Sure, done. On Tue, May 31, 2016 at 11:18 AM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > Hi Michael, > > Thanks! > > Actually, it looks like there are a few more quick changes I need you > to do. Simply at > https://github.com/Bioconductor-mirror/rtracklayer/blob/917973eb7e9f16bbcd6f6e4b9452f9e40d9a1e94/R/bigWig.R > replace path.expand() with expandPath(). I'm not sure this applies to > all current path.expand() calls, but at least it does for > https://github.com/Bioconductor-mirror/rtracklayer/blob/917973eb7e9f16bbcd6f6e4b9452f9e40d9a1e94/R/bigWig.R#L20 > > Best, > Leo > > > > >> library(recount); system.time( regions <- expressed_regions('SRP009615', >> 'chrY', cutoff = 5L) ) > 2016-05-31 14:11:52 loadCoverage: loading BigWig file > http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw > Error in seqinfo(con) : UCSC library operation failed > In addition: Warning message: > In seqinfo(con) : > Couldn't open http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw > Timing stopped at: 0.068 0.009 0.817 >> traceback() > 14: .Call(BWGFile_seqlengths, path.expand(path(x))) > 13: seqinfo(con) > 12: seqinfo(con) > 11: .local(con, format, text, ...) > 10: import(file, selection = range, as = "RleList") > 9: import(file, selection = range, as = "RleList") > 8: FUN(X[[i]], ...) > 7: lapply(as.list(X), FUN = FUN, ...) > 6: lapply(as.list(X), FUN = FUN, ...) > 5: lapply(bList, .loadCoverageBigWig, range = which, chr = chr, > verbose = verbose) > 4: lapply(bList, .loadCoverageBigWig, range = which, chr = chr, > verbose = verbose) > 3: loadCoverage(files = meanFile, chr = chr, chrlen = chrlen) > 2: expressed_regions("SRP009615", "chrY", cutoff = 5L) > 1: system.time(regions <- expressed_regions("SRP009615", "chrY", > cutoff = 5L)) >> 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 AQUA > language (EN) > collate en_US.UTF-8 > tz America/New_York > date 2016-05-31 > > Packages > --------------------------------------------------------------------------------------------------------------- > package * version date source > acepack 1.3-3.3 2014-11-24 CRAN (R 3.3.0) > AnnotationDbi 1.35.3 2016-05-27 Bioconductor > Biobase 2.33.0 2016-05-05 Bioconductor > BiocGenerics * 0.19.0 2016-05-05 Bioconductor > BiocParallel 1.7.2 2016-05-20 Bioconductor > biomaRt 2.29.2 2016-05-30 Bioconductor > Biostrings 2.41.1 2016-05-27 Bioconductor > bitops 1.0-6 2013-08-17 CRAN (R 3.3.0) > BSgenome 1.41.0 2016-05-05 Bioconductor > bumphunter 1.13.0 2016-05-05 Bioconductor > chron 2.3-47 2015-06-24 CRAN (R 3.3.0) > cluster 2.0.4 2016-04-18 CRAN (R 3.3.0) > codetools 0.2-14 2015-07-15 CRAN (R 3.3.0) > colorspace 1.2-6 2015-03-11 CRAN (R 3.3.0) > data.table 1.9.6 2015-09-19 CRAN (R 3.3.0) > DBI 0.4-1 2016-05-08 CRAN (R 3.3.0) > derfinder * 1.7.5 2016-05-20 Bioconductor > derfinderHelper 1.7.3 2016-05-20 Bioconductor > devtools 1.11.1 2016-04-21 CRAN (R 3.3.0) > digest 0.6.9 2016-01-08 CRAN (R 3.3.0) > doRNG 1.6 2014-03-07 CRAN (R 3.3.0) > foreach 1.4.3 2015-10-13 CRAN (R 3.3.0) > foreign 0.8-66 2015-08-19 CRAN (R 3.3.0) > Formula 1.2-1 2015-04-07 CRAN (R 3.3.0) > GenomeInfoDb * 1.9.1 2016-05-13 Bioconductor > GenomicAlignments 1.9.0 2016-05-05 Bioconductor > GenomicFeatures 1.25.12 2016-05-21 Bioconductor > GenomicFiles 1.9.7 2016-05-27 Bioconductor > GenomicRanges * 1.25.0 2016-05-05 Bioconductor > ggplot2 2.1.0 2016-03-01 CRAN (R 3.3.0) > gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0) > gtable 0.2.0 2016-02-26 CRAN (R 3.3.0) > Hmisc 3.17-4 2016-05-02 CRAN (R 3.3.0) > IRanges * 2.7.1 2016-05-27 Bioconductor > iterators 1.0.8 2015-10-13 CRAN (R 3.3.0) > lattice 0.20-33 2015-07-14 CRAN (R 3.3.0) > latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0) > locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.0) > magrittr 1.5 2014-11-22 CRAN (R 3.3.0) > Matrix 1.2-6 2016-05-02 CRAN (R 3.3.0) > matrixStats 0.50.2 2016-04-24 CRAN (R 3.3.0) > memoise 1.0.0 2016-01-29 CRAN (R 3.3.0) > munsell 0.4.3 2016-02-13 CRAN (R 3.3.0) > nnet 7.3-12 2016-02-02 CRAN (R 3.3.0) > pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0) > plyr 1.8.3 2015-06-12 CRAN (R 3.3.0) > qvalue 2.5.2 2016-05-20 Bioconductor > RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0) > Rcpp 0.12.5 2016-05-14 CRAN (R 3.3.0) > RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0) > recount * 0.99.0 2016-05-31 Bioconductor > registry 0.3 2015-07-08 CRAN (R 3.3.0) > reshape2 1.4.1 2014-12-06 CRAN (R 3.3.0) > rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0) > rpart 4.1-10 2015-06-29 CRAN (R 3.3.0) > Rsamtools 1.25.0 2016-05-05 Bioconductor > RSQLite 1.0.0 2014-10-25 CRAN (R 3.3.0) > rtracklayer 1.33.2 2016-05-31 Github > (Bioconductor-mirror/rtracklayer@917973e) > S4Vectors * 0.11.2 2016-05-27 Bioconductor > scales 0.4.0 2016-02-26 CRAN (R 3.3.0) > stringi 1.0-1 2015-10-22 CRAN (R 3.3.0) > stringr 1.0.0 2015-04-30 CRAN (R 3.3.0) > SummarizedExperiment 1.3.2 2016-05-20 Bioconductor > survival 2.39-4 2016-05-11 CRAN (R 3.3.0) > VariantAnnotation 1.19.1 2016-05-20 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) > xtable 1.8-2 2016-02-05 CRAN (R 3.3.0) > XVector 0.13.0 2016-05-05 Bioconductor > zlibbioc 1.19.0 2016-05-05 Bioconductor > > > > > On Tue, May 31, 2016 at 2:02 PM, Michael Lawrence > <lawrence.mich...@gene.com> wrote: >> 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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