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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
>
As a temporary fix you can use
chooseBioCmirror(local.only = TRUE)to select a Bioconductor mirror to install from.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'
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?I am having the exact same problem:
Any help would be greatly appreciated.