Awesome, thanks! On Tue, May 31, 2016 at 4:11 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > 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
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
