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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