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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel