version imcompatible between ORFik and biomartr

[Shiywa]

Hello, thanks for your job for ORFik. Recently, I found an error about version incompatible between ORFik and biomartr.

When I use getGenomeAndAnnotation to get genome from ensembl, I got an error information like:

Error in biomartr:::getENSEMBL.gtf(organism = organism, type = "dna",  : 
  参数没有用(id.type = assembly_type)

I found that getGenomeAndAnnotation get gtf files using getENSEMBL.gtf, but in the function:

 gtf <- get_genome_gtf(GTF, output.dir, organism, assembly_type, 
    db, gunzip, genome, optimize = optimize)

however, in the biomartr v1.0.7, the getENSEMBL.gtf has only four parameters like

getENSEMBL.gtf(organism, type = "dna", path, release = NULL)

maybe this function getGenomeAndAnnotation need to be improved.

sincerely !

[Roleren]

Hm, this is already fixed, which version of ORFik are you using ?

Anyway, just run:

library(devtools) # Install devtools if you do not have it
devtools::install_github("Roleren/ORFik") # Then restart R to flush old version and library(ORFik)

Let me know if it works :)

[Shiywa]

Fine, now I'm in R 4.2.0 and my ORFik is 1.16.6. I guess the error is due to the old version.

[Roleren]

Yes, so to explain the problem arises because CRAN and bioconductor are not synced in release windows.

We recently updated biomartr, but that does not propagate to bioconductor packages like ORFik. So there is no way around this failing in your case.

Did the new version work ? :)

[Shiywa]

Sorry, it didn't work. now my ORFik is 1.23.5. however, The function getGenomeAndAnnotation is similar to old version like :

    gtf <- get_genome_gtf(GTF, output.dir, organism, assembly_type, 
    db, gunzip, genome, optimize = optimize)

however, the error information is still like :

Error in biomartr:::getENSEMBL.gtf(organism = organism, type = "dna",  : 
  参数没有用(id.type = assembly_type)

my biomartr is 1.0.7, is it too old ?

sincerely !

[Roleren]

Did you restart R now?

[Shiywa]

Thanks for your help. This step is done after update ORFik and restart R.