----- 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