Hi Bioc-devel,
recount had been failing in recent months at bioc-release and
bioc-devel. I finally had the time to dive into it, and eventually
that led to an error on rtracklayer that I reported at
https://github.com/lawremi/rtracklayer/issues/83. Michael Lawrence
noticed that my R session information didn't show openssl being
loaded. In a message there, Michael speculated that maybe a change in
how the rtracklayer binaries were being built by Bioconductor could be
the source of the issue.
Here's a small reprex for the error:
library("GenomicRanges")
library("rtracklayer")
range <- GRanges(seqnames = "chrY", ranges = IRanges(1, 57227415))
rtracklayer::import("http://sciserver.org/public-data/recount2/data/SRP002001/bw/mean_SRP002001.bw";,
selection = reduce(range), as = "RleList")
And here's the error output:
Error in seqinfo(con) : UCSC library operation failed
In addition: Warning message:
In seqinfo(con) :
No openssl available in netConnectHttps for sciserver.org : 443
> traceback()
7: seqinfo(con)
6: seqinfo(con)
5: .local(con, format, text, ...)
4: import(FileForFormat(con), ...)
3: import(FileForFormat(con), ...)
2:
rtracklayer::import("http://sciserver.org/public-data/recount2/data/SRP002001/bw/mean_SRP002001.bw";,
selection = reduce(range), as = "RleList")
1:
rtracklayer::import("http://sciserver.org/public-data/recount2/data/SRP002001/bw/mean_SRP002001.bw";,
selection = reduce(range), as = "RleList")
> packageVersion("rtracklayer")
[1] ‘1.58.0’
I'm not sure what else I can do to help. As noted at
https://github.com/lawremi/rtracklayer/issues/83#issuecomment-1437585161,
recount / rtracklayer versions from BioC 3.11 do work with the same
links.
Thanks in advance.
Best,
Leo
Leonardo Collado Torres, Ph. D.
Investigator
LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com
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