Bug#1032975: igdiscover -- Broken, unusable package due to incomplete code in the binary package

2024-05-25 Thread Santiago Vila

tags 1032975 + ftbfs
thanks

Currently, this package FTBFS in unstable in this way:

dpkg-buildpackage
-

Command: dpkg-buildpackage --sanitize-env -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package igdiscover
dpkg-buildpackage: info: source version 0.11-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra 
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
dpkg-source: info: using options from igdiscover-0.11/debian/source/options: 
--extend-diff-ignore=^[^/]*[.]egg-info/
 fakeroot debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<>'
dh_auto_clean
pybuild --clean -i python{version} -p "3.12 3.11"
I: pybuild base:311: python3.12 setup.py clean
/<>/versioneer.py:485: SyntaxWarning: invalid escape sequence '\s'
  LONG_VERSION_PY['git'] = '''
Traceback (most recent call last):
  File "/<>/setup.py", line 15, in 
version = versioneer.get_version(),
  
  File "/<>/versioneer.py", line 1473, in get_version
return get_versions()["version"]
   ^^
  File "/<>/versioneer.py", line 1406, in get_versions
cfg = get_config_from_root(root)
  ^^
  File "/<>/versioneer.py", line 412, in get_config_from_root
parser = configparser.SafeConfigParser()
 ^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did 
you mean: 'RawConfigParser'?
E: pybuild pybuild:389: clean: plugin distutils failed with: exit code=1: 
python3.12 setup.py clean
dh_auto_clean: error: pybuild --clean -i python{version} -p "3.12 3.11" 
returned exit code 13
make[1]: *** [debian/rules:21: override_dh_auto_clean] Error 25
make[1]: Leaving directory '/<>'
make: *** [debian/rules:8: clean] Error 2
dpkg-buildpackage: error: fakeroot debian/rules clean subprocess returned exit 
status 2


To avoid an extra bug I'm tagging this one as ftbfs,
as part of the brokenness.

Thanks.



Bug#1032975: igdiscover -- Broken, unusable package due to incomplete code in the binary package

2023-03-15 Thread Andreas Tille
Hi Nilesh,

Am Wed, Mar 15, 2023 at 07:45:52AM +0530 schrieb Nilesh Patra:
> igdiscover vendors just a /usr/bin/igdiscover with is supposed to be
> nothing more than just a wrapper. The actual code is missing from the
> binary package (i.e. the python files) effectively making igdiscover
> useless.
> 
> Even after fixing that,

Thanks a lot for your work in the first place.

> igdiscover is still broken because of a broken
> Snakefile and it is not able to run the pipeline/workflow which is the
> main functionality here (it is a workflow tool).
> 
> Steps to check can be found here[1]. Remember to change merge tool to
> 'flash' (and apt-get install flash) before running `igdiscover run`.
> It chokes at not being able to find "igblastn" -- it might be originatin
> from ncbi-igblast.

As far as I understood igdiscover needs igblast (source package is
ncbi-igblast) and I was working together with Aaron to get this packaged.
The version of igdiscover in Git had probably fixed the binary code so
this dependency became more obvious.  The reason why I did not uploaded
it was the lack of igblast at the time when I was working in igdiscover.
Unfortunately I missed comming back once igblast was finally accepted
and thus igdiscover remained unfixed / not updated.

> I've fixed the first part (py files installation) and pushed changes to
> salsa in a different branch here[2]. I do not have any more time to look
> into it.

Thanks for all your work on this.

@Steffen, could you please raise your opinion what to do with this
package.  Is it worth to spent time in the old version of igdiscover or
should we simply release bookworm without it, fix the latest version and
upload it to backports once bookworm is released?  Possibly the latest
version is also just a bugfix release and you (Steffen) talk to the
release team giving good reasons why we need that version and why it is
important to have this package in Debian.

However, even the latest version in Salsa needs fixing.  I re-activated
the build-time tests to show the log in CI but somehow CI is not working
currently - feel free to clone and build yourself to see what happens.

IMHO igdiscover is not ready for release and we should probably remove
it from testing.

Kind regards
Andreas.

> [1]: https://docs.igdiscover.se/en/stable/testing.html
> [2]: https://salsa.debian.org/med-team/igdiscover/-/tree/bookworm-release

-- 
http://fam-tille.de



Bug#1032975: igdiscover -- Broken, unusable package due to incomplete code in the binary package

2023-03-14 Thread Nilesh Patra
Package: igdiscover
Version: 0.11-4
Severity: serious
Usertags: ftbfs-bookworm

Dear Maintainer,

igdiscover vendors just a /usr/bin/igdiscover with is supposed to be
nothing more than just a wrapper. The actual code is missing from the
binary package (i.e. the python files) effectively making igdiscover
useless.

Even after fixing that, igdiscover is still broken because of a broken
Snakefile and it is not able to run the pipeline/workflow which is the
main functionality here (it is a workflow tool).

Steps to check can be found here[1]. Remember to change merge tool to
'flash' (and apt-get install flash) before running `igdiscover run`.
It chokes at not being able to find "igblastn" -- it might be originatin
from ncbi-igblast.

I've fixed the first part (py files installation) and pushed changes to
salsa in a different branch here[2]. I do not have any more time to look
into it.

[1]: https://docs.igdiscover.se/en/stable/testing.html
[2]: https://salsa.debian.org/med-team/igdiscover/-/tree/bookworm-release

-- System Information:
Debian Release: bookworm/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-2-amd64 (SMP w/8 CPU threads; PREEMPT)
Locale: LANG=en_IN, LC_CTYPE=en_IN (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages igdiscover depends on:
ii  python3  3.11.1-2
pn  python3-cutadapt 
pn  python3-matplotlib   
ii  python3-numpy1:1.24.1-2+b1
pn  python3-pandas   
pn  python3-ruamel.yaml  
pn  python3-scipy
pn  python3-seaborn  
pn  python3-sqt  
pn  python3-xopen

igdiscover recommends no packages.

Versions of packages igdiscover suggests:
pn  igdiscover-doc  
pn  snakemake