Installation of the latest "GenomeInfoDb" fails with an error in attempting to extract the zip file. Is this a corrupted file or a problem with my Windows system? All previous installations on this computer proceeded smoothly. All other libraries from the Bioconductor install without a problem. However, without this, the entire Biostrings library is not functional!
# simple installation attempt leads to failure
> BiocManager::install("GenomeInfoDb")
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'GenomeInfoDb'
trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/GenomeInfoDb_1.28.1.zip'
Content type 'application/zip' length 4160116 bytes (4.0 MB)
downloaded 4.0 MB
The downloaded binary packages are in
C:\Users\XXXXXX\AppData\Local\Temp\RtmpctdRtV\downloaded_packages
Warning message:
In .inet_warning(msg) : error -3 in extracting from zip file
The two pertinent files, GenomeInfoDbData_1.2.6.targ.gz and GenomeInfoDb_1.28.1.zip1 are in the temp file as indicated above.
sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.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 tools_4.1.1
Please provide more information regarding your setup.
It may be that your username have special characters or spaces and it is interacting with R's unzip.
This seems to be a configuration issue.
Please provide more information regarding your setup. It may be that your username have special characters or spaces and it is interacting with R's unzip.
Best,
Marcel