Thanks for pointing out that buglet. Fixed. On Tue, May 31, 2016 at 10:55 AM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > 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
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