[Bioc-devel] Minor issue with rtracklayer
Leonardo Collado Torres
lcollado at jhu.edu
Thu Jul 14 17:25:48 CEST 2016
To complete my previous email, here's the issue:
> 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
> 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 "getCurlInfo"
>
> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.1 (2016-06-21)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2016-07-14
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 3.3.1)
Matrix 1.2-6 2016-05-02 CRAN (R 3.3.1)
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 * 1.33.10 2016-07-13 Github
(Bioconductor-mirror/rtracklayer at 7eaaa2d)
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
>
Importing getCurlInfo from RCurl in the namespace should fix this.
Thanks,
Leo
On Wed, Jul 13, 2016 at 4:05 PM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:
> 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
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