Re: Bug#980005: lumpy-sv: lumpyexpress fails with no args
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: debian@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"]
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