Message-ID: <CAP8VEO5S_42f_HCptgruka7X5ndPc-cuicipW8HDfjyhvyfY+g@mail.gmail.com>
Date: 2016-07-13T20:05:24Z
From: Leonardo Collado Torres
Subject: [Bioc-devel] Minor issue with rtracklayer
In-Reply-To: <CAOQ5NyfBJZX-d8K0h12c-=p6bnaZSFbe37N1aJF7s_0HOgaEzg@mail.gmail.com>
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