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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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Error with 'download.file' on Linux cluster #48

Closed lmweber closed 3 years ago

lmweber commented 3 years ago

This is a really amazing package, which has made some of our work much easier, thanks!

However I did get one error when running it on our Linux cluster, which I thought I would report here.

The error occurs when downloading genome info. I suspect it is a problem with running the base command download.file on a Linux cluster, although I am not completely sure. I know download.file has problems on Windows too.

The error message is as follows. It all works fine when running on my Mac laptop instead.

fetching genome info for GENCODE
Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz'
> download.file("http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz", destfile = "./testing.txt.gz", quiet = TRUE)
Error in download.file("http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz",  : 
  cannot open URL 'http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz'
lmweber commented 3 years ago

Oh, now it has worked! I logged out and back into our cluster, and tried again.

Maybe it was related to creating the cache directory for the first time.

Ok I think this is a non-issue then, sorry! I'll close the issue.

mikelove commented 3 years ago

I think it could have been an internet issue.

The genome info is a weak point, as the core mechanism for Bioc functions to get the genome info is via this USCS link. I think Ahub solves it, as we just grab the correct db with seqinfo. Maybe you GENCODE wasn’t in Ahub though? (Or are you using 3.11?)