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

[Martin Morgan]

I'd guess that your *docker* system is running out of resources, e.g., memory. I'm not sure how docker determines memory available, so don't really know how to solve this other than googling for things like 'how much memory does my docker image have' and 'how do I allocate more memory to docker'.

For the former I found https://docs.docker.com/engine/reference/commandline/stats/ and for me (running outside docker, with only the one container active) I had

$ docker stats --all
CONTAINER ID        NAME                CPU %               MEM USAGE / LIMIT     MEM %               NET I/O             BLOCK I/O           PIDS
db158ed3a1e9        hopeful_diffie      0.00%               124.5MiB / 1.944GiB   6.25%               24.2MB / 544kB      896MB / 1.09GB      6

The latter lead me to https://stackoverflow.com/questions/44533319/how-to-assign-more-memory-to-docker-container but I didn't explore the answers there...

Hope that helps; for what it's worth, the relevant part of the error message you post is I think

g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.

Martin

On 1/17/21, 2:33 PM, "Bioc-devel on behalf of David Jimenez-Morales" <bioc-devel-bounces using r-project.org on behalf of biodavidjm using gmail.com> wrote:

    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.

    R is a collaborative project with many contributors.
    Type 'contributors()' for more information and
    'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    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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