Hey everyone,
I am having some issues updating some packages. I am using Bioconductor 3.18 and sometimes, when I want to update my packages using BiocManager::install() (or, if I install a specific package), I am asked, if I want to update some packages. So far so normal and I mostly select all then. Most of the packages are updated, but some simply aren't. I don't get a warning or error for them, but if I rerun BiocManager::install(), they still show up as old packages. Right now it's Biostrings and edgeR. For month the package DBI showed up as old, until I simply installed it from source. I could do the same for Biostringsand edgeR, I guess, but I wonder why this happens and why I don't get any error/warning message. I guess this is because some updates are released and are not yet available precompiled for my arch (arm64; Apple Silicon).
The same also happens for some CRAN packages that simply don't update for some time, till some weeks later they can be updated.
Any explanation?
Here's my complete output:
> BiocManager::install()
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Old packages: 'Biostrings', 'edgeR'
Update all/some/none? [a/s/n]:
a
trying URL 'https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.3/Biostrings_2.70.1.tgz'
Content type 'application/x-gzip' length 14458224 bytes (13.8 MB)
==================================================
downloaded 13.8 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.3/edgeR_4.0.12.tgz'
Content type 'application/x-gzip' length 2916094 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
The downloaded binary packages are in
/var/folders/ws/vdb_nvyj35g9ck_srpvqpccm0000gn/T//Rtmpe0k3Id/downloaded_packages
And then, if I do it again:
> BiocManager::install()
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Old packages: 'Biostrings', 'edgeR'
Update all/some/none? [a/s/n]:
a
trying URL 'https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.3/Biostrings_2.70.1.tgz'
Content type 'application/x-gzip' length 14458224 bytes (13.8 MB)
==================================================
downloaded 13.8 MB
trying URL 'https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.3/edgeR_4.0.12.tgz'
Content type 'application/x-gzip' length 2916094 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
The downloaded binary packages are in
/var/folders/ws/vdb_nvyj35g9ck_srpvqpccm0000gn/T//Rtmpe0k3Id/downloaded_packages
Depending on where you are installing them from (RStudio directly or conda), you would likely get an error on the prompt telling why the packages were not updated. Or does that not happen?
I'm using with RStudio directly. I could also try to update them with R in the terminal directly, but I don't think, this would make a difference. I don't get any error. I updated the original post with my complete output.
This could probably explain it then - https://community.rstudio.com/t/packages-are-not-updating/166214
They have a different answer at bioconductor.