[Bioc-devel] Minor issue with rtracklayer

[Leonardo Collado Torres]

Thanks!

Actually, can you add getCurlInfo please? I missed it when checking
https://github.com/Bioconductor-mirror/rtracklayer/blob/master/R/web.R#L68-L84
versus https://github.com/Bioconductor-mirror/rtracklayer/blob/master/NAMESPACE#L30-L31

On Wed, Jul 13, 2016 at 3:55 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> 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