[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)
Leonardo Collado Torres
lcollado at jhu.edu
Tue Sep 30 17:13:20 CEST 2014
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 at 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 <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/
>>
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