[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)
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/
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