[BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error

[Henrik Hornshøj Jensen]

Hey,

Looks like it works again now with the developer versions of R (2.3) and AnnBuilder (1.9.11), although I had to try a couple of times before it ran all the way through. Also, I had to trim the accession IDs in the mybase file (e.g. NM_000962.2 to NM_000962) before I was able to get any mappings. Anyhow, it seems to work now. Thanks for the tip to use the developer version.

Henrik
 


-----Oprindelig meddelelse-----
Fra: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] På vegne af Seth Falcon
Sendt: Tuesday, February 07, 2006 4:02 PM
Til: bioconductor at stat.math.ethz.ch
Emne: Re: [BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error

Hi Henrik and Julien,

If you are still having troubles getting AnnBuilder to do what you want, please post again after having a look through the posting guide:
http://www.bioconductor.org/docs/postingGuide.html

>From your mails, I'm finding it difficult to help because I'm not
certain what code you are attempting to run, what the error output is, or what are the exact R and package versions you are using (sessionInfo()).

+ seth

On  7 Feb 2006, HenrikH.Jensen at agrsci.dk wrote:

>
> I am using the latest version, just updated everything.
>
> Did not try the developer version though.
>
> I also tried running my script with days in between, to see if the 
> error is caused by source where it downloads from. But this did not 
> help.
>
> Regards,
> Henrik
>
>
> -----Oprindelig meddelelse----- Fra:
> bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] På vegne af TEXTORIS 
> Julien Sendt: Tuesday, February 07, 2006 8:24 AM Til:
> bioconductor at stat.math.ethz.ch Emne: Re: [BioC] ABPkgBuilder
> (AnnBuilder) subscript out of bounds error
>
> I still have the same error with the latest version. 
>
> Julien
>
> Le Lundi 6 Février 2006 19:21, Ting-Yuan Liu a écrit :
>> Hi Henrik,
>>
>> Which version of AnnBuilder you are using?  I believe the "subscript 
>> out of bounds error" had been fixed.  If you tried the developmental 
>> version AnnBuilder, you should not get this error again.
>>
>> HTH,
>> Ting-Yuan
>> ______________________________________
>> Ting-Yuan Liu
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center Seattle, WA, USA 
>> ______________________________________
>>
>> On Mon, 6 Feb 2006, Henrik Hornshøj Jensen wrote:
>>> Anyone seen this error with ABPkgBuilder (AnnBuilder) and knows how 
>>> to resolve it?
>>>
>>>
>>> To build a data annotation package, this piece of code usually works 
>>> for me:
>>>
>>> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = 
>>> myBaseType, pkgName = myPkgName, pkgPath = myDir, organism = "Homo 
>>> sapiens", version = "2.0.0", author = list(author = "Henrik Hornshoj 
>>> <henrikh.jensen at agrsci.dk <mailto:henrikh.jensen at agrsci.dk> >", 
>>> maintainer = "Henrik Hornshoj <henrikh.jensen at agrsci.dk 
>>> <mailto:henrikh.jensen at agrsci.dk> >"), fromWeb = TRUE)
>>>
>>>
>>> But today I suddenly get the following error:
>>>
>>>
>>> Attaching package: 'GO'
>>>
>>>
>>> The following object(s) are masked from package:AnnBuilder :
>>>
>>> GO
>>>
>>> Warning message: Built for UCSC is not valid! in:
>>> getUCSCBuilt(organism) Failed to get data from URL:
>>> ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00191.gene
>>> <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00191.gene>
>>> Failed to get data from URL:
>>> ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00192.gene
>>> <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00192.gene> .  .
>>> Failed to get data from URL:
>>> ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99998.gene
>>> <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99998.gene>
>>> Failed to get data from URL:
>>> ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99999.gene
>>> <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99999.gene> [1] 
>>> "4010 2 2" Error in all(is.na(annotation[, "GO"])) : subscript out 
>>> of bounds
>>>
>>>
>>> Any suggestions are welcome!!
>>>
>>> Regards,
>>> Henrik Hornshj
>>>
>>> 	[[alternative HTML version deleted]]
>
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