Error Forging BSgenome Package

[sopeadeniji]

Hi, I got some errors and warnings after checking my BSgenome package. Please, could you help with explaining the errors and warnings in check.log? Code written below:

R CMD build BSgenome.Custulatus.NCBI.bCatUst1.pri.v2 R CMD check BSgenome.Custulatus.NCBI.bCatUst1.pri.v2_0.0.1.tar.gz

00check.log

Best, S.

[vjcitn]

I don't want to bring that log down onto my computer. Please extract the lines that indicate an error is occurring and place that text into the issue. Also, please provide the result of sessionInfo() after the error. Please be sure BiocManager::valid() returns TRUE for your system.

[sopeadeniji]

Error line below:

genome <- BSgenome.Custulatus.NCBI.bCatUst1.pri.v2 head(seqlengths(genome)) super_scaffold_1 scaffold_2_arrow_ctg1 super_scaffold_3 165774257 124776741 120187523 super_scaffold_5 scaffold_4_arrow_ctg1 scaffold_6_arrow_ctg1 77026709 76913702 63528738 genome[["1"]] Error in genome[["1"]] : no such sequence Calls: [[ -> [[ Execution halted

• checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems.
• checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr.
• DONE Status: 2 ERRORs, 2 WARNINGs, 3 NOTEs

BiocManager::valid() Bioconductor version '3.16'

• 4 packages out-of-date
• 0 packages too new

create a valid installation with

BiocManager::install(c( "BiocParallel", "DelayedArray", "GenomicRanges", "matrixStats" ), update = TRUE, ask = FALSE, force = TRUE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message: 4 packages out-of-date; 0 packages too new

[hpages]

Error in genome[["1"]] : no such sequence

Pretty clear no? This assembly has no sequence named 1. So your example fails because you are trying to load a sequence that doesn't exist.

You need to modify your example to use a valid sequence name.

See the sequence names in the "Full sequence report" here (in the leftmost column): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/819/885/GCF_009819885.2_bCatUst1.pri.v2/GCF_009819885.2_bCatUst1.pri.v2_assembly_report.txt

Alternatively, you can get the sequence names with getChromInfoFromNCBI("GCA_009819885.2")$SequenceName, as discussed here.

The code used in the example is supplied via the seed file. So you need to modify your seed file and forge the package again.

[sopeadeniji]

Thanks Herve, I figured I had to correct the seed file. How about the "LaTeX errors when creating PDF version"?

[hpages]

How about the "LaTeX errors when creating PDF version"?

That's just a WARNING. Maybe something is wrong with your LaTeX setup? Hard to know without having more details about your OS and LaTeX installation. Anyways, I don't know how much you care about generating the PDF manual, but if you don't care too much, you can always run R CMD check with the --no-manual flag. As long as this passes with no ERROR or WARNING, you should be good. Even some WARNINGs are acceptable, it all depends on the particular WARNING.

[sopeadeniji]

Got it, thanks.

[hpages]

Is it ok to close this?

[sopeadeniji]

Yes, it is.