[Bioc-devel] Minor issue with rtracklayer

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