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