[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)
Leonardo Collado Torres
lcollado at jhu.edu
Wed Oct 1 01:32:23 CEST 2014
Ahhhh!!! Thanks!
I forgot to check those help pages. The error messages didn't lead me
there, but I should have checked again regardless. Anyhow, maybe it
would be useful to check the OS in those functions and prompt a
warning or error that is more informative.
In my case, I added a warning in the functions that end up interacting
with BigWig files. For example:
if(.Platform$OS.type == 'windows') {
warning('As of rtracklayer 1.25.16, BigWig is not supported on
Windows. Thus loading data from BigWig files will most likely fail!')
}
As for Dan's linux, I don't know what is the solution in that case.
In the end, I made a data package with the BigWig files (only chr21
which I use in the examples) so users without internet connection can
still run the code in the vignettes of the packages I'm developing.
Those vignettes still show how you could get the data from the web if
you wanted. I also added the processed data in .RData files in the
data package, so Windows users could follow the examples.
Cheers,
Leo
On Tue, Sep 30, 2014 at 4:31 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
> Hi,
>
> Import and manipulation of BigWig files in rtracklayer make use of the Kent
> C library and are not supported on windows.
>
> This is documented at
>
> ?import.bw
> ?`BigWigFile-class`
>
> This problem isn't specific to an 'over the network' example. Trying to
> import() a local BigWig on Windows will also fail.
>
> Valerie
>
>
> On 09/30/2014 08:00 AM, Leonardo Collado Torres wrote:
>>
>> 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.
>>
>> 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
>>
>
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