Dear all,
I'm attempting to install Bioconductor packages with the same result, "installation of package ‘package name’ had non-zero exit status". Previously, i installed Bioconductor packages without any issues. Also, I can install CRAN packages normally.
The result of installation looks like this:
> BiocManager::install("org.Mm.eg.db") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt) Installing package(s) 'org.Mm.eg.db' installing the source package ‘org.Mm.eg.db’ trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Mm.eg.db_3.16.0.tar.gz' Content type 'application/x-gzip' length 79020899 bytes (75.4 MB) downloaded 75.4 MB The downloaded source packages are in ‘C:\Users\User\AppData\Local\Temp\RtmpSsYeYe\downloaded_packages’ Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.2.2/library packages: boot, foreign, Matrix, nlme, survival Old packages: 'Biobase', 'BiocParallel', 'Biostrings', 'cli', 'DelayedArray', 'GenomeInfoDbData', 'GO.db', 'IRanges', 'org.Hs.eg.db', 'reactome.db', 'S4Vectors', 'XVector', 'zlibbioc' Update all/some/none? [a/s/n]: n Warning message: In install.packages(...) : installation of package ‘org.Mm.eg.db’ had non-zero exit status
Start R as admin and run the following again
BiocManager::install("org.Mm.eg.db", force=T)
Dear Abhijeet Singh , thank you for your assistance. Unfortunately, this does not work. The result is the same.
Abhijeet Singh, thanks for all your help! After all attempts, the simplest solution was to repeat all the same on the Linux instead Windows OS :)
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