Sat 20 Mar 2021 11:42:33 PM +08 | scanpy 1.6.0

> Sat 20 Mar 2021 11:42:33 PM +08  (master)
robbi@debian: pts/1: /home/robbi/Documents/workplace/debian_packages/scanpy
└─ $ sudo -E pdebuild
I: Used distribution is sid.
I: Build architecture is amd64.
I: Used cpus for building: 7.
dpkg-checkbuilddeps: error: Unmet build dependencies: python3-all python3-h5py python3-tqdm python3-sklearn python3-statsmodels python3-networkx python3-natsort python3-joblib umap-learn python3-harmony python3-zarr python3-anndata python3-sinfo python3-setuptools-scm python3-legacy-api-wrap
W: Unmet build-dependency in source
dpkg-source: info: using options from scanpy/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
        install -d /home/robbi/Documents/workplace/debian_packages/scanpy/debian/.debhelper/generated/_source/home
        pybuild --clean -i python{version} -p 3.9
I: pybuild base:232: python3.9 setup.py clean
/usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'use_scm_version'
  warnings.warn(msg)
running clean
removing '/home/robbi/Documents/workplace/debian_packages/scanpy/.pybuild/cpython3_3.9_scanpy/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.9' does not exist -- can't clean it
        rm -rf .pybuild/
        find . -name \*.pyc -exec rm {} \;
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
        rm -f debian/debhelper-build-stamp
        rm -rf debian/.debhelper/
        rm -f -- debian/python3-scanpy.substvars debian/files
        rm -fr -- debian/python3-scanpy/ debian/tmp/
        find .  \( \( \
                \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
                \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
                 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
                 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
                 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
                \) -exec rm -f {} + \) -o \
                \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
dpkg-source: info: using options from scanpy/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building scanpy using existing ./scanpy_1.6.0.orig.tar.gz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building scanpy in scanpy_1.6.0-2.debian.tar.xz
dpkg-source: info: building scanpy in scanpy_1.6.0-2.dsc
I: Generating source changes file for original dsc
dpkg-genchanges: info: including full source code in upload
dpkg-source: info: using options from scanpy/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-source: info: unapplying avoid_setuptools_scm.patch
I: Used distribution is sid.
I: Build architecture is amd64.
I: Used cpus for building: 7.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Mar 20 23:43:10 +08 2021
I: pbuilder-time-stamp: 1616254990
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/sid-amd64-base.tgz]
I: copying local configuration
W: No local /etc/mailname to copy, relying on /var/cache/pbuilder/build/43226/etc/mailname to be correct
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: Mounting /var/cache/pbuilder/ccache
I: Mounting /var/cache/pbuilder/sid-amd64/result/
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: Copying source file
I: copying [../scanpy_1.6.0-2.dsc]
I: copying [../scanpy_1.6.0.orig.tar.gz]
I: copying [../scanpy_1.6.0-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (scanpy_1.6.0-2.dsc)
dpkg-source: info: extracting scanpy in scanpy-1.6.0
dpkg-source: info: unpacking scanpy_1.6.0.orig.tar.gz
dpkg-source: info: unpacking scanpy_1.6.0-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying avoid_setuptools_scm.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /var/cache/pbuilder/build/43226/tmp/hooks/D10pdebuild-result-repo starting
Reading package lists...
Building dependency tree...
Reading state information...
apt-utils is already the newest version (2.2.2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Get:1 file:/var/cache/pbuilder/sid-amd64/result ./ InRelease
Ign:1 file:/var/cache/pbuilder/sid-amd64/result ./ InRelease
Get:2 file:/var/cache/pbuilder/sid-amd64/result ./ Release [120 B]
Get:2 file:/var/cache/pbuilder/sid-amd64/result ./ Release [120 B]
Ign:2 file:/var/cache/pbuilder/sid-amd64/result ./ Release
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages [870 B]
Get:4 http://mirror.0x.sg/debian sid InRelease [154 kB]
Get:5 http://mirror.0x.sg/debian sid/main amd64 Packages.diff/Index [63.6 kB]
Get:6 http://mirror.0x.sg/debian sid/main amd64 Packages T-2021-03-20-0803.20-F-2021-03-19-0801.12.pdiff [29.3 kB]
Get:6 http://mirror.0x.sg/debian sid/main amd64 Packages T-2021-03-20-0803.20-F-2021-03-19-0801.12.pdiff [29.3 kB]
Fetched 247 kB in 3s (75.5 kB/s)
Reading package lists...
I: user script /var/cache/pbuilder/build/43226/tmp/hooks/D10pdebuild-result-repo finished
I: user script /var/cache/pbuilder/build/43226/tmp/hooks/D70results starting
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   python3-legacy-api-wrap
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
Get:1 file:/var/cache/pbuilder/sid-amd64/result ./ InRelease
Ign:1 file:/var/cache/pbuilder/sid-amd64/result ./ InRelease
Get:2 file:/var/cache/pbuilder/sid-amd64/result ./ Release [120 B]
Get:2 file:/var/cache/pbuilder/sid-amd64/result ./ Release [120 B]
Ign:2 file:/var/cache/pbuilder/sid-amd64/result ./ Release
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Ign:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages
Get:3 file:/var/cache/pbuilder/sid-amd64/result ./ Packages [733 B]
Hit:4 http://mirror.0x.sg/debian sid InRelease
Reading package lists...
I: user script /var/cache/pbuilder/build/43226/tmp/hooks/D70results finished
I: -> Attempting to satisfy build-dependencies
Note, using file '/build/scanpy_1.6.0-2.dsc''true'.
Processing triggers for libc-bin (2.31-9) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
apt-utils is already the newest version (2.2.2).
ccache is already the newest version (4.2-1).
debhelper is already the newest version (13.3.4).
lintian is already the newest version (2.104.0).
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
I: Copying back the cached apt archive contents
I: Building the package
I: Running cd /build/scanpy-1.6.0/ && env PATH="/usr/lib/ccache:/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc -sa && env PATH="/usr/lib/ccache:/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-genchanges -S '-sa' > ../scanpy_1.6.0-2_source.changes
dpkg-buildpackage: info: source package scanpy
dpkg-buildpackage: info: source version 1.6.0-2
dpkg-buildpackage: info: source distribution UNRELEASED
dpkg-buildpackage: info: source changed by Robbi Nespu <robbinespu@gmail.com>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
dpkg-source: info: using options from scanpy-1.6.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
        install -d /build/scanpy-1.6.0/debian/.debhelper/generated/_source/home
        pybuild --clean -i python{version} -p 3.9
I: pybuild base:232: python3.9 setup.py clean
running clean
removing '/build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.9' does not exist -- can't clean it
        rm -rf .pybuild/
        find . -name \*.pyc -exec rm {} \;
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
        rm -f debian/debhelper-build-stamp
        rm -rf debian/.debhelper/
        rm -f -- debian/python3-scanpy.substvars debian/files
        rm -fr -- debian/python3-scanpy/ debian/tmp/
        find .  \( \( \
                \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
                \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
                 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
                 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
                 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
                \) -exec rm -f {} + \) -o \
                \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
 dpkg-source -b .
dpkg-source: info: using options from scanpy-1.6.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-source: info: using source format '3.0 (quilt)''scanpy.egg-info/SOURCES.txt'
reading manifest file 'scanpy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching '.coveragerc'
warning: no previously-included files found matching '.editorconfig'
warning: no previously-included files found matching '.gitattributes'
warning: no previously-included files found matching '.gitignore'
warning: no previously-included files found matching '.readthedocs.yml'
warning: no previously-included files found matching '.travis.yml'
warning: no previously-included files found matching 'CONTRIBUTING.md'
no previously-included directories found matching 'docs'
writing manifest file 'scanpy.egg-info/SOURCES.txt'
   dh_auto_test -O--buildsystem=pybuild
        pybuild --test -i python{version} -p 3.9
I: pybuild base:232: cd /build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build; python3.9 -m unittest discover -v
/build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build/scanpy/api/__init__.py:3: FutureWarning:

In a future version of Scanpy, `scanpy.api` will be removed.
Simply use `import scanpy as sc` and `import scanpy.external as sce` instead.

  warnings.warn(
scanpy.api (unittest.loader._FailedTest) ... ERROR

======================================================================
ERROR: scanpy.api (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: scanpy.api
Traceback (most recent call last):
  File "/usr/lib/python3.9/unittest/loader.py", line 470, in _find_test_path
    package = self._get_module_from_name(name)
  File "/usr/lib/python3.9/unittest/loader.py", line 377, in _get_module_from_name
    __import__(name)
  File "/build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build/scanpy/api/__init__.py", line 27, in <module>
    from . import pl
  File "/build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build/scanpy/api/pl.py", line 1, in <module>
    from ..plotting._anndata import scatter, violin, ranking, clustermap, stacked_violin, heatmap, dotplot, matrixplot, tracksplot
ImportError: cannot import name 'stacked_violin' from 'scanpy.plotting._anndata' (/build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build/scanpy/plotting/_anndata.py)


----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)
E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd /build/scanpy-1.6.0/.pybuild/cpython3_3.9_scanpy/build; python3.9 -m unittest discover -v
        rm -fr -- /tmp/dh-xdg-rundir-8yGFya2D
dh_auto_test: error: pybuild --test -i python{version} -p 3.9 returned exit code 13
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
I: copying local configuratio