Debian Bug report logs - #868927
python-pybedtools FTBFS with more than one supported Python3 version

Toggle useless messages

Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Lucas Nussbaum <lucas@debian.org>

To: submit@bugs.debian.org

Subject: python-pybedtools: FTBFS: pybedtools/cbedtools.cxx:4:20: fatal error: Python.h: No such file or directory

Date: Wed, 19 Jul 2017 17:55:55 +0200

Source: python-pybedtools
Version: 0.7.8-1
Severity: serious
Tags: buster sid
User: debian-qa@lists.debian.org
Usertags: qa-ftbfs-20170719 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.6m -c pybedtools/cbedtools.cxx -o build/temp.linux-amd64-3.6/pybedtools/cbedtools.o
> cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
> pybedtools/cbedtools.cxx:4:20: fatal error: Python.h: No such file or directory
>  #include "Python.h"
>                     ^
> compilation terminated.
> error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
> E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1: /usr/bin/python3.6 setup.py build 
> dh_auto_build: pybuild --build --test-nose -i python{version} -p 3.6 3.5 returned exit code 13
> debian/rules:19: recipe for target 'override_dh_auto_build' failed
> make[1]: *** [override_dh_auto_build] Error 25

The full build log is available from:
   http://aws-logs.debian.net/2017/07/19/python-pybedtools_0.7.8-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.

Message #10 received at 868927@bugs.debian.org (full text, mbox, reply):

From: Adrian Bunk <bunk@debian.org>

To: 868927@bugs.debian.org

Subject: python-pybedtools FTBFS with more than one supported Python3 version

Date: Wed, 19 Jul 2017 20:45:33 +0300

Control: retitle -1 python-pybedtools FTBFS with more than one supported Python3 version
Control: tags -1 patch

Below is the fix (stolen from Ubuntu).

cu
Adrian


--- 0.7.8-1/debian/control	2017-01-14 09:51:01.000000000 +0000
+++ 0.7.8-1ubuntu1/debian/control	2017-06-26 10:59:20.000000000 +0000
@@ -7,9 +8,8 @@ Build-Depends: debhelper (>= 10),
                dh-python,
                bedtools,
                python3,
-               python3-all,
+               python3-all-dev,
                python3-setuptools,
-               python3-dev,
                python3-pysam,
                python3-matplotlib,
                python3-nose,

Message #19 received at 868927@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Adrian Bunk <bunk@debian.org>, 868927@bugs.debian.org

Subject: Re: Bug#868927: python-pybedtools FTBFS with more than one supported Python3 version

Date: Wed, 19 Jul 2017 21:37:35 +0200

Hi Adrian,

thanks for the patch.  I applied it in Git and also updated to the latest
upstream version.  However, when trying to build I'm running into

...
I: pybuild pybuild:219: cp /build/python-pybedtools-0.7.10/debian/mpl-expected.png /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/
I: pybuild base:184: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
E
======================================================================
ERROR: Failure: ModuleNotFoundError (No module named 'pysam.libchtslib')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/lib/python3/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 244, in load_module
    return load_package(name, filename)
  File "/usr/lib/python3.6/imp.py", line 216, in load_package
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 675, in _load
  File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/__init__.py", line 12, in <module>
    from . import contrib
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/contrib/__init__.py", line 3, in <module>
    from . import venn_maker
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/contrib/venn_maker.py", line 12, in <module>
    from pybedtools import helpers
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/helpers.py", line 13, in <module>
    import pysam
  File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 5, in <module>
    from pysam.libchtslib import *
ModuleNotFoundError: No module named 'pysam.libchtslib'

----------------------------------------------------------------------
Ran 1 test in 0.011s

FAILED (errors=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 3.5 returned exit code 13
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 25
...


I guess python-pysam is not yet build for Python3 3.6.

Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #24 received at 868927@bugs.debian.org (full text, mbox, reply):

From: Adrian Bunk <bunk@debian.org>

To: Andreas Tille <tille@debian.org>

Cc: 868927@bugs.debian.org

Subject: Re: Bug#868927: python-pybedtools FTBFS with more than one supported Python3 version

Date: Wed, 19 Jul 2017 22:47:09 +0300

On Wed, Jul 19, 2017 at 09:37:35PM +0200, Andreas Tille wrote:
>...
> I guess python-pysam is not yet build for Python3 3.6.

That's #867017/#867018, which seems to require that you update 
python-pysam to 0.11.2.2

> Kind regards
> 
>       Andreas.

cu
Adrian

-- 

       "Is there not promise of rain?" Ling Tan asked suddenly out
        of the darkness. There had been need of rain for many days.
       "Only a promise," Lao Er said.
                                       Pearl S. Buck - Dragon Seed

Message #29 received at 868927@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Adrian Bunk <bunk@debian.org>, 868927@bugs.debian.org

Subject: Re: Bug#868927: python-pybedtools FTBFS with more than one supported Python3 version

Date: Thu, 20 Jul 2017 07:56:02 +0200

Hi Adrian,

On Wed, Jul 19, 2017 at 10:47:09PM +0300, Adrian Bunk wrote:
> 
> That's #867017/#867018, which seems to require that you update 
> python-pysam to 0.11.2.2

Yes, I'm aware of it but I need to start the chain of dependencies
at htslib - samtools - python-pysam.

I'll try to work on this today.

Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #36 received at 868927@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 868927@bugs.debian.org

Subject: Re: Bug#868927: python-pybedtools FTBFS with more than one supported Python3 version

Date: Fri, 6 Oct 2017 21:50:25 +0200

On Wed, Jul 19, 2017 at 10:47:09PM +0300, Adrian Bunk wrote:
> On Wed, Jul 19, 2017 at 09:37:35PM +0200, Andreas Tille wrote:
> >...
> > I guess python-pysam is not yet build for Python3 3.6.
> 
> That's #867017/#867018, which seems to require that you update 
> python-pysam to 0.11.2.2

That's done now.  Unfortunately there is one remaining issue in the test
suite: 

...
I: pybuild base:184: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
..................................................................................................                                                                                        E.....................................................................................................................................................................................................................................................................................................................................................................................................S..
======================================================================
ERROR: pybedtools.test.test1.test_issue_178
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/test1.py", line 2108, in test_issue_178
    pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/contrib/bigwig.py", line 123, in bam_to_bigwig
    p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
  File "/usr/lib/python3.6/subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "/usr/lib/python3.6/subprocess.py", line 1344, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'bedGraphToBigWig': 'bedGraphToBigWig'

----------------------------------------------------------------------
Ran 491 tests in 12.192s

FAILED (SKIP=1, errors=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.6 3.5" returned exit code 13
...

Kind regards

       Andreas.

-- 
http://fam-tille.de

Message #43 received at 868927-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 868927-close@bugs.debian.org

Subject: Bug#868927: fixed in python-pybedtools 0.7.10-1

Date: Wed, 08 Nov 2017 08:56:32 +0000

Source: python-pybedtools
Source-Version: 0.7.10-1

We believe that the bug you reported is fixed in the latest version of
python-pybedtools, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 868927@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated python-pybedtools package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Wed, 08 Nov 2017 09:00:50 +0100
Source: python-pybedtools
Binary: python3-pybedtools
Architecture: source
Version: 0.7.10-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 python3-pybedtools - Python 3 wrapper around BEDTools for bioinformatics work
Closes: 868927
Changes:
 python-pybedtools (0.7.10-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
   * Build-Depends: python3-all-dev (Thanks for the hint to Adrian Bunk
     <bunk@debian.org>)
     Closes: #868927
   * Standards-Version: 4.1.1 (no changes needed)
   * do not uselessly parse d/changelog
   * hardening
   * Exclude test test_issue_178 since it fails for strange reasons (to be
     clarified with upstream)
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