Control: tags -1 confirmed Control: tags -1 help Hi,
I confirm I can reproduce the issue in a minimal chroot while the lumpyexpress command prints the help screen as expected. This smells like a missing dependency but I do not have any idea which one. It seems there is a similar known issue here https://stackoverflow.com/questions/65028261/attributeerror-module-importlib-has-no-attribute-util-ii but there is no answer here. Any idea how to fix this? Kind regards Andreas. On Tue, Jan 12, 2021 at 08:05:26PM +0000, Ken Yamaguchi wrote: > Package: lumpy-sv > Version: 0.3.1+dfsg-4 > Severity: important > X-Debbugs-Cc: deb...@knowledgesynthesis.com > > Dear Maintainer, > > I built a lumpy-sv Docker image with the attached Dockerfile. Running a > container for the image produces the following error: > > Sourcing executables from /etc/lumpy-sv/lumpyexpress.config ... > > Checking for required python modules (/usr/bin/python3)... > Traceback (most recent call last): > File "<string>", line 1, in <module> > AttributeError: module 'importlib' has no attribute 'util' > > Thanks, > Ken > > -- System Information: > Debian Release: bullseye/sid > APT prefers testing > APT policy: (500, 'testing') > Architecture: amd64 (x86_64) > > Kernel: Linux 4.19.0-13-amd64 (SMP w/4 CPU threads) > Kernel taint flags: TAINT_WARN > Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set > Shell: /bin/sh linked to /bin/dash > Init: unable to detect > > Versions of packages lumpy-sv depends on: > ii bamkit 0.0.1+git20170413.ccd079d-2 > ii libbamtools2.5.1 2.5.1+dfsg-7+b1 > ii libc6 2.31-9 > ii libgcc-s1 10.2.1-3 > ii libgzstream0 1.5+dfsg-5 > ii libhts3 1.11-4 > ii libstdc++6 10.2.1-3 > ii python3 3.9.1-1 > ii python3-numpy 1:1.19.4-1+b1 > ii python3-pysam 0.15.4+ds-3+b2 > ii samblaster 0.1.26-1 > ii samtools 1.11-1 > > Versions of packages lumpy-sv recommends: > pn sambamba <none> > > lumpy-sv suggests no packages. > > -- no debconf information > FROM debian:bullseye-slim > > RUN apt-get update && \ > apt-get -y --no-install-recommends full-upgrade && \ > apt-get -y --no-install-recommends install \ > lumpy-sv \ > && \ > rm -rf /var/lib/apt/lists/* > > RUN useradd -ms /bin/bash lumpy > > USER lumpy > > WORKDIR /home/lumpy > > CMD ["lumpyexpress"] > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
