Hm... weird. I can get it to work on our linux cluster.
> ## Attempt with 1 file ode_v10/bigwig/HSB97.AMY.bw')wnload.alleninstitute.org/brainspan/MRF_BigWig_Genc > seql <- seqlengths(bw) > > seql chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 249250621 135534747 135006516 133851895 115169878 107349540 102531392 90354753 chr17 chr18 chr19 chr2 chr20 chr21 chr22 chr3 81195210 78077248 59128983 243199373 63025520 48129895 51304566 198022430 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX 191154276 180915260 171115067 159138663 146364022 141213431 16571 155270560 chrY 59373566 > ## Then another file code_v10/bigwig/HSB114.A1C.bw')nload.alleninstitute.org/brainspan/MRF_BigWig_Gen > seql2 <- seqlengths(bw2) > > ## Check > identical(seql, seql2) [1] TRUE > > ## Session info > devtools::session_info() Session info------------------------------------------------------------------- setting value version R version 3.1.1 Patched (2014-09-27 r66697) system x86_64, linux-gnu ui X11 language (EN) collate en_US.UTF-8 tz <NA> Packages----------------------------------------------------------------------- package * version date source base64enc 0.1.2 2014-06-26 CRAN (R 3.1.0) BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1) BBmisc 1.7 2014-06-21 CRAN (R 3.1.0) BiocGenerics * 0.11.5 2014-09-17 Bioconductor BiocParallel 0.99.22 2014-09-26 Bioconductor Biostrings 2.33.14 2014-09-09 Bioconductor bitops 1.0.6 2013-08-17 CRAN (R 3.1.0) brew 1.0.6 2011-04-13 CRAN (R 3.1.0) checkmate 1.4 2014-09-03 CRAN (R 3.1.1) codetools 0.2.9 2014-08-21 CRAN (R 3.1.1) colorout * 1.0.2 2014-05-30 local DBI 0.3.1 2014-09-24 CRAN (R 3.1.1) devtools 1.6 2014-09-19 Github (hadley/devtools@45a6ac0) digest 0.6.4 2013-12-03 CRAN (R 3.1.0) fail 1.2 2013-09-19 CRAN (R 3.1.0) foreach 1.4.2 2014-04-11 CRAN (R 3.1.0) futile.logger 1.3.7 2014-01-25 CRAN (R 3.1.1) futile.options 1.0.0 2010-04-06 CRAN (R 3.1.1) GenomeInfoDb * 1.1.19 2014-09-09 Bioconductor GenomicAlignments 1.1.29 2014-09-17 Bioconductor GenomicRanges * 1.17.40 2014-09-17 Bioconductor IRanges * 1.99.28 2014-09-17 Bioconductor iterators 1.0.7 2014-04-11 CRAN (R 3.1.0) lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.1) RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1) Rsamtools 1.17.33 2014-09-09 Bioconductor RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.0) rstudioapi 0.1 2014-03-27 CRAN (R 3.1.1) rtracklayer * 1.25.16 2014-09-17 Bioconductor S4Vectors * 0.2.4 2014-09-15 Bioconductor sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1) stringr 0.6.2 2012-12-06 CRAN (R 3.1.0) XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0) XVector 0.5.8 2014-09-07 Bioconductor zlibbioc 1.11.1 2014-04-26 Bioconductor > On Tue, Sep 30, 2014 at 11:06 AM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > > > ----- Original Message ----- >> From: "Leonardo Collado Torres" <lcoll...@jhu.edu> >> To: bioc-devel@r-project.org >> Cc: "Dan" <dtene...@fhcrc.org> >> Sent: Tuesday, September 30, 2014 8:00:53 AM >> Subject: Cannot interact with a BigWig file on the web with rtracklayer >> (Windows specific) >> >> Hello, >> >> I ran into an issue interacting with BigWig files over the network >> with `rtracklayer`. For some reason, the issue is Windows-specific >> and >> I don't understand why. >> >> Basically, I run the short code at >> https://gist.github.com/lcolladotor/0ab8ab3d904d21110637 It works on >> a >> Mac, but it fails on Windows. The same is true for using >> rtracklayer::import(). >> >> Any help will be greatly appreciated. >> > > This fails for me on both linux and Windows. > > Here's the linux output: > >> suppressPackageStartupMessages(library('rtracklayer')) >> >> ## Attempt with 1 file >> bw <- >> BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB97.AMY.bw') >> seql <- seqlengths(bw) > Warning message: > In seqinfo(x) : Permission denied > Can't > open(/tmp/udcCache/http/download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB97.AMY.bw/bitmap, > O_RDWR) > Error in seqlengths(seqinfo(x)) : > error in evaluating the argument 'x' in selecting a method for function > 'seqlengths': Error in seqinfo(x) : UCSC library operation failed >> >> ## Then another file >> bw2 <- >> BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB114.A1C.bw') >> seql2 <- seqlengths(bw2) > Warning message: > In seqinfo(x) : Permission denied > Can't > open(/tmp/udcCache/http/download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB114.A1C.bw/bitmap, > O_RDWR) > Error in seqlengths(seqinfo(x)) : > error in evaluating the argument 'x' in selecting a method for function > 'seqlengths': Error in seqinfo(x) : UCSC library operation failed >> >> ## Check >> identical(seql, seql2) > Error in identical(seql, seql2) : object 'seql' not found >> >> ## Session info >> devtools::session_info() > Session > info------------------------------------------------------------------- > setting value > version R version 3.1.1 Patched (2014-09-25 r66681) > system x86_64, linux-gnu > ui X11 > language en_US: > collate en_US.UTF-8 > tz <NA> > > Packages----------------------------------------------------------------------- > package * version date source > base64enc 0.1.2 2014-06-26 CRAN (R 3.1.1) > BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1) > BBmisc 1.7 2014-06-21 CRAN (R 3.1.1) > BiocGenerics * 0.11.5 2014-09-30 Bioconductor > BiocParallel 0.99.24 2014-09-30 Bioconductor > Biostrings 2.33.14 2014-09-30 Bioconductor > bitops 1.0.6 2013-08-17 CRAN (R 3.1.1) > brew 1.0.6 2011-04-13 CRAN (R 3.1.1) > checkmate 1.4 2014-09-03 CRAN (R 3.1.1) > codetools 0.2.9 2014-08-21 CRAN (R 3.1.1) > DBI 0.3.1 2014-09-24 CRAN (R 3.1.1) > devtools 1.6 2014-09-23 CRAN (R 3.1.1) > digest 0.6.4 2013-12-03 CRAN (R 3.1.1) > fail 1.2 2013-09-19 CRAN (R 3.1.1) > foreach 1.4.2 2014-04-11 CRAN (R 3.1.1) > futile.logger 1.3.7 2014-01-25 CRAN (R 3.1.1) > futile.options 1.0.0 2010-04-06 CRAN (R 3.1.1) > GenomeInfoDb * 1.1.23 2014-09-30 Bioconductor > GenomicAlignments 1.1.30 2014-09-30 Bioconductor > GenomicRanges * 1.17.42 2014-09-30 Bioconductor > IRanges * 1.99.28 2014-09-30 Bioconductor > iterators 1.0.7 2014-04-11 CRAN (R 3.1.1) > lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.1) > RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1) > Rsamtools 1.17.34 2014-09-30 Bioconductor > RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.1) > rstudioapi 0.1 2014-03-27 CRAN (R 3.1.1) > rtracklayer * 1.25.16 2014-09-30 Bioconductor > S4Vectors * 0.2.4 2014-09-30 Bioconductor > sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1) > stringr 0.6.2 2012-12-06 CRAN (R 3.1.1) > XML 3.98.1.1 2013-06-20 CRAN (R 3.1.1) > XVector 0.5.8 2014-09-30 Bioconductor > zlibbioc 1.11.1 2014-09-30 Bioconductor >> > > > Dan > > >> Thanks, >> Leonardo >> >> >> ####### Windows info ########### >> >> > suppressPackageStartupMessages(library('rtracklayer')) >> > >> > ## Attempt with 1 file >> > bw <- >> > BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB97.AMY.bw') >> > seql <- seqlengths(bw) >> Warning message: >> In seqinfo(x) : Invalid argument >> Can't open >> http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB97.AMY.bw >> to read >> Error in seqlengths(seqinfo(x)) : >> error in evaluating the argument 'x' in selecting a method for >> function 'seqlengths': Error in seqinfo(x) : UCSC library operation >> failed >> > traceback() >> 3: seqlengths(seqinfo(x)) >> 2: seqlengths(bw) >> 1: seqlengths(bw) >> > >> > ## Then another file >> > bw2 <- >> > BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB114.A1C.bw') >> > seql2 <- seqlengths(bw2) >> Warning message: >> In seqinfo(x) : Invalid argument >> Can't open >> http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB114.A1C.bw >> to read >> Error in seqlengths(seqinfo(x)) : >> error in evaluating the argument 'x' in selecting a method for >> function 'seqlengths': Error in seqinfo(x) : UCSC library operation >> failed >> > >> > ## Check >> > identical(seql, seql2) >> Error in identical(seql, seql2) : object 'seql' not found >> > >> > ## Session info >> > devtools::session_info() >> Session >> info------------------------------------------------------------------------------------------------------------ >> setting value >> version R version 3.1.1 (2014-07-10) >> system x86_64, mingw32 >> ui Rgui >> language (EN) >> collate English_United States.1252 >> tz America/New_York >> >> Packages---------------------------------------------------------------------------------------------------------------- >> package * version date source >> base64enc 0.1.2 2014-06-26 CRAN (R 3.1.1) >> BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1) >> BBmisc 1.7 2014-06-21 CRAN (R 3.1.1) >> BiocGenerics * 0.11.5 2014-09-13 Bioconductor >> BiocParallel 0.99.22 2014-09-23 Bioconductor >> Biostrings 2.33.14 2014-09-07 Bioconductor >> bitops 1.0.6 2013-08-17 CRAN (R 3.1.0) >> brew 1.0.6 2011-04-13 CRAN (R 3.1.0) >> checkmate 1.4 2014-09-03 CRAN (R 3.1.1) >> codetools 0.2.9 2014-08-21 CRAN (R 3.1.1) >> DBI 0.3.1 2014-09-24 CRAN (R 3.1.1) >> devtools 1.6 2014-09-23 CRAN (R 3.1.1) >> digest 0.6.4 2013-12-03 CRAN (R 3.1.0) >> fail 1.2 2013-09-19 CRAN (R 3.1.0) >> foreach 1.4.2 2014-04-11 CRAN (R 3.1.0) >> futile.logger 1.3.7 2014-01-23 CRAN (R 3.1.1) >> futile.options 1.0.0 2010-04-06 CRAN (R 3.1.1) >> GenomeInfoDb * 1.1.23 2014-09-28 Bioconductor >> GenomicAlignments 1.1.30 2014-09-23 Bioconductor >> GenomicRanges * 1.17.42 2014-09-23 Bioconductor >> IRanges * 1.99.28 2014-09-10 Bioconductor >> iterators 1.0.7 2014-04-11 CRAN (R 3.1.0) >> lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.1) >> RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1) >> Rsamtools 1.17.34 2014-09-20 Bioconductor >> RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.0) >> rstudioapi 0.1 2014-03-27 CRAN (R 3.1.1) >> rtracklayer * 1.25.16 2014-09-10 Bioconductor >> S4Vectors * 0.2.4 2014-09-14 Bioconductor >> sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1) >> stringr 0.6.2 2012-12-06 CRAN (R 3.1.0) >> XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0) >> XVector 0.5.8 2014-09-07 Bioconductor >> zlibbioc 1.11.1 2014-05-09 Bioconductor >> > >> >> >> >> >> >> >> >> ########## Mac info ############ >> >> >> >> >> >> > suppressPackageStartupMessages(library('rtracklayer')) >> > >> > ## Attempt with 1 file >> > bw <- >> > BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB97.AMY.bw') >> > seql <- seqlengths(bw) >> > >> > ## Then another file >> > bw2 <- >> > BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB114.A1C.bw') >> > seql2 <- seqlengths(bw2) >> > >> > ## Check >> > identical(seql, seql2) >> [1] TRUE >> > >> > ## Session info >> > devtools::session_info() >> Session >> info------------------------------------------------------------------------------------------------------------------------ >> setting value >> version R version 3.1.1 (2014-07-10) >> system x86_64, darwin10.8.0 >> ui AQUA >> language (EN) >> collate en_US.UTF-8 >> tz America/New_York >> >> Packages---------------------------------------------------------------------------------------------------------------------------- >> package * version date source >> base64enc 0.1.2 2014-06-26 CRAN (R 3.1.0) >> BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1) >> BBmisc 1.7 2014-06-21 CRAN (R 3.1.0) >> BiocGenerics * 0.11.5 2014-09-13 Bioconductor >> BiocParallel 0.99.22 2014-09-24 Bioconductor >> Biostrings 2.33.14 2014-09-09 Bioconductor >> bitops 1.0.6 2013-08-17 CRAN (R 3.1.0) >> brew 1.0.6 2011-04-13 CRAN (R 3.1.0) >> checkmate 1.4 2014-09-03 CRAN (R 3.1.1) >> codetools 0.2.9 2014-08-21 CRAN (R 3.1.1) >> DBI 0.3.1 2014-09-24 CRAN (R 3.1.1) >> devtools 1.6 2014-09-23 CRAN (R 3.1.1) >> digest 0.6.4 2013-12-03 CRAN (R 3.1.0) >> fail 1.2 2013-09-19 CRAN (R 3.1.0) >> foreach 1.4.2 2014-04-11 CRAN (R 3.1.0) >> futile.logger 1.3.7 2014-01-23 CRAN (R 3.1.0) >> futile.options 1.0.0 2010-04-06 CRAN (R 3.1.0) >> GenomeInfoDb * 1.1.23 2014-09-28 Bioconductor >> GenomicAlignments 1.1.30 2014-09-23 Bioconductor >> GenomicRanges * 1.17.42 2014-09-23 Bioconductor >> IRanges * 1.99.28 2014-09-10 Bioconductor >> iterators 1.0.7 2014-04-11 CRAN (R 3.1.0) >> lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.0) >> RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1) >> Rsamtools 1.17.34 2014-09-20 Bioconductor >> RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.0) >> rstudioapi 0.1 2014-03-27 CRAN (R 3.1.0) >> rtracklayer * 1.25.16 2014-09-10 Bioconductor >> S4Vectors * 0.2.4 2014-09-14 Bioconductor >> sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1) >> stringr 0.6.2 2012-12-06 CRAN (R 3.1.0) >> XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0) >> XVector 0.5.8 2014-09-07 Bioconductor >> zlibbioc 1.11.1 2014-04-19 Bioconductor >> > >> >> >> >> >> >> Leonardo Collado Torres, PhD Candidate >> Department of Biostatistics >> Johns Hopkins University >> Bloomberg School of Public Health >> Website: http://www.biostat.jhsph.edu/~lcollado/ >> Blog: http://lcolladotor.github.io/ >> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel