I am trying to install DECIPHER. The installation appears to work, but when I go to load the package, I get an error that "there is no package called 'GenomeInfoDbData'". If I try to load GenomeInfoDbData, I get an error that saying GenomeInfoDbData had non-zero exit status.

> BiocManager::install("DECIPHER", force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: http://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.24), R 4.4.0 (2024-04-24
  ucrt)
Installing package(s) 'DECIPHER'
trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/DECIPHER_3.0.0.zip'
Content type 'application/zip' length 17987718 bytes (17.2 MB)
downloaded 17.2 MB

package 'DECIPHER' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\danab\AppData\Local\Temp\RtmpaQLjkg\downloaded_packages

> library(DECIPHER)
Loading required package: Biostrings
Loading required package: GenomeInfoDb
Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'GenomeInfoDbData'
Error: package 'GenomeInfoDb' could not be loaded

> BiocManager::install("GenomeInfoDbData", force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: http://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.24), 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

& was unexpected at this time.

The downloaded source packages are in
    'C:\Users\danab\AppData\Local\Temp\RtmpaQLjkg\downloaded_packages'
Warning message:
In install.packages(...) :
  installation of package 'GenomeInfoDbData' had non-zero exit status

> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

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/Chicago
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] XVector_0.44.0      IRanges_2.38.1      S4Vectors_0.42.1   
[4] BiocGenerics_0.50.0

loaded via a namespace (and not attached):
[1] httr_1.4.7          zlibbioc_1.50.0     BiocManager_1.30.24
[4] compiler_4.4.0      R6_2.5.1            tools_4.4.0        
[7] rstudioapi_0.16.0   UCSC.utils_1.0.0    jsonlite_1.8.8

The difference between installing DECIPHER and GenomeInfoDbData is that the former is a binary file and the latter is a source file that is installed using (under the hood) 'cmd.exe'.

If you google that error, you will run across lots of different people with the same error, but from doing different things (conda installs, Python installs, R package installs) but all are using the terminal prompt (e.g. cmd.exe). A quick test would be to hit the Windows button (bottom left of your keyboard, between Ctrl and Alt), then typing 'cmd' without the quotes and then hitting Enter. If you get a persistent terminal prompt it might not be what I think it is. If the terminal prompt immediately closes, you may have the problem outlined in this stackoverflow thread, which indicates that you might have something in your registry that you should correct.