Question

non-zero exit status when trying to install a package

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BioC123 • 0

@2a9ce85d

Last seen 2.5 years ago

Asia

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")

'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

Install • 3.0k views

ADD COMMENT • link 2.5 years ago BioC123 • 0

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I'm not able to reproduce this. Can you try again and if you encounter a similar error please provide your sessionInfo(). You could also check to make sure all package are up-to-date by running BiocManager::install() or BiocManager::valid() to ensure all needed dependencies match.

ADD REPLY • link 2.5 years ago shepherl 4.1k

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Thank you. Here is the more information you asked for:

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

BiocManager::valid()

TRUE

BiocManager::install()

Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt)

Thank you!

ADD REPLY • link 2.5 years ago BioC123 • 0