Deleted:Installation had non-zero exit status for all Bioconductor packages
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Anastasia • 0
@fec73fd9
Last seen 18 hours ago
Russia

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.

> 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
Bioconductor • 57 views
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