Hi all,

I was trying to install PANTHER.db on a Mac I have not used in a while. However, I was getting persistent errors. Since it had been a while since I've used this computer, I installed the latest version of Mac Ventura, R, and RStudio before updating the rest of the packages. This seemed to fix the issues I had installing other packages, such as TFutils and STRINGdb. However, it did not fix the error from attempting a PANTHER.db instillation.

I've tried restarting R, removing the Downloaded Package Cache, and updating the RSQLite and DBI packages. But nothing stops this error from occurring. I wanted to reach out before trying to do anything like re-installing everything from scratch or moving packages to a new folder path. Any insight anyone can provide would be greatly appreciated. Thank you for your time!

Best, Alan

> BiocManager::install("PANTHER.db")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Installing package(s) 'PANTHER.db'
installing the source package 'PANTHER.db'
trying URL 'https://bioconductor.org/packages/3.21/data/annotation/src/contrib/PANTHER.db_1.0.12.tar.gz'
Content type 'application/x-gzip' length 325416 bytes (317 KB)
==================================================
downloaded 317 KB

* installing *source* package 'PANTHER.db' ...
** this is package 'PANTHER.db' version '1.0.12'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
Error: database disk image is malformed
Execution halted
ERROR: loading failed
* removing '/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/PANTHER.db'
The downloaded source packages are in
    '/private/var/folders/4f/gvgsfhw11cdcdkb7cc55pnlh0000gn/T/RtmpKmrUx7/downloaded_packages'
Warning message:
In install.packages(...) :
  installation of package 'PANTHER.db' had non-zero exit status

> sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: x86_64-apple-darwin20
Running under: macOS Ventura 13.7.8

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.26 compiler_4.5.1      tools_4.5.1