Thanks, made the change.
On Wed, Jul 13, 2016 at 12:28 PM, Leonardo Collado Torres
<lcoll...@jhu.edu> wrote:
> 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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