Hi Michael, I forgot about pkg-util (just did a fresh BioC 3.3 install). I assumed the OS X binary would work out of the box.
Anyhow, I installed rtracklayer (release) manually and got another error (slightly different message now). $ svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/rtracklayer $ R CMD INSTALL rtracklayer Loading required package: colorout * installing to library ‘/Library/Frameworks/R.framework/Versions/3.3release/Resources/library’ * installing *source* package ‘rtracklayer’ ... checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... yes ## more output $ R > library('rtracklayer') > unshorten_url <- function(uri) { + require('RCurl') + opts <- list( + followlocation = TRUE, # resolve redirects + ssl.verifyhost = FALSE, # suppress certain SSL errors + ssl.verifypeer = FALSE, + nobody = TRUE, # perform HEAD request + verbose = FALSE + ) + curlhandle <- getCurlHandle(.opts = opts) + getURL(uri, curl = curlhandle) + info <- getCurlInfo(curlhandle) + rm(curlhandle) # release the curlhandle! + info$effective.url + } > url <- > unshorten_url('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw') Loading required package: RCurl Loading required package: bitops > url [1] "https://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5"; > x <- import.bw(url, as = 'RleList') Error in seqinfo(ranges) : UCSC library operation failed In addition: Warning message: In seqinfo(ranges) : Couldn't open https://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5 > x <- > import.bw('http://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5') Error in seqinfo(ranges) : UCSC library operation failed In addition: Warning messages: 1: In seqinfo(ranges) : TCP non-blocking connect() to content-na.drive.amazonaws.com timed-out in select() after 10000 milliseconds - Cancelling! 2: In seqinfo(ranges) : Couldn't open http://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5 > ## Reproducibility info > message(Sys.time()) 2016-05-05 17:38:30 > options(width = 120) > devtools::session_info() Session info ----------------------------------------------------------------------------------------------------------- setting value version R version 3.3.0 RC (2016-05-01 r70572) system x86_64, darwin13.4.0 ui X11 language (EN) collate en_US.UTF-8 tz America/New_York date 2016-05-05 Packages --------------------------------------------------------------------------------------------------------------- package * version date source Biobase 2.32.0 2016-05-04 Bioconductor BiocGenerics * 0.18.0 2016-05-04 Bioconductor BiocParallel 1.6.0 2016-05-04 Bioconductor Biostrings 2.40.0 2016-05-04 Bioconductor bitops * 1.0-6 2013-08-17 CRAN (R 3.3.0) colorout * 1.1-2 2016-05-05 Github (jalvesaq/colorout@6538970) devtools 1.11.1 2016-04-21 CRAN (R 3.3.0) digest 0.6.9 2016-01-08 CRAN (R 3.3.0) GenomeInfoDb * 1.8.0 2016-05-04 Bioconductor GenomicAlignments 1.8.0 2016-05-04 Bioconductor GenomicRanges * 1.24.0 2016-05-04 Bioconductor IRanges * 2.6.0 2016-05-04 Bioconductor memoise 1.0.0 2016-01-29 CRAN (R 3.3.0) RCurl * 1.95-4.8 2016-03-01 CRAN (R 3.3.0) Rsamtools 1.24.0 2016-05-04 Bioconductor rtracklayer * 1.32.0 2016-05-05 Bioconductor S4Vectors * 0.10.0 2016-05-04 Bioconductor SummarizedExperiment 1.2.0 2016-05-04 Bioconductor withr 1.0.1 2016-02-04 CRAN (R 3.3.0) XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0) XVector 0.12.0 2016-05-04 Bioconductor zlibbioc 1.18.0 2016-05-04 Bioconductor > On Thu, May 5, 2016 at 5:24 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > The URL redirection is something I can try to add. For the other error, you > need to get openssl installed and made visible to pkg-config, so that > rtracklayer finds it during its build process. > > Michael > > On Thu, May 5, 2016 at 2:01 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> Hi Michael, >> >> I have a use case that is similar to >> https://support.bioconductor.org/p/81267/#82142 and looks to me like >> it might need some changes in rtracklayer to work. That's why I'm >> posting it here this time. >> >> Basically, I'm trying to use rtracklayer to import a bigwig file over >> the web which is in a different type of url than before. Using >> utils::download.file() with the defaults doesn't work, I have to use >> method = 'curl' and extra = '-L'. >> >> More specifically, the original url >> http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw has an >> effective url >> https://content-na.drive.amazonaws.com/cdproxy/templink/i_aQAPZJkJ9d9lN1NO5DJJtlbpvAdgbNuc1SkqSTHFouFiZq5 >> >> Now, using the second url with utils::download.file() and default >> methods also doesn't work. It does on the browser though. >> >> >> As you can see, downloading the file doesn't work out of the box. >> Which I guess that it's not surprising that using rtracklayer I get >> errors like: >> >> In seqinfo(ranges) : >> No openssl available in netConnectHttps for >> content-na.drive.amazonaws.com : 443 >> >> You can find further details (code and log file) at >> https://gist.github.com/lcolladotor/c500dd79d49aed1ef33ade5417111453 >> >> Thanks, >> Leo > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
