kdkorthauer / dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
MIT License
54 stars 14 forks source link

Add missing `Suggests` entries #57

Closed martin-g closed 11 months ago

martin-g commented 11 months ago

It seems TxDb.Hsapiens.UCSC.hg19.knownGene and org.Hs.eg.db are transitive dependencies that must be explicitly declared for Bioc 3.18, because of _R_CHECK_SUGGESTSONLY=true

See https://support.bioconductor.org/p/9153573/#9153581 for more details.

Without these additions the R CMD check fails with:

Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (4 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (3 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (2 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (1 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Error in getAnnot("hg19") : Annotation could not be retrieved.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘dmrseq.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
kdkorthauer commented 11 months ago

Thank you for suggesting this change! I'm going to add it into the devel branch instead of master.

martin-g commented 11 months ago

Thank you, @kdkorthauer ! devel is what I actually meant! Have a nice weekend!

martin-g commented 11 months ago

https://bioconductor.org/checkResults/3.18/bioc-LATEST/dmrseq/ is fully green!