[Bioc-devel] graph package conflict with rtracklayer

Mainly for Martin:

Have you tried this with the current version(s)? I installed your pkgA
with the current trunk (well, plus a couple of my fixes but these are
asserted to only relate to reference classes ;-))

And:

 > setOldClass(c("file", "connection"))
 > options(error=recover)
 > require(pkgA)

Loading required package: pkgA

 > foo()

[1] "OK"

which AFAICS is the version of the bug you reported to me:

mtmorgan at linux-ibmc:/tmp> R

 > setOldClass(c("file", "connection"))
 > library(pkgA)
 > foo()

Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "fun", for signature
"file"

John


On 10/6/11 10:04 AM, Cook, Malcolm wrote:

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!

Thanks!

~Malcolm

-----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.

Look:

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)

locale:
[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