Building vignette `Pbase-data.Rmd` fails

sgibb commented 9 years ago

The build process of Pbase fails on the Bioc servers: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/Pbase/

Error message:

Quitting from lines 91-93 (Pbase-data.Rmd) Error: processing vignette 'Pbase-data.Rmd' failed with diagnostics: error in evaluating the argument 'value' in selecting a method for function 'setPar': Error: no slot of name "id" for this object of class "GenomeAxisTrack"

lgatto commented 9 years ago

Strange. I was able to run this code locally. I then tried to build/check under R-devel after running biocLite and got the following

This is Pbase version 0.5.2

Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: dbGetQuery(conn, SQL)
  error: error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'dbConn' not found
Calls: ::: -> get

Quitting from lines 38-42 (Pbase-data.Rmd) 
Error: processing vignette 'Pbase-data.Rmd' failed with diagnostics:
package or namespace load failed for 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Execution halted

Which I also get if I (re-)install TxDb.Hsapiens.UCSC.hg19.knownGene.

Let's wait a couple of days before following up.

sgibb commented 9 years ago

Pbase 0.5.4 builds fine.

lgatto / Pbase

Building vignette `Pbase-data.Rmd` fails #9