Hi,
I have a simple issue with rtracklayer::import.bw() which I believe
can be fixed by a one line edit to the NAMESPACE file.
The error is that url.exists() can't be found, which is part of RCurl.
> library(rtracklayer)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position,
rank, rbind, Reduce, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning messages:
1: package ‘rtracklayer’ was built under R version 3.3.1
2: package ‘GenomicRanges’ was built under R version 3.3.1
3: package ‘BiocGenerics’ was built under R version 3.3.1
4: package ‘S4Vectors’ was built under R version 3.3.1
> library(GenomicRanges)
> gr <- GRanges('chr1', IRanges(1, 1e5))
> x <-
> import.bw('http://duffel.rail.bio/recount/DRP000366/bw/mean_DRP000366.bw',
> selection = gr, as = 'RleList')
Error in expandURL(x) : could not find function "url.exists"
> options(width = 120)
> devtools::session_info()
Session info
-----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.0 RC (2016-05-01 r70572)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2016-07-13
Packages
---------------------------------------------------------------------------------------------------------------
package * version date source
Biobase 2.33.0 2016-05-05 Bioconductor
BiocGenerics * 0.19.2 2016-07-08 Bioconductor
BiocParallel 1.7.4 2016-06-17 Bioconductor
Biostrings 2.41.4 2016-06-17 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
devtools 1.12.0 2016-06-24 CRAN (R 3.3.0)
digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
GenomeInfoDb * 1.9.1 2016-05-13 Bioconductor
GenomicAlignments 1.9.5 2016-07-08 Bioconductor
GenomicRanges * 1.25.9 2016-06-26 Bioconductor
IRanges * 2.7.11 2016-06-22 Bioconductor
lattice 0.20-33 2015-07-14 CRAN (R 3.3.0)
Matrix 1.2-6 2016-05-02 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
Rsamtools 1.25.0 2016-05-05 Bioconductor
rtracklayer * 1.33.9 2016-07-08 Bioconductor
S4Vectors * 0.11.9 2016-07-08 Bioconductor
SummarizedExperiment 1.3.7 2016-07-08 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
XVector 0.13.6 2016-07-08 Bioconductor
zlibbioc 1.19.0 2016-05-05 Bioconductor
>
Modifying
https://github.com/Bioconductor-mirror/rtracklayer/blob/368e32110a4e515e7de27717399e69c193c827cc/NAMESPACE#L31
from:
postForm)
to
postForm, url.exists)
Should do it. Alternatively, changing
https://github.com/Bioconductor-mirror/rtracklayer/blob/368e32110a4e515e7de27717399e69c193c827cc/R/web.R#L69
from
if(!url.exists(uri))
to
if(!RCurl::url.exists(uri))
should fix this issue.
Best,
Leo
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