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Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting

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  Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting Lucas Nussbaum <lucas@debian.org> - 2021-10-24 14:40 +0200
    Processed: Re: Bug#997772: python-cogent: FTBFS: You must  configure the bibtex_bibfiles setting "Debian Bug Tracking System" <owner@bugs.debian.org> - 2021-11-02 08:10 +0100
    Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting Andreas Tille <tille@debian.org> - 2021-11-03 09:10 +0100
      Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting Nilesh Patra <nilesh@nileshpatra.info> - 2021-11-03 11:00 +0100
    Processed: Re: Bug#997772: python-cogent: FTBFS: You must  configure the bibtex_bibfiles setting "Debian Bug Tracking System" <owner@bugs.debian.org> - 2021-11-03 09:10 +0100
    Bug#997772: marked as done (python-cogent: FTBFS: You must  configure the bibtex_bibfiles setting) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2021-11-03 12:10 +0100

#307250 — Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting

Source: python-cogent
Version: 2021.5.7a+dfsg-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas@debian.org
Usertags: ftbfs-20211023 ftbfs-bookworm

Hi,

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


Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> sphinx-build -b html -d _build/doctrees   . _build/html
> Running Sphinx v4.2.0
> making output directory... done
> WARNING: html_static_path entry '_static' does not exist
> WARNING: The config value `today' has type `date', defaults to `str'.
> 
> Extension error:
> You must configure the bibtex_bibfiles setting
> make[2]: *** [Makefile:40: html] Error 2


The full build log is available from:
http://qa-logs.debian.net/2021/10/23/python-cogent_2021.5.7a+dfsg-2_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!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

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#308084 — Processed: Re: Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting

Processing control commands:

> tags -1 help
Bug #997772 [src:python-cogent] python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Added tag(s) help.
> tags -1 upstream
Bug #997772 [src:python-cogent] python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Added tag(s) upstream.
> forwarded -1 https://github.com/cogent3/cogent3/issues/977
Bug #997772 [src:python-cogent] python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Set Bug forwarded-to-address to 'https://github.com/cogent3/cogent3/issues/977'.

-- 
997772: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997772
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#308168

Control: tags -1 pending

Hi Stuart,

Am Wed, Nov 03, 2021 at 09:43:40AM +1100 schrieb Stuart Prescott:
> > > > Extension error:
> > > > You must configure the bibtex_bibfiles setting
> > > > make[2]: *** [Makefile:40: html] Error 2
> 
> this is sphinxcontrib-bibtex saying that you need to add the following to 
> doc/conf.py:
> 
> bibtex_bibfiles = "path/to/references.bib"
> 
> However I can't see a .bib file anywhere in the source. I also can't see any 
> code in the rst files or the docstrings that would actually use sphinxcontrib-
> bibtex so I'm not sure how this extension is actually used in these documents. 
> Perhaps it isn't actually needed at all.

Thanks for the good hint which helped me over this issue[1].  Unfortunately
now dh_auto_install has an issue that did not occured before:


   dh_auto_install -O--buildsystem=pybuild
I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3 
/usr/lib/python3/dist-packages/setuptools/dist.py:487: UserWarning: Normalizing '2021.5.7a' to '2021.5.7a0'
  warnings.warn(tmpl.format(**locals()))
running install
running build
running build_py
running install_lib
creating /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3
creating /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3/usr
...
byte-compiling /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages/cogent3/phylo/least_squares.py to least_squares.cpython-39.pyc
running install_egg_info
running egg_info
creating src/cogent3.egg-info
writing src/cogent3.egg-info/PKG-INFO
Traceback (most recent call last):
  File "/build/python-cogent-2021.5.7a+dfsg/setup.py", line 52, in <module>
    setup(
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 153, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 61, in run
    return orig.install.run(self)
  File "/usr/lib/python3.9/distutils/command/install.py", line 602, in run
    self.run_command(cmd_name)
  File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/install_egg_info.py", line 51, in run
    self.run_command('egg_info')
  File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line 292, in run
    writer(self, ep.name, os.path.join(self.egg_info, ep.name))
  File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line 635, in write_pkg_info
    metadata.write_pkg_info(cmd.egg_info)
  File "/usr/lib/python3.9/distutils/dist.py", line 1117, in write_pkg_info
    self.write_pkg_file(pkg_info)
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 182, in write_pkg_file
    license = rfc822_escape(self.get_license())
  File "/usr/lib/python3.9/distutils/util.py", line 476, in rfc822_escape
    lines = header.split('\n')
AttributeError: 'list' object has no attribute 'split'
E: pybuild pybuild:354: install: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py install --root /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3 
dh_auto_install: error: pybuild --install -i python{version} -p 3.9 --dest-dir /build/python-cogent-2021.5.7a\+dfsg/debian/tmp returned exit code 13


Any idea what might be wrong here?

Kind regards

     Andreas.


[1] https://salsa.debian.org/med-team/python-cogent/-/commit/43aa41a0fbce1643211bd69ec6ecaca209397753

-- 
http://fam-tille.de

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#308176

[Multipart message — attachments visible in raw view] — view raw

On 11/3/21 1:30 PM, Andreas Tille wrote:
> Control: tags -1 pending
> 
> Hi Stuart,
> 
> Am Wed, Nov 03, 2021 at 09:43:40AM +1100 schrieb Stuart Prescott:
>>>>> Extension error:
>>>>> You must configure the bibtex_bibfiles setting
>>>>> make[2]: *** [Makefile:40: html] Error 2
>>
>> this is sphinxcontrib-bibtex saying that you need to add the following to
>> doc/conf.py:
>>
>> bibtex_bibfiles = "path/to/references.bib"
>>
>> However I can't see a .bib file anywhere in the source. I also can't see any
>> code in the rst files or the docstrings that would actually use sphinxcontrib-
>> bibtex so I'm not sure how this extension is actually used in these documents.
>> Perhaps it isn't actually needed at all.
> 
> Thanks for the good hint which helped me over this issue[1].  Unfortunately
> now dh_auto_install has an issue that did not occured before:
> [...]

Pushed to salsa, and now it works as it should.
I leave the onus of checking and uploading onto you.

Regards,
Nilesh

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#308169 — Processed: Re: Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting

Processing control commands:

> tags -1 pending
Bug #997772 [src:python-cogent] python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Added tag(s) pending.

-- 
997772: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997772
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#308183 — Bug#997772: marked as done (python-cogent: FTBFS: You must configure the bibtex_bibfiles setting)

[Multipart message — attachments visible in raw view] — view raw

Your message dated Wed, 03 Nov 2021 11:04:41 +0000
with message-id <E1miE4P-000GYa-0T@fasolo.debian.org>
and subject line Bug#997772: fixed in python-cogent 2021.5.7a+dfsg-3
has caused the Debian Bug report #997772,
regarding python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
997772: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997772
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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