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.b...@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-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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel