Error when trying to install a package (non-zero exit status)

Question

[BioC123]

Hi,

I'm trying to install TxDb.Hsapiens.UCSC.hg38.knownGene package but I fail. Unfortunately, the error message is not so helpful. Any ideas how I can install the package? Thanks!

BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")

Here is the error I get:

getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://repo.miserver.it.umich.edu/cran Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'TxDb.Hsapiens.UCSC.hg38.knownGene' installing the source package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.15.0.tar.gz' Content type 'application/x-gzip' length 44812729 bytes (42.7 MB) downloaded 42.7 MB The downloaded source packages are in ‘C:\Users\AppData\Local\Temp\RtmpsPAYMJ\downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ had non-zero exit status

I'm using:

R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Thank you for your help!

[jv]

cross-posted: https://support.bioconductor.org/p/9144057/#9144070

[jv]

is that all of the output from the installation? Usually there is an error message further "up" in the output that will clarify why the install had non-zero exist status. The most common cause is a failed install of a dependency. For an example see https://support.bioconductor.org/p/119290/.

Then again, getOption("repos")' replaces Bioconductor standard repositories is not standard output when installing a Bioconductor package and I would suggest ruling out issues with your bioconductor package. Can we also see the results of sessionInfo()?

[BioC123]

Thank you. Here is the error message again:

Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'TxDb.Hsapiens.UCSC.hg38.knownGene'
installing the source package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.15.0.tar.gz'
Content type 'application/x-gzip' length 44812729 bytes (42.7 MB)
downloaded 42.7 MB


The downloaded source packages are in
        ‘C:\Users\AppData\Local\Temp\RtmpKWfcYV\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ had non-zero exit status

And here is the sessionInfo():

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.17 compiler_4.2.0      tools_4.2.0     

I also checked BiocManager::valid() and everything seems to be OK (TRUE).

Thanks again!

[jv]

Are you by any chance using Conda to manage your R environment? If so you could try installing this package via conda install instead. https://anaconda.org/bioconda/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene