pybigwig →
0.3.22+dfsg-1 →
armhf → 2023-09-15 13:18:30
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| pybigwig 0.3.22+dfsg-1 (armhf) Fri, 15 Sep 2023 13:05:04 +0000 |
+==============================================================================+
Package: pybigwig
Version: 0.3.22+dfsg-1
Source Version: 0.3.22+dfsg-1
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-585dee26-cc75-42d3-a3be-cadb906b7ff7' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
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 [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.6 MB]
Fetched 28.7 MB in 31s (930 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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: 'pybigwig' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pybigwig.git
Please use:
git clone https://salsa.debian.org/med-team/pybigwig.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 38.0 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main pybigwig 0.3.22+dfsg-1 (dsc) [2143 B]
Get:2 http://172.17.4.1/private trixie-staging/main pybigwig 0.3.22+dfsg-1 (tar) [31.6 kB]
Get:3 http://172.17.4.1/private trixie-staging/main pybigwig 0.3.22+dfsg-1 (diff) [4244 B]
Fetched 38.0 kB in 0s (423 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pybigwig-yiFrCO/pybigwig-0.3.22+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pybigwig-yiFrCO' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-2XjHAE/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-2XjHAE/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-2XjHAE/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2768 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core 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:
krb5-locales libpam-cap netbase sensible-utils sgml-base
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (18.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11771 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, libcurl4-gnutls-dev, zlib1g-dev, libbigwig-dev, python3-all, python3-all-dev, python3-numpy, python3-setuptools
Filtered Build-Depends: debhelper-compat (= 13), dh-python, libcurl4-gnutls-dev, zlib1g-dev, libbigwig-dev, python3-all, python3-all-dev, python3-numpy, python3-setuptools
dpkg-deb: building package 'sbuild-build-depends-pybigwig-dummy' in '/<<BUILDDIR>>/resolver-2XjHAE/apt_archive/sbuild-build-depends-pybigwig-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pybigwig-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-2XjHAE/apt_archive ./ Packages [633 B]
Fetched 2515 B in 1s (3507 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pybigwig 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:
krb5-locales libpam-cap netbase sgml-base
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbigwig-dev
libbigwig0 libblas3 libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libgfortran5 libicu72 libjs-jquery
libjs-sphinxdoc libjs-underscore liblapack3 libmagic-mgc libmagic1
libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev
libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all
python3-all-dev python3-dev python3-distutils python3-lib2to3
python3-minimal python3-numpy python3-pkg-resources python3-setuptools
python3.11 python3.11-dev python3.11-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev
groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv gfortran python3-pytest
python-setuptools-doc python3.11-venv python3.11-doc binfmt-support
Recommended packages:
curl | wget | lynx curl ca-certificates libarchive-cpio-perl
javascript-common publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbigwig-dev
libbigwig0 libblas3 libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libgfortran5 libicu72 libjs-jquery
libjs-sphinxdoc libjs-underscore liblapack3 libmagic-mgc libmagic1
libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev
libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal
libpython3.11-stdlib librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all
python3-all-dev python3-dev python3-distutils python3-lib2to3
python3-minimal python3-numpy python3-pkg-resources python3-setuptools
python3.11 python3.11-dev python3.11-minimal
sbuild-build-depends-pybigwig-dummy zlib1g-dev
0 upgraded, 70 newly installed, 0 to remove and 4 not upgraded.
Need to get 38.2 MB of archives.
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Get:2 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.2-6 [797 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.2-6 [1679 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.2-1 [26.0 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1668 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.2-6 [572 kB]
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Get:13 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.38.1-5 [78.5 kB]
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Get:15 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-2 [1342 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
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Get:18 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.44-3 [41.5 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-12 [156 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-3 [256 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
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Get:25 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
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Get:28 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
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Get:31 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3~deb12u1 [570 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-12 [1201 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
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Get:43 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
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Get:53 http://172.17.4.1/private trixie-staging/main armhf libexpat1-dev armhf 2.5.0-1 [130 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 12.2.0-14+rpi1 [238 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
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Get:57 http://172.17.4.1/private trixie-staging/main armhf libjs-sphinxdoc all 5.3.0-7 [131 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libpython3.11 armhf 3.11.2-6 [1667 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-dev armhf 3.11.2-6 [3364 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libpython3-dev armhf 3.11.2-1 [9248 B]
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Get:64 http://172.17.4.1/private trixie-staging/main armhf python3-all armhf 3.11.2-1 [1060 B]
Get:65 http://172.17.4.1/private trixie-staging/main armhf python3.11-dev armhf 3.11.2-6 [511 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf python3-dev armhf 3.11.2-1 [26.2 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf python3-all-dev armhf 3.11.2-1 [1068 B]
Get:68 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-1 [241 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf python3-numpy armhf 1:1.24.2-1 [3826 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-1 [468 kB]
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Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.6.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_12.4+rpi1+deb12u1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.38.1-5 bsdutils_1:2.38.1-5 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.6 debianutils_5.7-0.4 dh-autoreconf_20 dh-python_6.20230825 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-12 gettext-base_0.21-12 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 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libcurl3-gnutls_7.88.1-10+rpi1 libcurl4-gnutls-dev_7.88.1-10+rpi1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.270 libdebhelper-perl_13.11.6 libdpkg-perl_1.21.22+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.47.0-2 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14+rpi1 libgcc-s1_12.2.0-14+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14+rpi1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-2 libgomp1_12.2.0-14+rpi1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-2 libhogweed6_3.8.1-2 libicu72_72.1-3 libidn2-0_2.3.3-1+b2 libisl23_0.25-1 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_5.3.0-7 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 libksba8_1.6.3-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-5 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncursesw6_6.4-4 libnettle8_3.8.1-2 libnghttp2-14_1.52.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-2 libpam-cap_1:2.66-4 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-7 libpam0g_1.5.2-6 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpsl5_0.21.2-1 libpython3-all-dev_3.11.2-1 libpython3-dev_3.11.2-1 libpython3-stdlib_3.11.2-1 libpython3.11_3.11.2-6 libpython3.11-dev_3.11.2-6 libpython3.11-minimal_3.11.2-6 libpython3.11-stdlib_3.11.2-6 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.4-1+b2 libsemanage-common_3.5-1 libsemanage2_3.4-1+b2 libsepol1_3.1-1 libsepol2_3.4-2.1 libsmartcols1_2.38.1-5 libsqlite3-0_3.40.1-2 libss2_1.47.0-2 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.9-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-5 libxml2_2.9.14+dfsg-1.3~deb12u1 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 media-types_10.1.0 mount_2.38.1-5 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4-4 netbase_6.4 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.11.2-1 python3-all_3.11.2-1 python3-all-dev_3.11.2-1 python3-dev_3.11.2-1 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.11.2-1 python3-numpy_1:1.24.2-1 python3-pkg-resources_68.1.2-1 python3-setuptools_68.1.2-1 python3.11_3.11.2-6 python3.11-dev_3.11.2-6 python3.11-minimal_3.11.2-6 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pybigwig-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.06-4 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_37 util-linux_2.38.1-5 util-linux-extra_2.38.1-5 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Sun Jul 30 18:24:04 2023 UTC
gpgv: using RSA key 4D055C31E4812045F9010D75990D38367334D770
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pybigwig_0.3.22+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting pybigwig in /<<BUILDDIR>>/pybigwig-0.3.22+dfsg
dpkg-source: info: unpacking pybigwig_0.3.22+dfsg.orig.tar.gz
dpkg-source: info: unpacking pybigwig_0.3.22+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying prepareForExternalLibBigWig.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-585dee26-cc75-42d3-a3be-cadb906b7ff7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pybigwig
dpkg-buildpackage: info: source version 0.3.22+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from pybigwig-0.3.22+dfsg/debian/source/options: --extend-diff-ignore=^(.*\.egg-info/)
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:291: python3.11 setup.py clean
running clean
removing '/<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/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
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with python3 --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:291: python3.11 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:291: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest
copying pyBigWigTest/__init__.py -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest
copying pyBigWigTest/test.py -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest
running egg_info
creating pyBigWig.egg-info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '**/*.h'
adding license file 'LICENSE.txt'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
running build_ext
building 'pyBigWig' extension
creating build
creating build/temp.linux-armv7l-cpython-311
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pybigwig-0.3.22+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c pyBigWig.c -o build/temp.linux-armv7l-cpython-311/pyBigWig.o
pyBigWig.c: In function 'PyString_AsString':
pyBigWig.c:773:12: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
773 | return PyUnicode_AsUTF8(obj);
| ^~~~~~~~~~~~~~~~~~~~~
pyBigWig.c: In function 'Numeric2Uint':
pyBigWig.c:798:10: warning: comparison of integer expressions of different signedness: 'long int' and 'unsigned int' [-Wsign-compare]
798 | if(l > 0xFFFFFFFF) {
| ^
pyBigWig.c: In function 'pyBwAddHeader':
pyBigWig.c:883:20: warning: comparison of integer expressions of different signedness: 'long int' and 'unsigned int' [-Wsign-compare]
883 | if(zoomTmp > 0xFFFFFFFF) {
| ^
pyBigWig.c:897:32: warning: passing argument 1 of 'bwCreateChromList' from incompatible pointer type [-Wincompatible-pointer-types]
897 | bw->cl = bwCreateChromList(chroms, lengths, n);
| ^~~~~~
| |
| char **
In file included from pyBigWig.h:3,
from pyBigWig.c:3:
/usr/include/bigWig.h:497:51: note: expected 'const char * const*' but argument is of type 'char **'
497 | chromList_t *bwCreateChromList(const char* const* chroms, const uint32_t *lengths, int64_t n);
| ~~~~~~~~~~~~~~~~~~~^~~~~~
pyBigWig.c: In function 'PyAddIntervals':
pyBigWig.c:1251:29: warning: passing argument 2 of 'bwAddIntervals' from incompatible pointer type [-Wincompatible-pointer-types]
1251 | rv = bwAddIntervals(bw, cchroms, ustarts, uends, fvalues, n);
| ^~~~~~~
| |
| char **
/usr/include/bigWig.h:524:57: note: expected 'const char * const*' but argument is of type 'char **'
524 | int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *start, const uint32_t *end, const float *values, uint32_t n);
| ~~~~~~~~~~~~~~~~~~~^~~~~
pyBigWig.c:1257:19: warning: comparison of integer expressions of different signedness: 'Py_ssize_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare]
1257 | for(i=0; i<n; i++) free(cchroms[i]);
| ^
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/pybigwig-0.3.22+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pyBigWig.o -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/python3.11/config-3.11-arm-linux-gnueabihf -L/usr/lib/python3/dist-packages/numpy/core/include/../lib -L/usr/lib/arm-linux-gnueabihf -lBigWig -lm -lz -lpython3.11 -lcurl -lnpymath -o /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWig.cpython-311-arm-linux-gnueabihf.so
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:291: cd /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build; python3.11 -m unittest discover -v
----------------------------------------------------------------------
Ran 0 tests in 0.000s
OK
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/pybigwig-0.3.22+dfsg'
dh_auto_install
I: pybuild base:291: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig
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_py
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '**/*.h'
adding license file 'LICENSE.txt'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
running build_ext
running install_lib
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest
copying /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest/__init__.py -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest
copying /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest/test.py -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest
creating /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest/__pycache__
copying /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest/__pycache__/__init__.cpython-311.pyc -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest/__pycache__
copying /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWigTest/__pycache__/test.cpython-311.pyc -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest/__pycache__
copying /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/.pybuild/cpython3_3.11_pybigwig/build/pyBigWig.cpython-311-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages
byte-compiling /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWigTest/test.py to test.cpython-311.pyc
running install_egg_info
Copying pyBigWig.egg-info to /<<BUILDDIR>>/pybigwig-0.3.22+dfsg/debian/python3-pybigwig/usr/lib/python3.11/dist-packages/pyBigWig-0.3.22.egg-info
Skipping SOURCES.txt
running install_scripts
dh_numpy3
make[1]: Leaving directory '/<<BUILDDIR>>/pybigwig-0.3.22+dfsg'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_python3 -a -O--buildsystem=pybuild
dh_installsystemduser -a -O--buildsystem=pybuild
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
dh_compress -a -O--buildsystem=pybuild
dh_fixperms -a -O--buildsystem=pybuild
dh_missing -a -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -a -O--buildsystem=pybuild
dh_gencontrol -a -O--buildsystem=pybuild
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python3-pybigwig' in '../python3-pybigwig_0.3.22+dfsg-1_armhf.deb'.
dpkg-deb: building package 'python3-pybigwig-dbgsym' in '../python3-pybigwig-dbgsym_0.3.22+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../pybigwig_0.3.22+dfsg-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../pybigwig_0.3.22+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-source: info: using options from pybigwig-0.3.22+dfsg/debian/source/options: --extend-diff-ignore=^(.*\.egg-info/)
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-09-15T13:18:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pybigwig_0.3.22+dfsg-1_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sun, 30 Jul 2023 11:11:13 -0700
Source: pybigwig
Binary: python3-pybigwig python3-pybigwig-dbgsym
Architecture: armhf
Version: 0.3.22+dfsg-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Diane Trout <diane@ghic.org>
Description:
python3-pybigwig - Python 3 module for quick access to bigBed and bigWig files
Changes:
pybigwig (0.3.22+dfsg-1) unstable; urgency=medium
.
* New upstream release
* Refresh patches
* Remove commented out python 2 build dependencies from d/control
* Bump Standards-Version to 4.6.2. No changes needed.
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3fe972e98e92a06205b364b104c55a29d968306d 51172 python3-pybigwig-dbgsym_0.3.22+dfsg-1_armhf.deb
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Files:
75e03353bab8fa9ea9f02abfd2537cc9 6873 science optional pybigwig_0.3.22+dfsg-1_armhf.buildinfo
1278f77870596960f067a3de3299d066 51172 debug optional python3-pybigwig-dbgsym_0.3.22+dfsg-1_armhf.deb
a12d196936f309952f7f3b7f64cbcde6 33636 science optional python3-pybigwig_0.3.22+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python3-pybigwig-dbgsym_0.3.22+dfsg-1_armhf.deb
-----------------------------------------------
new Debian package, version 2.0.
size 51172 bytes: control archive=552 bytes.
409 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: python3-pybigwig-dbgsym
Source: pybigwig
Version: 0.3.22+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 71
Depends: python3-pybigwig (= 0.3.22+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for python3-pybigwig
Build-Ids: 13ebf934be44096c3f0bf50de9348049c40eb89e
drwxr-xr-x root/root 0 2023-07-30 18:11 ./
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python3-pybigwig_0.3.22+dfsg-1_armhf.deb
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new Debian package, version 2.0.
size 33636 bytes: control archive=1808 bytes.
1795 bytes, 31 lines control
753 bytes, 8 lines md5sums
279 bytes, 12 lines * postinst #!/bin/sh
392 bytes, 12 lines * prerm #!/bin/sh
Package: python3-pybigwig
Source: pybigwig
Version: 0.3.22+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 113
Depends: python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3 (<< 3.12), python3 (>= 3.11~), python3:any, libbigwig0 (>= 0.4.6), libc6 (>= 2.4), libpython3.11 (>= 3.11.0)
Section: science
Priority: optional
Homepage: https://github.com/dpryan79/pyBigWig
Description: Python 3 module for quick access to bigBed and bigWig files
This is a Python extension, written in C, for quick access to bigBed files,
and access to and creation of bigWig files.
.
The bigWig format was originally created in the context of genome
browsers. There, computing exact summary statistics for a given interval
is less important than quickly being able to compute an approximate
statistic. Because of this, bigWig files contain not only interval-value
associations, but also `sum of values`/`sum of squared values`/`minimum
value`/`maximum value`/`number of bases covered` for equally sized
bins of various sizes. These different sizes are referred to as "zoom
levels". The smallest zoom level has bins that are 16 times the mean
interval size in the file and each subsequent zoom level has bins 4 times
larger than the previous. This methodology is used in Kent's tools and,
therefore, likely used in almost every currently existing bigWig file.
.
When a bigWig file is queried for a summary statistic, the size of the
interval is used to determine whether to use a zoom level and, if so,
which one. The optimal zoom level is that which has the largest bins no
more than half the width of the desired interval. If no such zoom level
exists, the original intervals are instead used for the calculation.
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-rw-r--r-- root/root 1 2023-07-30 18:11 ./usr/lib/python3/dist-packages/pyBigWig-0.3.22.egg-info/dependency_links.txt
-rw-r--r-- root/root 22 2023-07-30 18:11 ./usr/lib/python3/dist-packages/pyBigWig-0.3.22.egg-info/top_level.txt
-rw-r--r-- root/root 63440 2023-07-30 18:11 ./usr/lib/python3/dist-packages/pyBigWig.cpython-311-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2023-07-30 18:11 ./usr/lib/python3/dist-packages/pyBigWigTest/
-rw-r--r-- root/root 0 2023-04-07 18:29 ./usr/lib/python3/dist-packages/pyBigWigTest/__init__.py
-rw-r--r-- root/root 13185 2023-04-07 18:29 ./usr/lib/python3/dist-packages/pyBigWigTest/test.py
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drwxr-xr-x root/root 0 2023-07-30 18:11 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-07-30 18:11 ./usr/share/doc/python3-pybigwig/
-rw-r--r-- root/root 843 2023-07-30 18:11 ./usr/share/doc/python3-pybigwig/changelog.Debian.gz
-rw-r--r-- root/root 1461 2023-07-30 18:10 ./usr/share/doc/python3-pybigwig/copyright
+------------------------------------------------------------------------------+
| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 1036
Build-Time: 88
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 652
Job: pybigwig_0.3.22+dfsg-1
Machine Architecture: armhf
Package: pybigwig
Package-Time: 799
Source-Version: 0.3.22+dfsg-1
Space: 1036
Status: successful
Version: 0.3.22+dfsg-1
--------------------------------------------------------------------------------
Finished at 2023-09-15T13:18:23Z
Build needed 00:13:19, 1036k disc space