Package: singularity-container Version: 3.9.9+ds1-1+b1 Severity: important X-Debbugs-Cc: offri...@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
