I think you'd better have just one SNPlocs.* package in your searchlist for
the diagnosis to be as simple as possible.  But  I will stop chattering as
HP will surely know the answer.

On Thu, Sep 15, 2011 at 3:53 PM, Tim Triche, Jr. <ttriche@usc.edu> wrote:

> Sure, and since you might know the answer...
>
> How come the standard policy for SNPlocs package is to use (e.g.) $ch1, but
> for BSgenomes, it's $chr1?
>
> I've been computing overlaps this morning and keep having to change
> seqlevels() to do it without warnings being raised.
>
> thanks,
>
> --t
>
>
>
> On Thu, Sep 15, 2011 at 12:20 PM, Vincent Carey <
> stvjc@channing.harvard.edu> wrote:
>
>> Can you give the sessionInfo() where this occurred?  Also I'd recommend
>> triggering the error with
>> options(error=recover) on so the stack can be seen.
>>
>> On Thu, Sep 15, 2011 at 3:15 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote:
>>
>>> Hi Herve (and others),
>>>
>>> in an attempt to update annotations for some probes, and after taking
>>> your
>>> workshop at Bioc2011, I have been playing with Biostrings, BSgenomes,
>>> GRanges, et al, mostly to good effect (thank you and others for writing
>>> and
>>> documenting them, they're terrific once the learning curve flattens out).
>>>  However, I rebuilt the SNPlocs package following instructions you long
>>> ago
>>> posted for Paul Shannon, and I think I have hit a wall in that respect.
>>>  I
>>> put the offending package (and some others) up:
>>>
>>> http://flaver.com/annotations/  (in case you need the actual package for
>>> an
>>> autopsy)
>>>
>>> When I load and inject SNPlocs.Hsapiens.dbSNP.20101109, your package of
>>> build 132, everything goes as planned: I can inject the hard mask with
>>> polymorphisms where they're supposed to be, and everything is hunkey
>>> dorey.
>>>  When I do this after building (without apparent incident) the b134 based
>>> SNPlocs.Hsapiens.dbSNP.20110815_0.99.3 , after editing the scripts to
>>> look
>>> for 'GRCh37.p2' instead of 'GRCh37' and rebuilding, I get the following
>>> error:
>>>
>>> Error in x %in% SNPlocs_seqnames :
>>>  error in evaluating the argument 'table' in selecting a method for
>>> function '%in%': Error in getSNPcount() : internal error: 'SNPcount' data
>>> set is broken.
>>>       Please contact the maintainer of the
>>> SNPlocs.Hsapiens.dbSNP.20110815
>>> package.
>>>
>>> This seems odd, since the internal regression tests all passed when I
>>> built
>>> the package.  But, obviously I must have missed something somewhere!
>>>
>>> Any thoughts?
>>>
>>> Thanks!
>>>
>>>
>>>
>>> --
>>> If people do not believe that mathematics is simple, it is only because
>>> they
>>> do not realize how complicated life is.
>>> John von Neumann<
>>> http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html
>>> >
>>>
>>>        [[alternative HTML version deleted]]
>>>
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>>>
>>
>>
>
>
> --
> When you emerge in a few years, you can ask someone what you missed, and
> you'll find it can be summed up in a few minutes.
>
> Derek Sivers <http://sivers.org/berklee>
>
>

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