[Bioc-devel] bug tracker (was: graph package conflict with rtracklayer)
On 10/06/2011 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!
Hi Malcolm -- tried to disentangle the bug tracker from the other parts of the post. There is no overall bug tracker; it is worth exploring, though no promises. Any feedback from other developers? I think my reservation is that only some would adopt the practice, meaning that the developer and the conscientious bug reporter interested in knowing whether an issued had been reported / resolved would have to look both on the list and in the tracker. Thanks for the suggestion! Martin
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
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