Failing on Bioconductor builders.

[lshep]

I tired to send an email to both ps562@cam.ac.uk and pstempor@gmail.com (not if you are reachable by only the later it should be updated in the DESCRIPTION of the package)

Your package has been failing since 06/29/20. we are beginning the deprecation process for your package. Please see the build reports at :

bioconductor.org/checkResults/devel/bioc-LATEST/seqplots
bioconductor.org/checkResults/release/bioc-LATEST/seqplots

We are proceeding with deprecation of your package. The package will remain deprecated until the package is fixed to build and check cleanly on the Bioconductor builders AND you formally request undeprecation to lori.shepherd@roswellpark.org or on bioc-devel@bioconductor.orgIf the package remains deprecated, at the time of the Spring release (normally April/May) the package will be removed from Bioconductor 3.14

[cmuyehara]

Hey,

The problem is in the getRef function:

getREF <- function(genome) {
    
    if( file.exists(file.path(Sys.getenv('root'), 'genomes', genome)) ) {
        REF <- Biostrings::readDNAStringSet( file.path(Sys.getenv('root'), 'genomes', genome) )
        names(REF) <- gsub(' .+', '', names(REF))
    } else {
        
        GENOMES <- BSgenome::installed.genomes(
            splitNameParts=TRUE)$provider_version
        if( length(GENOMES) ) 
            names(GENOMES) <- gsub('^BSgenome.', '', BSgenome::installed.genomes())
        if( !length(GENOMES) ) stop('No genomes installed!')
        
        pkg <- paste0('BSgenome.', names(GENOMES[GENOMES %in% genome]))[[1]]
        suppressPackageStartupMessages(
            library(pkg, character.only = TRUE, quietly=TRUE)
        )
        REF <- get(pkg)
    }
    return(REF)
}

You're checking to see if the genome is installed with

GENOMES <- BSgenome::installed.genomes(
            splitNameParts=TRUE)$provider_version

BSGenome::installed.genomes doesn't return the provider_version field anymore - it was removed 6mos ago. Your call is returning NULL and it thinks there aren't any genomes installed. You just need to index something else in that object. I think that's the only problem.

See here for the relevant commit in BSGenome.
Bioconductor/BSgenome@cf83a90

---

Addendum:
Actually, it looks like the field was just renamed to genome. So if you change provider_version to genome it will fix the problem.