repos argument not kept
Closed this issue · 7 comments
I am using BiocManager
for managing the installation of packages.
I would like to make use of both bspm
for CRAN
packages and BiocManager
for Bioconductor packages.
It seems that bspm::enable()
shim does not keep the input's repos
argument, seen at
https://github.com/Enchufa2/bspm/blob/5d9f5f1b786807efa7c249dd81ddedd18579b33d/R/integration.R#L53
leading to the error below.
> BiocManager::repositories()
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
BioCsoft
"https://bioconductor.org/packages/3.16/bioc"
BioCann
"https://bioconductor.org/packages/3.16/data/annotation"
BioCexp
"https://bioconductor.org/packages/3.16/data/experiment"
BioCworkflows
"https://bioconductor.org/packages/3.16/workflows"
BioCbooks
"https://bioconductor.org/packages/3.16/books"
CRAN
"https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"
> install.packages("BSgenome", repos = BiocManager::repositories())
[truncated]
Available system packages...
Error in dbs[bins, "Version"] : subscript out of bounds
Thanks for the report. Could you please try the fix in the fix/51
branch?
This is with @eddelbuettel's r2u
docker image:
> install.packages("BSgenome", repos = BiocManager::repositories())
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
Available system packages as root...
There are binary versions available but the source versions are later:
binary source
BSgenome 1.66.1 1.66.2
GenomeInfoDb 1.34.4 1.34.6
GenomicRanges 1.50.1 1.50.2
GenomeInfoDbData 1.2.8 1.2.9
BiocParallel 1.32.4 1.32.5
Do you want to install later versions from sources? (Yes/no/cancel)
Thanks for the quick fix @Enchufa2
It looks good!
I'm not sure why I get a different version of BSgenome under the binary
column. Is this due to the version of R that I am using (R 4.2.1
)?
There are binary versions available but the source versions are later:
binary source
BSgenome 1.62.0 1.66.2
With the container (using R 4.2.2
) I can see the versions that you have above.
Note. For binary generation, it would be best to use the packages that are restricted and defined by BiocManager
so to avoid 'old' binaries in the binary
column shown here (which is incompatible with R 4.2.1
; it's an R 4.1.0
package).
What's your OS version and what repo are you using for the binaries? That's probably the difference.
I am using:
$ lsb_release -a
Distributor ID: Ubuntu
Description: Ubuntu 22.04.1 LTS
Release: 22.04
Codename: jammy
> dbb <- bspm::available_sys()
> dbb[rownames(dbb) == "bsgenome", ]
Package Version Repository
"bsgenome" "1.62.0" "Ubuntu"
> packageVersion("bspm")
[1] '0.4.0.1'
I guess I'm using these repos in:
sources.list.d/
deb https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu/ jammy main
sources.list
deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/