I'm trying to install a package on Bioconductor called "Herper" and it requires "hdf5r" to be updated. I'm trying to update using compilation to get the most recent version of this package. Previously, I had issues with finding the hdf5 library but was able to rectify this by first installing hdf5 using homebrew and then using the following code to specify the location of the hdf5 library.
install.packages("hdf5r", configure.args = "--with-hdf5=/opt/homebrew/Cellar/hdf5/1.12.2_2/bin/h5cc")
Now I'm getting a new error where R is trying to find the object 'hdf5r.so'.
Here is where I believe things start going wrong:
ld: warning: ignoring file /opt/homebrew/Cellar/hdf5/1.12.2_2/lib/libhdf5_hl.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/Cellar/hdf5/1.12.2_2/lib/libhdf5.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-hdf5r/00new/hdf5r/libs
** 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
Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so, 0x0006): symbol not found in flat namespace (_H5P_CLS_ATTRIBUTE_CREATE_ID_g)
Error: loading failed
Execution halted
ERROR: loading failed
I'm quite new to coding, so I believe the 00LOCK folders are temporary folders? Because I cannot find the path that R is searching for. Let me know if you guys have any solutions to this!
Cheers, G