So this might not be a Bioconductor question per se, but the error revealed itself when trying to install a Bioconductor package.
When trying to install DESeq2, I am failing because the dependency 'SummarizedExperiment' will not install. The console error messages seem to indicate shell errors where basic commands such as 'rm' and 'mv' are not being found.
When I check R's PATH using Sys.getenv() , the PATH looks normal and has the place where these commands are.
I have a sneaking suspicion that Apple did this to me. I updated my OS from Mojave to Catalina, and ever since whenever I open a Terminal window I have a message saying:
The default interactive shell is now zsh.
To update your account to use zsh, please runchsh -s /bin/zsh
For more details, please visit https://support.apple.com/kb/HT208050.
Behind the scenes when R is trying to do my install, is it falling into a shell that doesn't even know where rm and mv are? If so, any ideas on how to fix this?
R version 4.0.0, Bioconductor version 3.11. Full console information below with sessionInfo() at bottom.
> BiocManager::install("DESeq2") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24) Installing package(s) 'DESeq2' also installing the dependency ‘SummarizedExperiment’ There is a binary version available but the source version is later: binary source needs_compilation SummarizedExperiment 1.18.1 1.18.2 FALSE trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/DESeq2_1.28.1.tgz' Content type 'application/x-gzip' length 1887714 bytes (1.8 MB) ================================================== downloaded 1.8 MB The downloaded binary packages are in /var/folders/82/x9hk21dx19jfp44kk7njvcqc0000gn/T//RtmpQAF98w/downloaded_packages installing the source package ‘SummarizedExperiment’ trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/SummarizedExperiment_1.18.2.tar.gz' Content type 'application/x-gzip' length 1520747 bytes (1.5 MB) ================================================== downloaded 1.5 MB * installing *source* package ‘SummarizedExperiment’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading sh: rm: command not found ** help *** installing help indices ** building package indices sh: rm: command not found ** installing vignettes ** testing if installed package can be loaded from temporary location sh: rm: command not found sh: mv: command not found Warning in system(paste("mv -f", shQuote(instdir), shQuote(dirname(final_instdir)))) : error in running command ERROR: moving to final location failed sh: rm: command not found The downloaded source packages are in ‘/private/var/folders/82/x9hk21dx19jfp44kk7njvcqc0000gn/T/RtmpQAF98w/downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘SummarizedExperiment’ had non-zero exit status sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  BiocManager_1.30.10 compiler_4.0.0 tools_4.0.0