[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Sep 30 17:06:26 CEST 2014
----- 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/
>
More information about the Bioc-devel
mailing list