Question

BiocManager::install() does not work anymore

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Julie • 0

@julie-24031

Last seen 2.5 years ago

Belgium

I just updated my R version from 4.0.2 to 4.1.1. I could install packages by BiocManager::install() while I was using R 4.0.2. However, I cannot install packages by BiocManager::install() while I am using R 4.1.1. I am able to install packages by using install.packages, but BiocManager::install() does not work in my computer for R 4.1.1. Please see the error message below.

Thank you very much in advance! Kindest regards, Julie


> install.packages("BiocManager")
Installing package into ‘C:/Users/julie/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/BiocManager_1.30.16.zip'
Content type 'application/zip' length 328865 bytes (321 KB)
downloaded 321 KB

package ‘BiocManager’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\julie\AppData\Local\Temp\Rtmp6naDm7\downloaded_packages
> BiocManager::install("limma")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/




sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252   
[3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C                  
[5] LC_TIME=Dutch_Belgium.1252    

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

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.16 compiler_4.1.1      fastmap_1.1.0       htmltools_0.5.2    
 [5] tools_4.1.1         yaml_2.2.1          rmarkdown_2.11      knitr_1.36         
 [9] xfun_0.26           digest_0.6.28       rlang_0.4.11        evaluate_0.14      
>

Install PackageType • 2.6k views

ADD COMMENT • link updated 2.5 years ago by shepherl 3.8k • written 2.5 years ago by Julie • 0

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As a temporary fix you can use chooseBioCmirror(local.only = TRUE) to select a Bioconductor mirror to install from.

ADD REPLY • link 2.5 years ago Mike Smith ★ 6.5k

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chooseBioCmirror(local.only = TRUE)  
install.packages("BiocManager")
BiocManager::install("limma")

This gives the same error:

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Installing package(s) 'BiocVersion', 'limma'

ADD REPLY • link 2.5 years ago Julie • 0

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The server has been restored. Could you please try again now that the repositories should be accessible? If not, also do not see an ERROR message just a message that indicates a repository is being replaced? After installing BiocManager, what does BiocManager::valid() produce?

ADD REPLY • link 2.5 years ago shepherl 3.8k

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I am having the exact same problem:

   BiocManager::install("edgeR")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'BiocVersion', 'edgeR'
also installing the dependencies ‘limma’, ‘locfit’

Any help would be greatly appreciated.

ADD REPLY • link 2.5 years ago wellitonboots • 0