Hi Michael, We tried getting things to work with Amazon Cloud Drive (see Abhi's efforts at https://github.com/nellore/duffel/commits/master). But we now have the data hosted elsewhere where the links work properly.
I just noted a small mistake on rtracklayer:::expandPath(). See: > startsWith('http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw', > 'http||ftp') [1] FALSE > startsWith('http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw', > 'http') [1] TRUE The fix is simple. At https://github.com/Bioconductor-mirror/rtracklayer/blob/c4b842bc4daa4b9db26cb86f3284cf8cf5c32ebd/R/web.R#L62-L66, change it to: expandPath <- function(x) { if (startsWith(x, "http") | startsWith(x, "ftp")) expandURL(x) else path.expand(x) } Best, Leo On Thu, May 5, 2016 at 8:10 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > I checked in something that tries to find openssl automatically on the Mac. > > It looks like AWS is for some reason returning 404 for the HEAD command that > the UCSC library uses the get info about the file like the content size. > Same thing happens when I play around in Firefox's developer tools. The > error response header claims a JSON content type, but no JSON is actually > sent, so there is no further description of the error. I think this is a bug > in Amazon. > > Seems like for now you'll need to download the file first. > > Michael > > On Thu, May 5, 2016 at 2:46 PM, Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> 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