[Bioc-devel] bug tracker (was: graph package conflict with rtracklayer)

[Martin Morgan]

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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> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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