[BioC] SNPcounts error in SNPlocs.Hsapiens.dbSNP.20110815_0.99.3 (i.e., my attempt to update SNPlocs to dbSNP build 134)

[Tim Triche, Jr.]

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 at 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 at 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>
-------------- next part --------------
> sessionInfo()
R Under development (unstable) (2011-09-10 r56986)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.17    
 [2] IlluminaHumanMethylation450k.db_1.4.9 
 [3] plyr_1.6                              
 [4] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2
 [5] ChIPpeakAnno_2.0.5                    
 [6] gplots_2.10.1                         
 [7] KernSmooth_2.23-6                     
 [8] caTools_1.12                          
 [9] bitops_1.0-4.1                        
[10] gdata_2.8.2                           
[11] limma_3.9.16                          
[12] org.Hs.eg.db_2.5.0                    
[13] GO.db_2.5.0                           
[14] RSQLite_0.9-4                         
[15] DBI_0.2-5                             
[16] AnnotationDbi_1.15.15                 
[17] BSgenome.Ecoli.NCBI.20080805_1.3.17   
[18] multtest_2.9.1                        
[19] Biobase_2.13.9                        
[20] biomaRt_2.9.2                         
[21] SNPlocs.Hsapiens.dbSNP.20110815_0.99.3
[22] BSgenome_1.21.3                       
[23] Biostrings_2.21.9                     
[24] GenomicRanges_1.5.35                  
[25] IRanges_1.11.26                       
[26] BiocInstaller_1.1.27                  
[27] gtools_2.6.2                          

loaded via a namespace (and not attached):
[1] MASS_7.3-14     RCurl_1.6-10    splines_2.14.0  survival_2.36-9
[5] tcltk_2.14.0    tools_2.14.0    XML_3.4-3