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

[David Jimenez-Morales]

Martin, your suspicion was right: it was just insufficient memory available
for docker in my system.

Thank you very much!
David

On Sun, Jan 17, 2021 at 1:58 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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.
>
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>     Type 'demo()' for some demos, 'help()' for on-line help, or
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>     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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