Hello,
At the moment, the source file https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.40.1.tar.gz does not exit (dead link), which prevents me from installing bioconductor packages in R 4.4.3.
I installed manually the zip version (1.40.0 https://www.bioconductor.org/packages/release/bioc/bin/windows/contrib/4.4/BiocParallel_1.40.0.zip) for Windows, but then it R considers it as too old and I am back to square one:
BiocManager::install("BiocParallel")
Old packages: 'BiocParallel' Update all/some/none? [a/s/n]: a
There is a binary version available but the source version is later: binary source needs_compilation BiocParallel 1.40.0 1.40.1 TRUE
installing the source package 'BiocParallel'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocParallel_1.40.1.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocParallel_1.40.1.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocParallel_1.40.1.tar.gz': HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'BiocParallel' failed
Could you put the file BiocParallel_1.40.1.tar.gz online?
Thanks :)
I'm not sure why the source package isn't currently available, but when you get the to question
Old packages: 'BiocParallel' Update all/some/none? [a/s/n]:can you just answernfor no? Then it won't try to updateBiocParalleland you won't it the error. You should be fine to keep the existing version for now.Your approach works, but it implies manually rejecting the update of BiocParallel at each use of
BiocManager::install(), which is pretty annoying.Thank you for your question. We are aware of the issue and are in process of resolving.