[Bioc-devel] graph package conflict with rtracklayer

Cook, Malcolm MEC at stowers.org
Thu Oct 6 19:04:25 CEST 2011

Hi Michael & Martin,

Michael replied to my problem (stated below) that:

	"This issue has been reported before. The resolution was that there are odd things going on in the methods package. Pretty sure we reported this to John."

Ah, yes, now I see it has been reported, with Martin replying (on 12/2010  in https://stat.ethz.ch/pipermail/bioconductor/2010-December/036755.html)

	" I forwarded an example to John Chambers, and will report back ..." 
Pending a resolution, is there any advice for a best workaround aside from not loading both `graph` and `rtracklayer` libraries.

Also, off topic, but, is there any advice on tracking status of issues with bioconductor packages other than emailing to the list and package authors?  The CPAN (for perl) offers an 'rt bug tracker' which forwards posted issues to developers.  Something like that might be a grand addition!



-----Original Message-----
From: bioc-devel-bounces at r-project.org [mailto:bioc-devel-bounces at r-project.org] On Behalf Of Cook, Malcolm
Sent: Friday, June 10, 2011 2:57 PM
To: 'Michael Lawrence'
Cc: 'bioc-devel at r-project.org'; 'bioc-sig-sequencing at r-project.org'
Subject: [Bioc-devel] graph package conflict with rtracklayer

Michael & Robert,

If I load the graph package prior to rtracklayer, import.bed generates an error and fails.  It otherwise succeeds if I don't load the graph package.

It happens both with rtracklayer from svn and production.


In a fresh session:

> library(graph)
> library(rtracklayer)
Loading required package: RCurl
Loading required package: bitops
> b <- import.bed('my.bed')
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "import.ucsc", for signature "file"
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rtracklayer_1.13.3 RCurl_1.5-0        bitops_1.0-4.1     graph_1.30.0      

loaded via a namespace (and not attached):
[1] BSgenome_1.20.0     Biostrings_2.20.1   GenomicRanges_1.4.6
[4] IRanges_1.10.4      XML_3.4-0           tools_2.13.0       

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