restfulr::download.file usage results in warning

[mjsteinbaugh]

Hi @lawremi ,

I noticed with rtracklayer 1.56.0 on R 4.2 / Bioconductor 3.15 that loading rtracklayer now results in this warning:

replacing previous import 'utils::download.file' by 'restfulr::download.file'

Would it be possible to rename this conflict in restfulr?

Best,
Mike

[mjsteinbaugh]

Issue #69 is also somewhat related

[lawremi]

The download.file() generic was removed from restfulr 5 years ago. I don't think that version made it onto CRAN. However, I must have fixed a CRAN issue using an older checkout, so now there's a really old but new version on CRAN. Oops. The annoying thing is that I failed to upload the fixes to GitHub, and that computer is on the other side of the world from me right now. I probably shouldn't even try developing software anymore.

[mjsteinbaugh]

PS thanks again for rtracklayer, it's awesome

[almeidasilvaf]

Hi, @lawremi

I have the same problems reported in this issue and in #69 when trying to pass URLs to import(). I think the problem is indeed because you pushed a broken version of restfulr to CRAN. It was working fine for me yesterday in the morning, but then I had to upgrade GenomicRanges and all its dependencies were upgraded, including rtracklayer and restfulr. After the upgrade, import() does not work with URLs anymore.

I tried to install the previous version of restfulr from GitHub, but I could not find the repo. Is restfulr not in a GitHub repo?

For those who are reading this issue and, like me, need an urgent solution for this bug, here is a workaround:

# Example GFF3 file
url <- "ftp://ftp.psb.ugent.be/pub/plaza/plaza_pico_03/GFF/ppa/annotation.selected_transcript.exon_features.ppa.gff3.gz"

# Download GFF3 file to tempdir
dfile <- file.path(tempdir(), basename(x))
utils::download.file(x, dfile) # download GFF3 file to

# Read GFF3 file as GRanges object
ranges <- rtracklayer::import(dfile)

# Leave no traces
unlink(dfile)

[lawremi]

restfulr 0.15 is on its way to CRAN.

[lawremi]

I think this should be resolved now? Please reopen if not.

[mjsteinbaugh]

Looks to be fixed, thanks!