Unable to install bioconductor packages
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Entering edit mode
emsie25 • 0
@b7eca502
Last seen 6 weeks ago
United States

I have used Bioconductor packages before without any issue installing them, but I just upgraded to R v 4.1.0 and I am unable to connect to the URL . I think the issue is with R, but I'm not sure at this point (I can install non-bioconductor packages with no problem).

If I try to install a Bioconductor package manually:

if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")

Warning: unable to access index for repository https://cran.fhcrc.org/src/contrib:
  cannot open URL 'https://cran.fhcrc.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.fhcrc.org/bin/macosx/contrib/4.1:
  cannot open URL 'https://cran.fhcrc.org/bin/macosx/contrib/4.1/PACKAGES'
Warning message:
package ‘BiocManager’ is not available for this version of R

If I try to install through the R package installer:
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
Warning: unable to access index for repository http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1:
  cannot open URL 'http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1/PACKAGES'
Warning: unable to access index for repository http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1:
  cannot open URL 'http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://cran.fhcrc.org/bin/macosx/contrib/4.1:
  cannot open URL 'https://cran.fhcrc.org/bin/macosx/contrib/4.1/PACKAGES'
Warning: dependencies ‘GO.db’, ‘SparseM’, ‘matrixStats’, ‘ALL’, ‘hgu95av2.db’, ‘hgu133a.db’, ‘xtable’ are not available
trying URL 'http://www.bioconductor.org/packages/3.13/bioc/bin/macosx/contrib/4.1/topGO_2.44.0.tgz'
Content type 'application/x-gzip' length 2123289 bytes (2.0 MB)
==================================================
downloaded 2.0 MB


The downloaded binary packages are in
    /var/folders/46/f4bybyjd599ghrw6dsdmlkgc0000gn/T//RtmphkrHGb/downloaded_packages
Warning: unable to access index for repository http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1:
  cannot open URL 'http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1/PACKAGES'

sessionInfo( )

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0
Bioconductor • 201 views
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1
Entering edit mode
Mike Smith ★ 5.0k
@mike-smith
Last seen 10 hours ago
EMBL Heidelberg / de.NBI

There looks like maybe two different problems here. Let's try fixing the installation of BiocManager first, and then maybe everything will be resolved.

When I visit https://cran.fhcrc.org in a web browser I get a warning about the certificate being invalid and the option to "proceed anyway". I wonder if R is experiencing the same problem but not giving you any choice but to fail.

Do you know why you are trying to connect to https://cran.fhcrc.org to install the packages? It could be that R gave you a list and you selected that option, or it might be set somewhere on your system. If you know why, then I would change that and try again. If you don't know why that server was selected, I would suggest running the command chooseCRANmirror() and picking one of the options that isn't the FHCRC mirror.

Then try installing BiocManager again with install.packages("BiocManager")


I don't see it in your example, but I guess from the rest of the error messages you're then ultimately trying to run BiocManager::install("topGO"). Hopefully getting a working copy of BiocManager will allow that to work, but if not please report back here with any progress.

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