Bug#1012469: marked as done (singularity-container: Broken handling of Docker environment variables in Singularity)
Your message dated Fri, 17 Jun 2022 06:03:52 +0000
with message-id <E1o255E-0004zT-6I@fasolo.debian.org>
and subject line Bug#1012469: fixed in singularity-container 3.10.0+ds2-3
has caused the Debian Bug report #1012469,
regarding singularity-container: Broken handling of Docker environment variables in Singularity
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.
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--
1012469: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012469
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: singularity-container
Version: 3.9.9+ds1-1+b1
Severity: important
X-Debbugs-Cc: offringa@gmail.com
Dear Maintainer,
Using Debian's singularity to pull a Docker container somehow removes the
environment variables that are set in the Dockerfile (using ENV) from the
container. This bug is not present in 3.9.9 upstream, so it has to do with how
it is packaged in Debian.
The issue is also discussed here, and there is concluded it is a Debian issue:
https://github.com/sylabs/singularity/issues/852
An example run that displays the problems:
$ singularity pull --name astronrd_linc.sif docker://astronrd/linc
$ singularity exec --contain --cleanenv astronrd_linc.sif bash
Singularity> echo $PYTHONPATH
Singularity> echo $LINC_DATA_ROOT
Singularity>
Both these variables are set in the Docker container, but are no longer set
when the docker container is pulled using Debian's singularity. The correct
output should be:
Singularity> echo $PYTHONPATH
/usr/local/bin
Singularity> echo $LINC_DATA_ROOT
/usr/local/share/linc
Singularity's own package for 3.9.9 does this correctly (and various other
versions were tested as well, see link to github issue above)
Kind regards,
André
-- System Information:
Debian Release: bookworm/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.17.0-1-amd64 (SMP w/16 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages singularity-container depends on:
ii ca-certificates 20211016
ii containernetworking-plugins 1.1.0+ds1-1+b1
ii libc6 2.33-7
ii libseccomp2 2.5.4-1
ii squashfs-tools 1:4.5.1-1
Versions of packages singularity-container recommends:
ii e2fsprogs 1.46.5-2
singularity-container suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: singularity-container
Source-Version: 3.10.0+ds2-3
Done: Nilesh Patra <nilesh@debian.org>
We believe that the bug you reported is fixed in the latest version of
singularity-container, 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 1012469@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nilesh@debian.org> (supplier of updated singularity-container 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: SHA512
Format: 1.8
Date: Fri, 17 Jun 2022 11:03:52 +0530
Source: singularity-container
Architecture: source
Version: 3.10.0+ds2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team <debian-hpc@lists.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Closes: 1012469
Changes:
singularity-container (3.10.0+ds2-3) unstable; urgency=medium
.
* Team upload.
* Modify oci patch to return right imgspec
(Closes: #1012469)
* Add desc to patches
* d/u/metadata: Make yamllint happy
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