[Bioc-devel] Minor issue with rtracklayer

[Michael Lawrence]

Thanks, made the change.

On Wed, Jul 13, 2016 at 12:28 PM, Leonardo Collado Torres
<lcollado at 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