[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)
Michael Lawrence
lawrence.michael at gene.com
Tue Sep 30 22:30:48 CEST 2014
The answer on Windows is simple: BigWig is not supported on that platform.
There is probably a simple fix, if someone were to just go into Windows and
use gdb to fix the Windows implementation of the abstraction layer.
The problem on Dans' linux seems to be lack of permission for writing to
/tmp.
A possible answer is to switch Jim Kent's library to the Java
implementation of BigWig, but that would be a lot of work and seems risky.
On Tue, Sep 30, 2014 at 8:06 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>
> ----- Original Message -----
> > From: "Leonardo Collado Torres" <lcollado at jhu.edu>
> > To: bioc-devel at r-project.org
> > Cc: "Dan" <dtenenba at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list