Hello, I am trying to install GenomeInfoDb in a new renv. I am able to install BiocManager itself as well as the dependencies for some of the other packages. I am having an issue during the installation of GenomeInfoDbData specifically. I'm not sure what to make of it...any insight would be greatly appreciated.
> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
BioCsoft: https://bioconductor.org/packages/3.19/bioc
BioCann: https://bioconductor.org/packages/3.19/data/annotation
BioCexp: https://bioconductor.org/packages/3.19/data/experiment
BioCworkflows: https://bioconductor.org/packages/3.19/workflows
BioCbooks: https://bioconductor.org/packages/3.19/books
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package 'GenomeInfoDbData'
trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/GenomeInfoDbData_1.2.12.tar.gz'
Content type 'application/x-gzip' length 12558310 bytes (12.0 MB)
downloaded 12.0 MB
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
The downloaded source packages are in
'C:\Users\userName\AppData\Local\Temp\RtmpUHlYpn\downloaded_packages'
Warning message:
In install.packages(...) :
installation of package 'GenomeInfoDbData' had non-zero exit status
My session info...
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] BiocManager_1.30.23
loaded via a namespace (and not attached):
[1] compiler_4.4.0 tools_4.4.0 renv_1.0.7
Hello,
As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what is wrong with my Windows installation.