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-boun...@r-project.org on behalf of biodavi...@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@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
