Version incompatibilities?
Closed this issue · 4 comments
I can't seem to load the qiime2R package. I've successfully installed it, but when I try to load it, I get this error:
library(qiime2R)
Error: package or namespace load failed for ‘qiime2R’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/.../Library/R/3.6/library/Rhdf5lib/libs/Rhdf5lib.so':
dlopen(/Users/.../Library/R/3.6/library/Rhdf5lib/libs/Rhdf5lib.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
Referenced from: /Users/.../Library/R/3.6/library/Rhdf5lib/libs/Rhdf5lib.so
Reason: image not found
My best (somewhat inexperienced) guess is version incompatibilities? Any insight would be appreciated!
I checked this on my OS X mojave machine and I did not have this issue with 3.6.0. I am wondering if uninstalling or updating your Rhdf5lib might help BiocManager::install("Rhdf5lib"). I am thinking something funny happened in your update from 3.5 to 3.6.
Unfortunately I get the exact same error (described above) on two different OSX machines, so it's not just an update error on one machine. I tried running BiocManager::install("Rhdf5lib") and get this:
Warning message:
package ‘Rdhf5lib’ is not available (for R version 3.6.0)
Hmm, I checked this on two more macs, a second mojave, and a high sierra and I can't replicate the error. Given that you got the error that Rdhf5lib isn't available, I wonder if you need to update your BiocManager as well. I currently have BiocManager_1.30.4 (Bioconductor version 3.9) and Rhdf5lib_1.6.0. Please let me know what happens.
Jordan
Got it! I had to update BiocManager and THEN Rhdf5lib, both at the System level (not the user level). Thank you!