp.linux-armv7l-cpython-312/python
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c align.c -o build/temp.linux-armv7l-cpython-312/align.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
align.c: In function ‘mm_get_hplen_back’:
align.c:365:43: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
365 | if (mm_seq4_get(mi->S, i) != c) break;
| ^~
align.c: In function ‘mm_seed_ext_score’:
align.c:552:56: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
552 | re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len;
| ^~~~~~~~~~~~
align.c: In function ‘mm_align1’:
align.c:646:59: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
646 | re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len;
| ^~~~~~
align.c:698:65: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
698 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re;
| ^
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c bseq.c -o build/temp.linux-armv7l-cpython-312/bseq.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c esterr.c -o build/temp.linux-armv7l-cpython-312/esterr.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c format.c -o build/temp.linux-armv7l-cpython-312/format.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c hit.c -o build/temp.linux-armv7l-cpython-312/hit.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
hit.c: In function ‘mm_hit_sort’:
hit.c:190:55: warning: variable ‘no_cigar’ set but not used [-Wunused-but-set-variable]
190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0;
| ^~~~~~~~
hit.c:190:40: warning: variable ‘has_cigar’ set but not used [-Wunused-but-set-variable]
190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0;
| ^~~~~~~~~
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c index.c -o build/temp.linux-armv7l-cpython-312/index.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
index.c: In function ‘mm_idx_name2id’:
index.c:149:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
149 | return k == kh_end(h)? -1 : kh_val(h, k);
| ^~
index.c: In function ‘mm_idx_gen’:
index.c:382:70: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
382 | pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
| ^~~~~~~~~~~~~~~
index.c: In function ‘mm_idx_dump’:
index.c:483:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
483 | for (i = 0; i < 1<<mi->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<<mi->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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c kalloc.c -o build/temp.linux-armv7l-cpython-312/kalloc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
kalloc.c: In function ‘km_stat_print’:
kalloc.c:222:42: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:53: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:66: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:78: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:91: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~
| |
| size_t {aka unsigned int}
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extd2_sse.c -o build/temp.linux-armv7l-cpython-312/ksw2_extd2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
6 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_exts2_sse.c -o build/temp.linux-armv7l-cpython-312/ksw2_exts2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
6 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extz2_sse.c -o build/temp.linux-armv7l-cpython-312/ksw2_extz2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
5 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c ksw2_ll_sse.c -o build/temp.linux-armv7l-cpython-312/ksw2_ll_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c kthread.c -o build/temp.linux-armv7l-cpython-312/kthread.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c lchain.c -o build/temp.linux-armv7l-cpython-312/lchain.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
lchain.c: In function ‘mg_chain_bk_end’:
lchain.c:18:37: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
18 | s = i < 0? z[k].x : (int32_t)z[k].x - f[i];
| ^~~~~~~~~~~~~~~~~~~~~~
lchain.c: In function ‘mg_chain_backtrack’:
lchain.c:51:46: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
51 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
| ^~~~~~~~~~~~~~~~~~~~~~
lchain.c:66:46: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
66 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
| ^~~~~~~~~~~~~~~~~~~~~~
lchain.c: In function ‘mg_lchain_dp’:
lchain.c:190:56: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘long long int’ [-Wsign-compare]
190 | if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) {
| ^
lchain.c:204:57: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘long long int’ [-Wsign-compare]
204 | if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i]))
| ^~
lchain.c: In function ‘mg_lchain_rmq’:
lchain.c:295:117: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
295 | while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) {
| ^
lchain.c:304:155: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
304 | while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) {
| ^
lchain.c:356:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
356 | if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root);
| ^
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c map.c -o build/temp.linux-armv7l-cpython-312/map.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
map.c: In function ‘mm_dust_minier’:
map.c:48:70: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
48 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32;
| ^
map.c:49:64: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
49 | int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v];
| ^
map.c: In function ‘mm_map_frag’:
map.c:365:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
map.c:365:70: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
map.c:365:82: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c misc.c -o build/temp.linux-armv7l-cpython-312/misc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c options.c -o build/temp.linux-armv7l-cpython-312/options.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c pe.c -o build/temp.linux-armv7l-cpython-312/pe.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c python/mappy.c -o build/temp.linux-armv7l-cpython-312/python/mappy.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
python/mappy.c: In function ‘__Pyx_PyInt_AndObjC’:
python/mappy.c:15248:36: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
15248 | if ((intval & PyLong_MASK) == intval) {
| ^~
python/mappy.c:15250:71: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
15250 | long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1));
| ^~~~~~~~~~
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c sdust.c -o build/temp.linux-armv7l-cpython-312/sdust.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c seed.c -o build/temp.linux-armv7l-cpython-312/seed.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
seed.c: In function ‘mm_seed_mz_flt’:
seed.c:9:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
9 | if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return;
| ^~
seed.c: In function ‘mm_seed_select’:
seed.c:65:28: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
65 | if (a[i].n > max_occ) ++m;
| ^
seed.c:68:38: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
68 | if (i == n || a[i].n <= max_occ) {
| ^~
seed.c:71:54: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
71 | int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1;
| ^~~
seed.c:81:60: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
81 | if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap
| ^
seed.c:90:52: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
90 | if (a[j].n > max_max_occ)
| ^
seed.c: In function ‘mm_collect_matches’:
seed.c:109:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
109 | for (i = 0; i < n_m0; ++i)
| ^
seed.c:110:36: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
110 | if (m[i].n > max_occ)
| ^
seed.c:113:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) {
| ^
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c sketch.c -o build/temp.linux-armv7l-cpython-312/sketch.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.12 -c splitidx.c -o build/temp.linux-armv7l-cpython-312/splitidx.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/align.o build/temp.linux-armv7l-cpython-312/bseq.o build/temp.linux-armv7l-cpython-312/esterr.o build/temp.linux-armv7l-cpython-312/format.o build/temp.linux-armv7l-cpython-312/hit.o build/temp.linux-armv7l-cpython-312/index.o build/temp.linux-armv7l-cpython-312/kalloc.o build/temp.linux-armv7l-cpython-312/ksw2_extd2_sse.o build/temp.linux-armv7l-cpython-312/ksw2_exts2_sse.o build/temp.linux-armv7l-cpython-312/ksw2_extz2_sse.o build/temp.linux-armv7l-cpython-312/ksw2_ll_sse.o build/temp.linux-armv7l-cpython-312/kthread.o build/temp.linux-armv7l-cpython-312/lchain.o build/temp.linux-armv7l-cpython-312/map.o build/temp.linux-armv7l-cpython-312/misc.o build/temp.linux-armv7l-cpython-312/options.o build/temp.linux-armv7l-cpython-312/pe.o build/temp.linux-armv7l-cpython-312/python/mappy.o build/temp.linux-armv7l-cpython-312/sdust.o build/temp.linux-armv7l-cpython-312/seed.o build/temp.linux-armv7l-cpython-312/sketch.o build/temp.linux-armv7l-cpython-312/splitidx.o -L/usr/lib/arm-linux-gnueabihf -lz -lm -lpthread -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/mappy.cpython-312-arm-linux-gnueabihf.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-armv7l-cpython-311
creating build/temp.linux-armv7l-cpython-311/python
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
align.c: In function ‘mm_get_hplen_back’:
align.c:365:43: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
365 | if (mm_seq4_get(mi->S, i) != c) break;
| ^~
align.c: In function ‘mm_seed_ext_score’:
align.c:552:56: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
552 | re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len;
| ^~~~~~~~~~~~
align.c: In function ‘mm_align1’:
align.c:646:59: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
646 | re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len;
| ^~~~~~
align.c:698:65: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
698 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re;
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c bseq.c -o build/temp.linux-armv7l-cpython-311/bseq.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c esterr.c -o build/temp.linux-armv7l-cpython-311/esterr.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c format.c -o build/temp.linux-armv7l-cpython-311/format.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c hit.c -o build/temp.linux-armv7l-cpython-311/hit.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
hit.c: In function ‘mm_hit_sort’:
hit.c:190:55: warning: variable ‘no_cigar’ set but not used [-Wunused-but-set-variable]
190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0;
| ^~~~~~~~
hit.c:190:40: warning: variable ‘has_cigar’ set but not used [-Wunused-but-set-variable]
190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0;
| ^~~~~~~~~
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c index.c -o build/temp.linux-armv7l-cpython-311/index.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
index.c: In function ‘mm_idx_name2id’:
index.c:149:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
149 | return k == kh_end(h)? -1 : kh_val(h, k);
| ^~
index.c: In function ‘mm_idx_gen’:
index.c:382:70: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
382 | pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
| ^~~~~~~~~~~~~~~
index.c: In function ‘mm_idx_dump’:
index.c:483:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
483 | for (i = 0; i < 1<<mi->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<<mi->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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c kalloc.c -o build/temp.linux-armv7l-cpython-311/kalloc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
kalloc.c: In function ‘km_stat_print’:
kalloc.c:222:42: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:53: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:66: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:78: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~~
| |
| size_t {aka unsigned int}
kalloc.c:222:91: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
| ~~^
| |
| long int
| %d
223 | st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
| ~~~~~~~~~~
| |
| size_t {aka unsigned int}
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_extd2_sse.c -o build/temp.linux-armv7l-cpython-311/ksw2_extd2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
6 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_exts2_sse.c -o build/temp.linux-armv7l-cpython-311/ksw2_exts2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
6 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_extz2_sse.c -o build/temp.linux-armv7l-cpython-311/ksw2_extz2_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined
5 | #define SIMDE_ENABLE_NATIVE_ALIASES
|
<command-line>: note: this is the location of the previous definition
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c ksw2_ll_sse.c -o build/temp.linux-armv7l-cpython-311/ksw2_ll_sse.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c kthread.c -o build/temp.linux-armv7l-cpython-311/kthread.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c lchain.c -o build/temp.linux-armv7l-cpython-311/lchain.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
lchain.c: In function ‘mg_chain_bk_end’:
lchain.c:18:37: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
18 | s = i < 0? z[k].x : (int32_t)z[k].x - f[i];
| ^~~~~~~~~~~~~~~~~~~~~~
lchain.c: In function ‘mg_chain_backtrack’:
lchain.c:51:46: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
51 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
| ^~~~~~~~~~~~~~~~~~~~~~
lchain.c:66:46: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
66 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
| ^~~~~~~~~~~~~~~~~~~~~~
lchain.c: In function ‘mg_lchain_dp’:
lchain.c:190:56: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘long long int’ [-Wsign-compare]
190 | if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) {
| ^
lchain.c:204:57: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘long long int’ [-Wsign-compare]
204 | if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i]))
| ^~
lchain.c: In function ‘mg_lchain_rmq’:
lchain.c:295:117: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
295 | while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) {
| ^
lchain.c:304:155: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
304 | while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) {
| ^
lchain.c:356:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
356 | if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root);
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c map.c -o build/temp.linux-armv7l-cpython-311/map.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
map.c: In function ‘mm_dust_minier’:
map.c:48:70: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare]
48 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32;
| ^
map.c:49:64: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
49 | int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v];
| ^
map.c: In function ‘mm_map_frag’:
map.c:365:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
map.c:365:70: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
map.c:365:82: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
365 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
| ~~^ ~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c misc.c -o build/temp.linux-armv7l-cpython-311/misc.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c options.c -o build/temp.linux-armv7l-cpython-311/options.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c pe.c -o build/temp.linux-armv7l-cpython-311/pe.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c python/mappy.c -o build/temp.linux-armv7l-cpython-311/python/mappy.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
python/mappy.c: In function ‘__Pyx_PyInt_AndObjC’:
python/mappy.c:15248:36: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
15248 | if ((intval & PyLong_MASK) == intval) {
| ^~
python/mappy.c:15250:71: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
15250 | long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1));
| ^~~~~~~~~~
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c sdust.c -o build/temp.linux-armv7l-cpython-311/sdust.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c seed.c -o build/temp.linux-armv7l-cpython-311/seed.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
seed.c: In function ‘mm_seed_mz_flt’:
seed.c:9:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
9 | if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return;
| ^~
seed.c: In function ‘mm_seed_select’:
seed.c:65:28: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
65 | if (a[i].n > max_occ) ++m;
| ^
seed.c:68:38: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
68 | if (i == n || a[i].n <= max_occ) {
| ^~
seed.c:71:54: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
71 | int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1;
| ^~~
seed.c:81:60: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
81 | if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap
| ^
seed.c:90:52: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
90 | if (a[j].n > max_max_occ)
| ^
seed.c: In function ‘mm_collect_matches’:
seed.c:109:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
109 | for (i = 0; i < n_m0; ++i)
| ^
seed.c:110:36: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
110 | if (m[i].n > max_occ)
| ^
seed.c:113:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c sketch.c -o build/temp.linux-armv7l-cpython-311/sketch.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.11 -c splitidx.c -o build/temp.linux-armv7l-cpython-311/splitidx.o -DHAVE_KALLOC -DKSW_SSE2_ONLY -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/bseq.o build/temp.linux-armv7l-cpython-311/esterr.o build/temp.linux-armv7l-cpython-311/format.o build/temp.linux-armv7l-cpython-311/hit.o build/temp.linux-armv7l-cpython-311/index.o build/temp.linux-armv7l-cpython-311/kalloc.o build/temp.linux-armv7l-cpython-311/ksw2_extd2_sse.o build/temp.linux-armv7l-cpython-311/ksw2_exts2_sse.o build/temp.linux-armv7l-cpython-311/ksw2_extz2_sse.o build/temp.linux-armv7l-cpython-311/ksw2_ll_sse.o build/temp.linux-armv7l-cpython-311/kthread.o build/temp.linux-armv7l-cpython-311/lchain.o build/temp.linux-armv7l-cpython-311/map.o build/temp.linux-armv7l-cpython-311/misc.o build/temp.linux-armv7l-cpython-311/options.o build/temp.linux-armv7l-cpython-311/pe.o build/temp.linux-armv7l-cpython-311/python/mappy.o build/temp.linux-armv7l-cpython-311/sdust.o build/temp.linux-armv7l-cpython-311/seed.o build/temp.linux-armv7l-cpython-311/sketch.o build/temp.linux-armv7l-cpython-311/splitidx.o -L/usr/lib/arm-linux-gnueabihf -lz -lm -lpthread -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/mappy.cpython-311-arm-linux-gnueabihf.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 '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
debian/test_script
[M::mm_idx_gen::0.004*1.46] collected minimizers
[M::mm_idx_gen::0.006*1.84] sorted minimizers
[M::main::0.006*1.80] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.007*1.71] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.008*1.64] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569
[M::worker_pipeline::0.301*1.02] 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: 0.303 sec; CPU: 0.308 sec; Peak RSS: 0.003 GB
[M::mm_idx_gen::0.004*1.51] collected minimizers
[M::mm_idx_gen::0.006*1.89] sorted minimizers
[M::main::0.010*1.53] 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::0.011*1.49] 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: 0.013 sec; CPU: 0.018 sec; Peak RSS: 0.003 GB
[M::main::0.006*1.19] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.007*1.14] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.008*1.11] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569
[M::worker_pipeline::0.361*1.00] 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: 0.364 sec; CPU: 0.365 sec; Peak RSS: 0.004 GB
rm test.sam
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
dh_auto_install --buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/mappy.cpython-312-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/dist-packages/mappy-2.27.egg-info
Skipping SOURCES.txt
running install_scripts
creating /<<PKGBUILDDIR>>/debian/tmp/usr/bin
copying build/scripts-3.12/minimap2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/bin
changing mode of /<<PKGBUILDDIR>>/debian/tmp/usr/bin/minimap2.py to 755
I: pybuild base:311: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/mappy.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 -> /<<PKGBUILDDIR>>/debian/tmp/usr/bin
changing mode of /<<PKGBUILDDIR>>/debian/tmp/usr/bin/minimap2.py to 755
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman --language=C
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_fixperms -a
dh_missing -a
dh_dwz -a
debian/rules override_dh_strip
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_strip
ranlib /<<PKGBUILDDIR>>/debian/libminimap2-dev/usr/lib/libminimap2.a
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/minimap2/usr/bin/minimap2 was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libminimap2-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_armhf.deb'.
dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_armhf.deb'.
dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_armhf.deb'.
dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_armhf.deb'.
dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../minimap2_2.27+dfsg-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../minimap2_2.27+dfsg-1_armhf.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)
--------------------------------------------------------------------------------
Build finished at 2024-06-11T12:47:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
minimap2_2.27+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Mon, 18 Mar 2024 17:12:17 +0100
Source: minimap2
Binary: libminimap2-dev minimap2 minimap2-dbgsym python3-mappy python3-mappy-dbgsym
Architecture: armhf
Version: 2.27+dfsg-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
libminimap2-dev - development headers for libminimap
minimap2 - versatile pairwise aligner for genomic and spliced nucleotide seq
python3-mappy - Python3 interface minimap2
Closes: 1046060
Changes:
minimap2 (2.27+dfsg-1) unstable; urgency=medium
.
* Team upload.
* d/rules, d/clean: simply cleanup code.
* d/rules: clean using pybuild. Closes: #1046060
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Files:
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d5a01453982ed9b54e4ba1cb57de7617 277176 debug optional minimap2-dbgsym_2.27+dfsg-1_armhf.deb
08333edff04ad2738d34ef7dacfa917c 12095 science optional minimap2_2.27+dfsg-1_armhf.buildinfo
9a4e931f4abd0bbd1114f56b1a0b2eee 394452 science optional minimap2_2.27+dfsg-1_armhf.deb
c78699556b461325176fdaf1f1f55398 1053744 debug optional python3-mappy-dbgsym_2.27+dfsg-1_armhf.deb
54e65470c273c6d418445375d458f434 188808 python optional python3-mappy_2.27+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: minimap2
Binary: libminimap2-dev minimap2 minimap2-dbgsym python3-mappy python3-mappy-dbgsym
Architecture: armhf
Version: 2.27+dfsg-1
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 11 Jun 2024 12:47:21 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
adduser (= 3.137),
aglfn (= 1.7+git20191031.4036a9c-2),
apt (= 2.9.3),
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13.2+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
binutils (= 2.41-6+rpi1+b1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1+b1),
binutils-common (= 2.41-6+rpi1+b1),
bsdextrautils (= 2.40.1-4+rpi1),
bsdutils (= 1:2.40.1-4+rpi1),
build-essential (= 12.10),
bzip2 (= 1.0.8-5.1),
coreutils (= 9.4-3.1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-14+rpi1),
cpp-13 (= 13.2.0-16.1+rpi1),
cpp-13-arm-linux-gnueabihf (= 13.2.0-16.1+rpi1),
cython3 (= 3.0.10+dfsg-5),
d-shlibs (= 0.106),
dash (= 0.5.12-8),
debconf (= 1.5.86),
debhelper (= 13.15.3),
debianutils (= 5.17),
dh-autoreconf (= 20),
dh-python (= 6.20240422),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1),
dirmngr (= 2.2.43-7),
dpkg (= 1.22.6+rpi1),
dpkg-dev (= 1.22.6+rpi1),
dwz (= 0.15-1+b2),
file (= 1:5.45-3),
findutils (= 4.9.0-6),
fontconfig (= 2.15.0-1.1),
fontconfig-config (= 2.15.0-1.1),
fonts-dejavu-core (= 2.37-8),
fonts-dejavu-mono (= 2.37-8),
fonts-gfs-baskerville (= 1.1-6),
fonts-gfs-porson (= 1.1-7),
fonts-lmodern (= 2.005-1),
fonts-urw-base35 (= 20200910-8),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-16.1+rpi1),
g++-13-arm-linux-gnueabihf (= 13.2.0-16.1+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-14+rpi1),
gcc-12-base (= 12.3.0-14+rpi1),
gcc-13 (= 13.2.0-16.1+rpi1),
gcc-13-arm-linux-gnueabihf (= 13.2.0-16.1+rpi1),
gcc-13-base (= 13.2.0-16.1+rpi1),
gcc-14-base (= 14-20240221-2.1+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
ghostscript (= 10.03.1~dfsg-1),
gnupg (= 2.2.43-7),
gnupg-l10n (= 2.2.43-7),
gnuplot-data (= 6.0.0+dfsg1-3),
gnuplot-nox (= 6.0.0+dfsg1-3),
gpg (= 2.2.43-7),
gpg-agent (= 2.2.43-7),
gpgconf (= 2.2.43-7),
gpgsm (= 2.2.43-7),
gpgv (= 2.2.43-7),
grep (= 3.11-4),
groff-base (= 1.23.0-4),
gzip (= 1.12-1.1),
hostname (= 3.23+nmu2),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libabsl20230802 (= 20230802.1-4),
libacl1 (= 2.3.2-2+rpi1),
libaom3 (= 3.8.2-3),
libapache-pom-java (= 29-2),
libapt-pkg6.0t64 (= 2.9.3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 14-20240221-2.1+rpi1),
libassuan0 (= 2.5.6-1),
libatomic1 (= 14-20240221-2.1+rpi1),
libattr1 (= 1:2.5.2-1),
libaudit-common (= 1:3.1.2-2),
libaudit1 (= 1:3.1.2-2),
libavahi-client3 (= 0.8-13+b2),
libavahi-common-data (= 0.8-13+b2),
libavahi-common3 (= 0.8-13+b2),
libavif16 (= 1.0.4-3),
libbinutils (= 2.41-6+rpi1+b1),
libblkid1 (= 2.40.1-4+rpi1),
libbrotli1 (= 1.1.0-2),
libbsd0 (= 0.12.2-1),
libbz2-1.0 (= 1.0.8-5.1),
libc-bin (= 2.38-8+rpi1),
libc-dev-bin (= 2.38-8+rpi1),
libc6 (= 2.38-8+rpi1),
libc6-dev (= 2.38-8+rpi1),
libcairo2 (= 1.18.0-3+b1),
libcap-ng0 (= 0.8.5-1),
libcap2 (= 1:2.66-5),
libcc1-0 (= 14-20240221-2.1+rpi1),
libcom-err2 (= 1.47.1-1),
libcommons-logging-java (= 1.3.0-1),
libcommons-parent-java (= 56-1),
libcrypt-dev (= 1:4.4.36-4),
libcrypt1 (= 1:4.4.36-4),
libctf-nobfd0 (= 2.41-6+rpi1+b1),
libctf0 (= 2.41-6+rpi1+b1),
libcups2t64 (= 2.4.7-1.2),
libdatrie1 (= 0.2.13-3),
libdav1d7 (= 1.4.2-1+rpi1),
libdb5.3t64 (= 5.3.28+dfsg2-7),
libdbus-1-3 (= 1.14.10-4+b1),
libde265-0 (= 1.0.15-1+rpi1+b1),
libdebconfclient0 (= 0.272),
libdebhelper-perl (= 13.15.3),
libdeflate0 (= 1.20-1),
libdpkg-perl (= 1.22.6+rpi1),
libedit2 (= 3.1-20240517-1),
libelf1t64 (= 0.191-1+rpi1),
libexpat1 (= 2.6.2-1),
libexpat1-dev (= 2.6.2-1),
libffi8 (= 3.4.6-1),
libfile-stripnondeterminism-perl (= 1.14.0-1),
libfontbox-java (= 1:1.8.16-5),
libfontconfig1 (= 2.15.0-1.1),
libfontenc1 (= 1:1.1.8-1),
libfreetype6 (= 2.13.2+dfsg-1+b4),
libfribidi0 (= 1.0.13-3+b1),
libgav1-1 (= 0.19.0-2+rpi1),
libgcc-12-dev (= 12.3.0-14+rpi1),
libgcc-13-dev (= 13.2.0-16.1+rpi1),
libgcc-s1 (= 14-20240221-2.1+rpi1),
libgcrypt20 (= 1.10.3-3),
libgd3 (= 2.3.3-9+b3),
libgdbm-compat4t64 (= 1.23-5.1+b1),
libgdbm6t64 (= 1.23-5.1+b1),
libglib2.0-0t64 (= 2.80.2-2),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30t64 (= 3.8.5-4),
libgomp1 (= 14-20240221-2.1+rpi1),
libgpg-error0 (= 1.49-2),
libgraphite2-3 (= 1.3.14-2),
libgs-common (= 10.03.1~dfsg-1),
libgs10 (= 10.03.1~dfsg-1),
libgs10-common (= 10.03.1~dfsg-1),
libgssapi-krb5-2 (= 1.20.1-6+b4),
libharfbuzz0b (= 8.3.0-2+b1),
libheif-plugin-dav1d (= 1.17.6-1+b1),
libheif-plugin-libde265 (= 1.17.6-1+b1),
libheif1 (= 1.17.6-1+b1),
libhogweed6t64 (= 3.9.1-2.2),
libice6 (= 2:1.0.10-1+b1),
libicu72 (= 72.1-4+b1),
libidn12 (= 1.42-2),
libidn2-0 (= 2.3.7-2),
libijs-0.35 (= 0.35-15.1+b1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjbig0 (= 2.1-6.1+b1),
libjbig2dec0 (= 0.20-1+b2),
libjpeg62-turbo (= 1:2.1.5-3),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-sphinxdoc (= 7.2.6-8),
libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
libk5crypto3 (= 1.20.1-6+b4),
libkeyutils1 (= 1.6.3-3),
libkpathsea6 (= 2023.20230311.66589-9),
libkrb5-3 (= 1.20.1-6+b4),
libkrb5support0 (= 1.20.1-6+b4),
libksba8 (= 1.6.6-1),
liblcms2-2 (= 2.14-2+b1),
libldap-2.5-0 (= 2.5.17+dfsg-1+rpi1),
liblerc4 (= 4.0.0+ds-4+b1),
liblua5.4-0 (= 5.4.6-3+b1),
liblz4-1 (= 1.9.4-2+rpi1),
liblzma5 (= 5.6.1+really5.4.5-1),
libmagic-mgc (= 1:5.45-3),
libmagic1t64 (= 1:5.45-3),
libmd0 (= 1.1.0-2),
libmount1 (= 2.40.1-4+rpi1),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.5-2),
libnettle8t64 (= 3.9.1-2.2),
libnpth0t64 (= 1.6-3.1),
libnsl2 (= 1.3.0-3+b1),
libopenjp2-7 (= 2.5.0-2+b3),
libp11-kit0 (= 0.25.3-5),
libpam-modules (= 1.5.3-7),
libpam-modules-bin (= 1.5.3-7),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7),
libpango-1.0-0 (= 1.52.2+ds-1),
libpangocairo-1.0-0 (= 1.52.2+ds-1),
libpangoft2-1.0-0 (= 1.52.2+ds-1),
libpaper-utils (= 1.1.29),
libpaper1 (= 1.1.29),
libpcre2-8-0 (= 10.42-4+b1),
libpdfbox-java (= 1:1.8.16-5),
libperl5.38t64 (= 5.38.2-4),
libpipeline1 (= 1.5.7-2),
libpixman-1-0 (= 0.42.2-1+b1),
libpng16-16t64 (= 1.6.43-5),
libpotrace0 (= 1.16-2),
libptexenc1 (= 2023.20230311.66589-9),
libpython3-all-dev (= 3.11.8-1),
libpython3-dev (= 3.11.8-1),
libpython3-stdlib (= 3.11.8-1),
libpython3.11-dev (= 3.11.9-1+b1),
libpython3.11-minimal (= 3.11.9-1+b1),
libpython3.11-stdlib (= 3.11.9-1+b1),
libpython3.11t64 (= 3.11.9-1+b1),
libpython3.12-dev (= 3.12.3-1+b1),
libpython3.12-minimal (= 3.12.3-1+b1),
libpython3.12-stdlib (= 3.12.3-1+b1),
libpython3.12t64 (= 3.12.3-1+b1),
librav1e0 (= 0.7.1-2),
libreadline8t64 (= 8.2-4),
libsasl2-2 (= 2.1.28+dfsg1-6),
libsasl2-modules-db (= 2.1.28+dfsg1-6),
libseccomp2 (= 2.5.5-1+rpi1),
libselinux1 (= 3.5-2+b2),
libsemanage-common (= 3.5-1),
libsemanage2 (= 3.5-1+b1),
libsepol2 (= 3.5-2+b1),
libsframe1 (= 2.41-6+rpi1+b1),
libsharpyuv0 (= 1.4.0-0.1),
libsimde-dev (= 0.8.2-1),
libsm6 (= 2:1.2.3-1+b1),
libsmartcols1 (= 2.40.1-4+rpi1),
libsqlite3-0 (= 3.45.3-1),
libssl3t64 (= 3.2.1-3),
libstdc++-13-dev (= 13.2.0-16.1+rpi1),
libstdc++6 (= 14-20240221-2.1+rpi1),
libsvtav1enc1d1 (= 1.7.0+dfsg-2),
libsynctex2 (= 2023.20230311.66589-9),
libsystemd0 (= 255.3-1+rpi1+b1),
libtasn1-6 (= 4.19.0-3+b2),
libteckit0 (= 2.5.12+ds1-1),
libtexlua53-5 (= 2023.20230311.66589-9),
libthai-data (= 0.1.29-2),
libthai0 (= 0.1.29-2),
libtiff6 (= 4.5.1+git230720-4),
libtinfo6 (= 6.5-2),
libtirpc-common (= 1.3.4+ds-1.3),
libtirpc3t64 (= 1.3.4+ds-1.3),
libtool (= 2.4.7-7),
libubsan1 (= 14-20240221-2.1+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 255.3-1+rpi1+b1),
libunistring5 (= 1.2-1),
libuuid1 (= 2.40.1-4+rpi1),
libwebp7 (= 1.4.0-0.1),
libwebpmux3 (= 1.4.0-0.1),
libx11-6 (= 2:1.8.7-1),
libx11-data (= 2:1.8.7-1),
libxau6 (= 1:1.0.9-1),
libxaw7 (= 2:1.0.14-1+b2),
libxcb-render0 (= 1.17.0-2),
libxcb-shm0 (= 1.17.0-2),
libxcb1 (= 1.17.0-2),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1+b1),
libxi6 (= 2:1.8.1-1),
libxml2 (= 2.9.14+dfsg-1.3+b4),
libxmu6 (= 2:1.1.3-3+b2),
libxpm4 (= 1:3.5.17-1+b1),
libxrender1 (= 1:0.9.10-1.1+b1),
libxt6t64 (= 1:1.2.1-1.2),
libxxhash0 (= 0.8.2-2+b1),
libyuv0 (= 0.0.1888.20240509-4),
libzstd1 (= 1.5.5+dfsg2-2),
libzzip-0-13t64 (= 0.13.72+dfsg.1-1.2),
linux-libc-dev (= 6.5.6-1+rpi1+b1),
login (= 1:4.13+dfsg1-4),
lsb-base (= 11.6+rpi1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.1-1),
mawk (= 1.3.4.20240123-1),
media-types (= 10.1.0),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2),
netbase (= 6.4),
passwd (= 1:4.13+dfsg1-4),
patch (= 2.7.6-7),
perl (= 5.38.2-4),
perl-base (= 5.38.2-4),
perl-modules-5.38 (= 5.38.2-4),
pinentry-curses (= 1.2.1-3),
po-debconf (= 1.0.21+nmu1),
poppler-data (= 0.4.12-1),
preview-latex-style (= 13.2-1),
python3 (= 3.11.8-1),
python3-all (= 3.11.8-1),
python3-all-dev (= 3.11.8-1),
python3-dev (= 3.11.8-1),
python3-distutils (= 3.12.3-3.1),
python3-lib2to3 (= 3.12.3-3.1),
python3-minimal (= 3.11.8-1),
python3-pkg-resources (= 68.1.2-2),
python3-setuptools (= 68.1.2-2),
python3.11 (= 3.11.9-1+b1),
python3.11-dev (= 3.11.9-1+b1),
python3.11-minimal (= 3.11.9-1+b1),
python3.12 (= 3.12.3-1+b1),
python3.12-dev (= 3.12.3-1+b1),
python3.12-minimal (= 3.12.3-1+b1),
raspbian-archive-keyring (= 20120528.2),
readline-common (= 8.2-4),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.22),
sysvinit-utils (= 3.09-1),
t1utils (= 1.41-4),
tar (= 1.35+dfsg-3),
tex-common (= 6.18),
texlive-base (= 2023.20240207-1),
texlive-binaries (= 2023.20230311.66589-9),
texlive-font-utils (= 2023.20240207-1),
texlive-fonts-recommended (= 2023.20240207-1),
texlive-lang-greek (= 2023.20240207-1),
texlive-latex-base (= 2023.20240207-1),
texlive-latex-extra (= 2023.20240207-1),
texlive-latex-recommended (= 2023.20240207-1),
texlive-pictures (= 2023.20240207-1),
texlive-science (= 2023.20240207-1),
tzdata (= 2024a-4),
ucf (= 3.0043+nmu1),
usr-is-merged (= 39),
util-linux (= 2.40.1-4+rpi1),
x11-common (= 1:7.7+23),
xdg-utils (= 1.1.3-4.1),
xfonts-encodings (= 1:1.0.4-2.2),
xfonts-utils (= 1:7.7+6),
xz-utils (= 5.6.1+really5.4.5-1),
zlib1g (= 1:1.3.dfsg+really1.3.1-1),
zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1710778337"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libminimap2-dev_2.27+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 125312 bytes: control archive=1344 bytes.
1034 bytes, 23 lines control
970 bytes, 17 lines md5sums
Package: libminimap2-dev
Source: minimap2
Version: 2.27+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 360
Depends: zlib1g-dev
Section: libdevel
Priority: optional
Homepage: https://github.com/lh3/minimap2
Description: development headers for libminimap
Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate up
to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
or Direct RNA reads against a reference genome; (4) aligning Illumina
single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-
genome alignment between two closely related species with divergence
below ~15%.
.
This package contains the C library headers for using minimap in custom tools,
along with a static library.
drwxr-xr-x root/root 0 2024-03-18 16:12 ./
drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/
drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/include/
-rw-r--r-- root/root 1811 2024-03-12 17:20 ./usr/include/bseq.h
-rw-r--r-- root/root 2630 2024-03-12 17:20 ./usr/include/kalloc.h
-rw-r--r-- root/root 4400 2024-03-12 17:20 ./usr/include/kdq.h
-rw-r--r-- root/root 3969 2024-03-12 17:20 ./usr/include/ketopt.h
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-rw-r--r-- root/root 3132 2024-03-18 16:12 ./usr/share/doc/libminimap2-dev/copyright
minimap2-dbgsym_2.27+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 277176 bytes: control archive=536 bytes.
382 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: minimap2-dbgsym
Source: minimap2
Version: 2.27+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 294
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Section: debug
Priority: optional
Description: debug symbols for minimap2
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lrwxrwxrwx root/root 0 2024-03-18 16:12 ./usr/share/doc/minimap2-dbgsym -> minimap2
minimap2_2.27+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 394452 bytes: control archive=1496 bytes.
1433 bytes, 27 lines control
981 bytes, 14 lines md5sums
Package: minimap2
Version: 2.27+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 534
Depends: libc6 (>= 2.34), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: https://github.com/lh3/minimap2
Description: versatile pairwise aligner for genomic and spliced nucleotide sequences
Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate up
to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
or Direct RNA reads against a reference genome; (4) aligning Illumina
single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-
genome alignment between two closely related species with divergence
below ~15%.
.
For ~10kb noisy reads sequences, minimap2 is tens of times faster than
mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It
is more accurate on simulated long reads and produces biologically
meaningful alignment ready for downstream analyses. For >100bp Illumina
short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
as accurate on simulated data. Detailed evaluations are available from
the minimap2 paper or the preprint.
drwxr-xr-x root/root 0 2024-03-18 16:12 ./
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-rw-r--r-- root/root 347 2020-01-10 15:56 ./usr/share/doc/minimap2/run-unit-test
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-rw-r--r-- root/root 8195 2024-03-18 16:12 ./usr/share/man/man1/minimap2.1.gz
python3-mappy-dbgsym_2.27+dfsg-1_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 1053744 bytes: control archive=660 bytes.
439 bytes, 12 lines control
305 bytes, 3 lines md5sums
Package: python3-mappy-dbgsym
Source: minimap2
Version: 2.27+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1113
Depends: python3-mappy (= 2.27+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for python3-mappy
Build-Ids: 27cda52d833c3eaeba5f7213d0d37741a611f16e 6d6ddb8d4226d736ff485c255f310894c032b54f
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lrwxrwxrwx root/root 0 2024-03-18 16:12 ./usr/share/doc/python3-mappy-dbgsym -> python3-mappy
python3-mappy_2.27+dfsg-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 188808 bytes: control archive=1560 bytes.
1057 bytes, 22 lines control
860 bytes, 10 lines md5sums
273 bytes, 12 lines * postinst #!/bin/sh
386 bytes, 12 lines * prerm #!/bin/sh
Package: python3-mappy
Source: minimap2
Version: 2.27+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 753
Depends: libc6 (>= 2.34), zlib1g (>= 1:1.2.3.3), python3 (<< 3.13), python3 (>= 3.11~), python3:any
Section: python
Priority: optional
Homepage: https://github.com/lh3/minimap2
Description: Python3 interface minimap2
Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate up
to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
or Direct RNA reads against a reference genome; (4) aligning Illumina
single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-
genome alignment between two closely related species with divergence
below ~15%.
.
This package contains the Python3 interface for using minimap2.
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 22272
Build-Time: 197
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 1849
Job: minimap2_2.27+dfsg-1
Machine Architecture: armhf
Package: minimap2
Package-Time: 2288
Source-Version: 2.27+dfsg-1
Space: 22272
Status: successful
Version: 2.27+dfsg-1
--------------------------------------------------------------------------------
Finished at 2024-06-11T12:47:22Z
Build needed 00:38:08, 22272k disk space