sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-02.freexian.com
+==============================================================================+
| pairtools 1.0.3-1+bd1 (arm64) Tue, 05 Nov 2024 19:45:45 +0000 |
+==============================================================================+
Package: pairtools
Version: 1.0.3-1+bd1
Source Version: 1.0.3-1
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any
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Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9940 kB]
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Reading package lists...
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The following packages will be upgraded:
bsdextrautils bsdutils libaudit-common libaudit1 libblkid1 libmount1
libsmartcols1 libuuid1 login mount util-linux
11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
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Get:11 http://deb.debian.org/debian sid/main arm64 login arm64 1:4.16.0-2+really2.40.2-10 [79.8 kB]
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Local sources
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| Install package build dependencies |
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Setup apt archive
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Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, cython3, python3-setuptools, python3-bioframe, python3-click, python3-exceptiongroup, python3-numpy, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-pytest, python3-scipy, libhts-dev, python3-yaml, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, cython3, python3-setuptools, python3-bioframe, python3-click, python3-exceptiongroup, python3-numpy, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-pytest, python3-scipy, libhts-dev, python3-yaml, 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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Install main build dependencies (apt-based resolver)
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Installing build dependencies
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Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot
fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libblas3
libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64
libevent-2.1-7t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgcc-14-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64
libgnutls-openssl27t64 libgnutls28-dev libgraphite2-3 libharfbuzz0b
libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libimagequant0
libisl23 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4
liblsan0 liblzma-dev libmpc3 libmpfr6 libncursesw6 libnghttp2-dev
libnghttp3-dev libngtcp2-crypto-gnutls-dev libngtcp2-dev libnsl2
libopenjp2-7 libp11-kit-dev libpkgconf3 libpng16-16t64 libpsl-dev
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev
libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libpython3.13
libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0
libraqm0 librtmp-dev libsharpyuv0 libssh2-1-dev libssl-dev libstdc++-14-dev
libtasn1-6-dev libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6
libtool libtsan2 libubsan1 libunbound8 libwebp7 libwebpdemux2 libwebpmux3
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1
libxslt1.1 libxss1 libzstd-dev linux-libc-dev m4 media-types nettle-dev
pkgconf pkgconf-bin po-debconf python-matplotlib-data python3 python3-all
python3-all-dev python3-appdirs python3-attr python3-autocommand
python3-bioframe python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-click python3-colorama python3-contourpy
python3-cycler python3-dateutil python3-decorator python3-dev
python3-exceptiongroup python3-fonttools python3-fs python3-idna
python3-inflect python3-iniconfig python3-jaraco.context
python3-jaraco.functools python3-jaraco.text python3-kiwisolver python3-lxml
python3-lz4 python3-matplotlib python3-minimal python3-more-itertools
python3-mpmath python3-numpy python3-packaging python3-pandas
python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources
python3-pluggy python3-pyparsing python3-pysam python3-pytest
python3-requests python3-scipy python3-setuptools python3-six python3-sympy
python3-tk python3-typeguard python3-typing-extensions python3-tz
python3-ufolib2 python3-urllib3 python3-yaml python3-zipp python3.12
python3.12-dev python3.12-minimal python3.12-tk python3.13 python3.13-dev
python3.13-minimal python3.13-tk rpcsvc-proto tk8.6-blt2.5 unicode-data
x11-common zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
cpp-14-doc cython-doc dh-make flit python3-build python3-installer
python3-wheel gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
gdb-aarch64-linux-gnu libc-devtools glibc-doc libcurl4-doc libidn-dev
libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data
gnutls-bin gnutls-doc libjs-jquery-ui-docs liblcms2-utils liblzma-doc
libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc tcl8.6 tk8.6
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl
python3-doc python3-venv python-attr-doc python-charset-normalizer-doc
python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo
python3-gobject python3-pyqt5 python3-sip python3-tornado
texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2
gfortran python-numpy-doc python-pandas-doc python3-statsmodels
python-pil-doc python-pyparsing-doc python3-cryptography python3-openssl
python3-socks python-requests-doc python-scipy-doc python-setuptools-doc
texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.12-venv
python3.12-doc binfmt-support python3.13-venv python3.13-doc
Recommended packages:
bzip2-doc manpages manpages-dev libarchive-cpio-perl javascript-common
libgpm2 libtasn1-doc libltdl-dev libmail-sendmail-perl python3-bs4
python3-cssselect python3-html5lib python3-bottleneck python3-numexpr
python3-odf python3-openpyxl python3-tables python3-jinja2 python3-olefile
python3-pygments isympy-common
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot
fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libblas3
libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64
libevent-2.1-7t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgcc-14-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64
libgnutls-openssl27t64 libgnutls28-dev libgraphite2-3 libharfbuzz0b
libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libimagequant0
libisl23 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui
libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4
liblsan0 liblzma-dev libmpc3 libmpfr6 libncursesw6 libnghttp2-dev
libnghttp3-dev libngtcp2-crypto-gnutls-dev libngtcp2-dev libnsl2
libopenjp2-7 libp11-kit-dev libpkgconf3 libpng16-16t64 libpsl-dev
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev
libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libpython3.13
libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0
libraqm0 librtmp-dev libsharpyuv0 libssh2-1-dev libssl-dev libstdc++-14-dev
libtasn1-6-dev libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6
libtool libtsan2 libubsan1 libunbound8 libwebp7 libwebpdemux2 libwebpmux3
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1
libxslt1.1 libxss1 libzstd-dev linux-libc-dev m4 media-types nettle-dev
pkgconf pkgconf-bin po-debconf python-matplotlib-data python3 python3-all
python3-all-dev python3-appdirs python3-attr python3-autocommand
python3-bioframe python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-click python3-colorama python3-contourpy
python3-cycler python3-dateutil python3-decorator python3-dev
python3-exceptiongroup python3-fonttools python3-fs python3-idna
python3-inflect python3-iniconfig python3-jaraco.context
python3-jaraco.functools python3-jaraco.text python3-kiwisolver python3-lxml
python3-lz4 python3-matplotlib python3-minimal python3-more-itertools
python3-mpmath python3-numpy python3-packaging python3-pandas
python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources
python3-pluggy python3-pyparsing python3-pysam python3-pytest
python3-requests python3-scipy python3-setuptools python3-six python3-sympy
python3-tk python3-typeguard python3-typing-extensions python3-tz
python3-ufolib2 python3-urllib3 python3-yaml python3-zipp python3.12
python3.12-dev python3.12-minimal python3.12-tk python3.13 python3.13-dev
python3.13-minimal python3.13-tk rpcsvc-proto
sbuild-build-depends-main-dummy tk8.6-blt2.5 unicode-data x11-common
zlib1g-dev
0 upgraded, 214 newly installed, 0 to remove and 0 not upgraded.
Need to get 145 MB/180 MB of archives.
After this operation, 835 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [996 B]
Get:2 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-2 [808 kB]
Get:6 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ cython3 3.0.11+dfsg-1+debusine1 [2724 kB]
Get:7 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
Get:8 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ libpython3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:9 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:10 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:11 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:12 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-2 [90.1 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-2 [1939 kB]
Get:14 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-numpy 1:1.26.4+ds-11+bd1 [3816 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2+b1 [125 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-2 [1902 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-2 [671 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0-1 [849 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:24 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-scipy 1.13.1-5+nocheck1 [18.1 MB]
Get:25 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:29 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-pandas-lib 2.2.3+dfsg-5+bd1 [6022 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:31 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-pysam 0.22.1+ds-2+debusine1 [3880 kB]
Get:32 file:/<<BUILDDIR>>/resolver-FBEncw/apt_archive ./ python3-yaml 6.0.2-1+debusine1 [149 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.10-1 [337 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.10-1 [788 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B]
Get:53 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.6-1 [2449 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b2 [680 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b3 [50.5 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8 [9166 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-8 [1284 B]
Get:63 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:64 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:65 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-8 [42.2 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:74 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:76 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:77 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB]
Get:79 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:81 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:82 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:83 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:88 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:98 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 75.2.0-1 [731 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20241024 [109 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 libbrotli-dev arm64 1.1.0-2+b5 [308 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libunbound8 arm64 1.22.0-1 [553 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 libgnutls-dane0t64 arm64 3.8.6-2+b1 [437 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libgnutls-openssl27t64 arm64 3.8.6-2+b1 [437 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 libgnutls28-dev arm64 3.8.6-2+b1 [1398 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libcurl4-gnutls-dev arm64 8.10.1-2 [456 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-2 [142 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-2 [1982 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-2 [4788 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-2 [505 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 python3-attr all 24.2.0-1 [68.4 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 python3-pil arm64 10.4.0-1 [480 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 python3.12-tk arm64 3.12.7-2 [111 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 python3.13-tk arm64 3.13.0-1 [101 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 python3-tk arm64 3.12.6-1 [9428 B]
Get:182 http://deb.debian.org/debian sid/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 python3-cycler all 0.12.1-1 [9496 B]
Get:186 http://deb.debian.org/debian sid/main arm64 python3-brotli arm64 1.1.0-2+b5 [307 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.1-2 [30.9 kB]
Get:188 http://deb.debian.org/debian sid/main arm64 python3-six all 1.16.0-7 [16.4 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 python3-fs all 2.4.16-4 [95.4 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b5 [25.3 kB]
Get:192 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:193 http://deb.debian.org/debian sid/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 unicode-data all 15.1.0-1 [8547 kB]
Get:197 http://deb.debian.org/debian sid/main arm64 python3-fonttools arm64 4.54.1-4 [1356 kB]
Get:198 http://deb.debian.org/debian sid/main arm64 python3-kiwisolver arm64 1.4.7-2 [56.7 kB]
Get:199 http://deb.debian.org/debian sid/main arm64 python3-packaging all 24.1-1 [45.8 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 python3-matplotlib arm64 3.8.3-3 [5509 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get:202 http://deb.debian.org/debian sid/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get:203 http://deb.debian.org/debian sid/main arm64 python3-charset-normalizer arm64 3.4.0-1 [112 kB]
Get:204 http://deb.debian.org/debian sid/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get:205 http://deb.debian.org/debian sid/main arm64 python3-urllib3 all 2.0.7-2 [111 kB]
Get:206 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:207 http://deb.debian.org/debian sid/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get:208 http://deb.debian.org/debian sid/main arm64 python3-bioframe all 0.4.1-1 [71.6 kB]
Get:209 http://deb.debian.org/debian sid/main arm64 python3-colorama all 0.4.6-4 [36.2 kB]
Get:210 http://deb.debian.org/debian sid/main arm64 python3-click all 8.1.7-2 [94.3 kB]
Get:211 http://deb.debian.org/debian sid/main arm64 python3-exceptiongroup all 1.2.2-1 [19.7 kB]
Get:212 http://deb.debian.org/debian sid/main arm64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:213 http://deb.debian.org/debian sid/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:214 http://deb.debian.org/debian sid/main arm64 python3-pytest all 8.3.3-1 [249 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:arm64 (2.6.3-2) ...
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Setting up python3-minimal (3.12.6-1+debusine1) ...
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.6-1
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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: pairtools
Binary: python3-pairtools, python3-pairtools-examples
Architecture: any
Version: 1.0.3-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Antoni Villalonga <antoni@friki.cat>
Homepage: https://github.com/mirnylab/pairtools
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/pairtools
Vcs-Git: https://salsa.debian.org/med-team/pairtools.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-pytest
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, cython3, python3-setuptools, python3-bioframe, python3-click, python3-exceptiongroup, python3-numpy, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-pytest <!nocheck>, python3-scipy, libhts-dev, python3-yaml <!nocheck>
Package-List:
python3-pairtools deb python optional arch=any
python3-pairtools-examples deb python optional arch=any
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LnQJPAM1VP0=
=d4i+
-----END PGP SIGNATURE-----
gpgv: Signature made Mon Dec 11 14:44:59 2023 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pairtools_1.0.3-1.dsc: no acceptable signature found
dpkg-source: info: extracting pairtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pairtools_1.0.3.orig.tar.gz
dpkg-source: info: unpacking pairtools_1.0.3-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying makefile
dpkg-source: info: applying fix-spelling
dpkg-source: info: applying tests-to-python3
dpkg-source: info: applying fix-pysam-ftbfs.patch
dpkg-source: info: applying do-not-run-coverage.patch
dpkg-source: info: applying no_install_depends_cython.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.0.3-1+bd1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mDebusine Rebuild <debusine@example.net> -B -rfakeroot
dpkg-buildpackage: info: source package pairtools
dpkg-buildpackage: info: source version 1.0.3-1+bd1
dpkg-buildpackage: info: source distribution sid
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --with numpy3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:311: python3.13 setup.py clean
/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>>/pairtools/lib/dedup_cython.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/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>>/pairtools/lib/parse_pysam.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
/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>>/pairtools/lib/regions.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling /<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.pyx because it changed.
Compiling /<<PKGBUILDDIR>>/pairtools/lib/regions.pyx because it changed.
Compiling /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.pyx because it changed.
[1/3] Cythonizing /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.pyx
[2/3] Cythonizing /<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.pyx
[3/3] Cythonizing /<<PKGBUILDDIR>>/pairtools/lib/regions.pyx
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
I: pybuild base:311: python3.12 setup.py clean
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
rm -f pairtools/lib/*.c pairtools/lib/regions.cpp
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with numpy3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config
/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>>/pairtools/lib/dedup_cython.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/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>>/pairtools/lib/parse_pysam.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
/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>>/pairtools/lib/regions.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling /<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.pyx because it changed.
Compiling /<<PKGBUILDDIR>>/pairtools/lib/regions.pyx because it changed.
Compiling /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.pyx because it changed.
[1/3] Cythonizing /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.pyx
[2/3] Cythonizing /<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.pyx
[3/3] Cythonizing /<<PKGBUILDDIR>>/pairtools/lib/regions.pyx
running config
I: pybuild base:311: python3.12 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.13 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools
copying pairtools/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools
copying pairtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools
copying pairtools/_logging.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/filterbycov.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/dedup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/phase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/scaling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/pairsam_format.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/headerops.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/restrict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
copying pairtools/lib/fileio.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/filterbycov.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/dedup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/phase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/scaling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/merge.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/split.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/flip.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/sort.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/restrict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/markasdup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
copying pairtools/cli/parse2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/cli
running build_ext
building 'pairtools.lib.parse_pysam' extension
creating build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib
aarch64-linux-gnu-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipairtools/lib -I/usr/lib/python3/dist-packages/pysam -I/usr/lib/python3/dist-packages/pysam/include/samtools -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.c -o build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.o
/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.c:3259:9: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations]
3259 | Py_UNICODE *as_pyunicodes;
| ^~~~~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib/parse_pysam.cpython-313-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-313-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-313-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-313-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-313-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-313-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-313-aarch64-linux-gnu.so
building 'pairtools.lib.regions' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /<<PKGBUILDDIR>>/pairtools/lib/regions.cpp -o build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib/regions.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from /<<PKGBUILDDIR>>/pairtools/lib/regions.cpp:1302:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
/<<PKGBUILDDIR>>/pairtools/lib/regions.cpp:2634:21: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations]
2634 | Py_UNICODE *as_pyunicodes;
| ^~~~~~~~~~~~~
In file included from /usr/include/python3.13/unicodeobject.h:1014,
from /usr/include/python3.13/Python.h:79,
from /<<PKGBUILDDIR>>/pairtools/lib/regions.cpp:30:
/usr/include/python3.13/cpython/unicodeobject.h:10:37: note: declared here
10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE;
| ^~~~~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib/regions.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib/regions.cpython-313-aarch64-linux-gnu.so
building 'pairtools.lib.dedup_cython' extension
aarch64-linux-gnu-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.c -o build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.c:1240:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pairtools/lib/dedup_cython.cpython-313-aarch64-linux-gnu.so
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools
copying pairtools/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools
copying pairtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools
copying pairtools/_logging.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/filterbycov.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/dedup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/phase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/scaling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/pairsam_format.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/headerops.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/restrict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
copying pairtools/lib/fileio.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/filterbycov.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/dedup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/header.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/phase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/select.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/scaling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/merge.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/split.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/flip.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/sort.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/restrict.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/markasdup.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
copying pairtools/cli/parse2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/cli
running build_ext
building 'pairtools.lib.parse_pysam' extension
creating build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib
aarch64-linux-gnu-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipairtools/lib -I/usr/lib/python3/dist-packages/pysam -I/usr/lib/python3/dist-packages/pysam/include/samtools -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.c -o build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.o
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/parse_pysam.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-312-aarch64-linux-gnu.so
building 'pairtools.lib.regions' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /<<PKGBUILDDIR>>/pairtools/lib/regions.cpp -o build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/regions.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from /<<PKGBUILDDIR>>/pairtools/lib/regions.cpp:1302:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/regions.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/regions.cpython-312-aarch64-linux-gnu.so
building 'pairtools.lib.dedup_cython' extension
aarch64-linux-gnu-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.c -o build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from /<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.c:1240:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/dedup_cython.o -L/usr/lib/aarch64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/dedup_cython.cpython-312-aarch64-linux-gnu.so
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- --system=custom --test-args="export CURPY={interpreter}; \
cd {build_dir} && {interpreter} -m pytest -v"
I: pybuild base:311: export CURPY=python3.13; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build && python3.13 -m pytest -v
============================= test session starts ==============================
platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build
configfile: pytest.ini
testpaths: tests
plugins: typeguard-4.4.1
collecting ... collected 17 items / 2 errors
==================================== ERRORS ====================================
___________________ ERROR collecting tests/test_headerops.py ___________________
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/tests/test_headerops.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_headerops.py:2: in <module>
from pairtools.lib import headerops
pairtools/lib/__init__.py:1: in <module>
from . import fileio
pairtools/lib/fileio.py:2: in <module>
import pipes
E ModuleNotFoundError: No module named 'pipes'
____________________ ERROR collecting tests/test_select.py _____________________
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/tests/test_select.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_select.py:6: in <module>
from pairtools.lib import pairsam_format
pairtools/lib/__init__.py:1: in <module>
from . import fileio
pairtools/lib/fileio.py:2: in <module>
import pipes
E ModuleNotFoundError: No module named 'pipes'
=========================== short test summary info ============================
ERROR tests/test_headerops.py
ERROR tests/test_select.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 2 errors in 0.51s ===============================
E: pybuild pybuild:389: test: plugin custom failed with: exit code=2: export CURPY=python3.13; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build && python3.13 -m pytest -v
I: pybuild base:311: export CURPY=python3.12; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build && python3.12 -m pytest -v
============================= test session starts ==============================
platform linux -- Python 3.12.7+, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
configfile: pytest.ini
testpaths: tests
plugins: typeguard-4.4.1
collecting ... collected 31 items
tests/test_dedup.py::test_mock_pairsam PASSED [ 3%]
tests/test_filterbycov.py::test_mock_pairs PASSED [ 6%]
tests/test_flip.py::test_flip PASSED [ 9%]
tests/test_header.py::test_generate PASSED [ 12%]
tests/test_headerops.py::test_make_standard_header PASSED [ 16%]
tests/test_headerops.py::test_samheaderops PASSED [ 19%]
tests/test_headerops.py::test_merge_pairheaders PASSED [ 22%]
tests/test_headerops.py::test_merge_different_pairheaders PASSED [ 25%]
tests/test_headerops.py::test_force_merge_pairheaders PASSED [ 29%]
tests/test_headerops.py::test_merge_samheaders PASSED [ 32%]
tests/test_headerops.py::test_merge_headers PASSED [ 35%]
tests/test_markasdup.py::test_mock_pairsam PASSED [ 38%]
tests/test_merge.py::test_mock_pairsam PASSED [ 41%]
tests/test_parse.py::test_python_version PASSED [ 45%]
tests/test_parse.py::test_mock_pysam PASSED [ 48%]
tests/test_parse.py::test_mock_pysam_parse_all PASSED [ 51%]
tests/test_parse2.py::test_mock_pysam_parse2_read PASSED [ 54%]
tests/test_parse2.py::test_mock_pysam_parse2_pair PASSED [ 58%]
tests/test_restrict.py::test_restrict PASSED [ 61%]
tests/test_scaling.py::test_scaling PASSED [ 64%]
tests/test_select.py::test_preserve PASSED [ 67%]
tests/test_select.py::test_equal PASSED [ 70%]
tests/test_select.py::test_csv PASSED [ 74%]
tests/test_select.py::test_wildcard PASSED [ 77%]
tests/test_select.py::test_regex PASSED [ 80%]
tests/test_select.py::test_chrom_subset PASSED [ 83%]
tests/test_select.py::test_remove_columns PASSED [ 87%]
tests/test_sort.py::test_mock_pairsam PASSED [ 90%]
tests/test_split.py::test_split PASSED [ 93%]
tests/test_stats.py::test_mock_pairsam PASSED [ 96%]
tests/test_stats.py::test_merge_stats PASSED [100%]
=============================== warnings summary ===============================
pairtools/lib/fileio.py:2
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/fileio.py:2: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13
import pipes
pairtools/lib/stats.py:928
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/stats.py:928: SyntaxWarning: invalid escape sequence '\w'
"""Extract the name of the tile for each read name in the series
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================= 31 passed, 2 warnings in 39.04s ========================
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13 3.12" --system=custom "--test-args=export CURPY={interpreter}; cd {build_dir} && {interpreter} -m pytest -v" returned exit code 13
make[1]: *** [debian/rules:16: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-05T19:49:47Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: arm64
Build Type: any
Build-Space: 21760
Build-Time: 85
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 109
Job: /tmp/debusine-fetch-exec-upload-6jyuinkw/pairtools_1.0.3-1.dsc
Machine Architecture: arm64
Package: pairtools
Package-Time: 242
Source-Version: 1.0.3-1
Space: 21760
Status: attempted
Version: 1.0.3-1+bd1
--------------------------------------------------------------------------------
Finished at 2024-11-05T19:49:47Z
Build needed 00:04:02, 21760k disk space