[Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive
Leonardo Collado Torres
lcollado at jhu.edu
Thu May 5 23:46:29 CEST 2016
Hi Michael,
I forgot about pkg-util (just did a fresh BioC 3.3 install). I assumed
the OS X binary would work out of the box.
Anyhow, I installed rtracklayer (release) manually and got another
error (slightly different message now).
$ svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/rtracklayer
$ R CMD INSTALL rtracklayer
Loading required package: colorout
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.3release/Resources/library’
* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
## more output
$ R
> library('rtracklayer')
> unshorten_url <- function(uri) {
+ require('RCurl')
+ opts <- list(
+ followlocation = TRUE, # resolve redirects
+ ssl.verifyhost = FALSE, # suppress certain SSL errors
+ ssl.verifypeer = FALSE,
+ nobody = TRUE, # perform HEAD request
+ verbose = FALSE
+ )
+ curlhandle <- getCurlHandle(.opts = opts)
+ getURL(uri, curl = curlhandle)
+ info <- getCurlInfo(curlhandle)
+ rm(curlhandle) # release the curlhandle!
+ info$effective.url
+ }
> url <- unshorten_url('http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw')
Loading required package: RCurl
Loading required package: bitops
> url
[1] "https://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5"
> x <- import.bw(url, as = 'RleList')
Error in seqinfo(ranges) : UCSC library operation failed
In addition: Warning message:
In seqinfo(ranges) :
Couldn't open
https://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5
> x <- import.bw('http://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5')
Error in seqinfo(ranges) : UCSC library operation failed
In addition: Warning messages:
1: In seqinfo(ranges) :
TCP non-blocking connect() to content-na.drive.amazonaws.com
timed-out in select() after 10000 milliseconds - Cancelling!
2: In seqinfo(ranges) :
Couldn't open
http://content-na.drive.amazonaws.com/cdproxy/templink/usTQCr2pAaI3tTps4AFQuz1H9kmm23EDYy39SQ3ke5EuFiZq5
> ## Reproducibility info
> message(Sys.time())
2016-05-05 17:38:30
> 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 X11
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2016-05-05
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
Biobase 2.32.0 2016-05-04 Bioconductor
BiocGenerics * 0.18.0 2016-05-04 Bioconductor
BiocParallel 1.6.0 2016-05-04 Bioconductor
Biostrings 2.40.0 2016-05-04 Bioconductor
bitops * 1.0-6 2013-08-17 CRAN (R 3.3.0)
colorout * 1.1-2 2016-05-05 Github (jalvesaq/colorout at 6538970)
devtools 1.11.1 2016-04-21 CRAN (R 3.3.0)
digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
GenomeInfoDb * 1.8.0 2016-05-04 Bioconductor
GenomicAlignments 1.8.0 2016-05-04 Bioconductor
GenomicRanges * 1.24.0 2016-05-04 Bioconductor
IRanges * 2.6.0 2016-05-04 Bioconductor
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 1.24.0 2016-05-04 Bioconductor
rtracklayer * 1.32.0 2016-05-05 Bioconductor
S4Vectors * 0.10.0 2016-05-04 Bioconductor
SummarizedExperiment 1.2.0 2016-05-04 Bioconductor
withr 1.0.1 2016-02-04 CRAN (R 3.3.0)
XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
XVector 0.12.0 2016-05-04 Bioconductor
zlibbioc 1.18.0 2016-05-04 Bioconductor
>
On Thu, May 5, 2016 at 5:24 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> The URL redirection is something I can try to add. For the other error, you
> need to get openssl installed and made visible to pkg-config, so that
> rtracklayer finds it during its build process.
>
> Michael
>
> On Thu, May 5, 2016 at 2:01 PM, Leonardo Collado Torres <lcollado at jhu.edu>
> wrote:
>>
>> Hi Michael,
>>
>> I have a use case that is similar to
>> https://support.bioconductor.org/p/81267/#82142 and looks to me like
>> it might need some changes in rtracklayer to work. That's why I'm
>> posting it here this time.
>>
>> Basically, I'm trying to use rtracklayer to import a bigwig file over
>> the web which is in a different type of url than before. Using
>> utils::download.file() with the defaults doesn't work, I have to use
>> method = 'curl' and extra = '-L'.
>>
>> More specifically, the original url
>> http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw has an
>> effective url
>> https://content-na.drive.amazonaws.com/cdproxy/templink/i_aQAPZJkJ9d9lN1NO5DJJtlbpvAdgbNuc1SkqSTHFouFiZq5
>>
>> Now, using the second url with utils::download.file() and default
>> methods also doesn't work. It does on the browser though.
>>
>>
>> As you can see, downloading the file doesn't work out of the box.
>> Which I guess that it's not surprising that using rtracklayer I get
>> errors like:
>>
>> In seqinfo(ranges) :
>> No openssl available in netConnectHttps for
>> content-na.drive.amazonaws.com : 443
>>
>> You can find further details (code and log file) at
>> https://gist.github.com/lcolladotor/c500dd79d49aed1ef33ade5417111453
>>
>> Thanks,
>> Leo
>
>
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