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] P? 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] P? 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 F?vrier 2006 19:21, Ting-Yuan Liu a ?crit?:
>> 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 Hornsh?j 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 allis.na(annotation[, "GO"])) : subscript out
>>> of bounds
>>>
>>>
>>> Any suggestions are welcome!!
>>>
>>> Regards,
>>> Henrik Hornshj
>>>
>>> [[alternative HTML version deleted]]
>
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