[Bioc-devel] Unable to install bioconductor package in bioconductor docker

[David Jimenez-Morales]

Dear bio

I am trying to install the bioconductor package "mzR" in the following
bioconductor docker containers without success:

bioconductor/bioconductor_docker:RELEASE_3_12
bioconductor/bioconductor_docker:RELEASE_3_11
bioconductor/bioconductor_docker:devel
(and also tried, tidyverse:3.6.1)

Nitash Turaga was able to install it successfully on the devel docker (
bioconductor/bioconductor_docker:devel), however I tried without success,
which doesn't make any sense at all.

These are the commands that I tried:

--> docker --version
Docker version 20.10.2, build 2291f61

--> docker pull bioconductor/bioconductor_docker:devel
devel: Pulling from bioconductor/bioconductor_docker
Digest:
sha256:824f99a380856434491dbe83242171986147a608fac0c6be3050c65d6deb2274
Status: Image is up to date for bioconductor/bioconductor_docker:devel
docker.io/bioconductor/bioconductor_docker:devel


docker run -it --rm bioconductor/bioconductor_docker:devel /bin/bash

root using 5d6bbd03317a:/# R

R Under development (unstable) (2021-01-14 r79832) -- "Unsuffered
Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Bioconductor version 3.13 (BiocManager 1.30.10), ?BiocManager::install for
help

> BiocManager::install("mzR")
Bioconductor version 3.13 (BiocManager 1.30.10), R Under development
(unstable)
  (2021-01-14 r79832)
Installing package(s) 'mzR'

... (after compilation)

/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/usr/local/lib/R/etc/Makeconf:177: pwiz/data/common/Unimod.o]
Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/usr/local/lib/R/site-library/mzR’

The downloaded source packages are in
‘/tmp/RtmpM0suak/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘mzR’ had non-zero exit status

Questions:

- Any idea why it cannot be installed in the release Bioconductor dockers?
- how is possible that Nitesh can install it and I cannot in the exact same
bioconductor dev version?

Thanks a lot
David

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