This is a test version of Biostars. For the public version, visit https://www.biostars.org.
bioconductor caches fails to load/corrupted for annotation databases

I'm unable to load annotation databases such as transcription databases due to corrupt caches. The problem still persists after reinstalling packages

I tried following leads in this biconductor post but doesn't solve the problem. Any suggestions would be gladly appreciated. Thanks

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Error: package or namespace load failed for ‘AnnotationDbi’:
 .onLoad failed in loadNamespace() for 'RSQLite', details:
  call: is_old_cache(cache)
  error: cannot open file '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cachem/R/cachem.rdb': No such file or directory
Error: package ‘AnnotationDbi’ could not be loaded
In addition: Warning message:
In is_old_cache(cache) : restarting interrupted promise evaluation

AnnotationHub()
Error in AnnotationHub() : could not find function "AnnotationHub"

library(BiocFileCache)
Loading required package: dbplyr
Error: package or namespace load failed for ‘BiocFileCache’:
 .onLoad failed in loadNamespace() for 'RSQLite', details:
  call: is_old_cache(cache)
  error: cannot open file '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cachem/R/cachem.rdb': No such file or directory
In addition: Warning message:
In is_old_cache(cache) : restarting interrupted promise evaluation
txdb.hsapiens.ucsc.hg19.knowngene biocfilecache annotationdbi r

Try restarting your R session.

0 answers

No answers yet.

Log in to answer this question.