[BioC] an error in AnnotationForge

[Marc Carlson]

Hi Peter,

Maybe this will help you?

http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/SQLForge.pdf

Almost all of the packages in Bioconductor have vignettes, which you can 
find by navigating to them by using the web site here:

http://www.bioconductor.org/packages/2.12/BiocViews.html

And then clicking on their various landing pages.


OR you can navigate to them by using help.start() to display the 
documentation for packages that you have installed.


   Marc



On 04/22/2013 07:26 AM, James W. MacDonald wrote:
> Hi Peter,
>
> On 4/21/2013 10:25 PM, Wang Peter wrote:
>> source("http://bioconductor.org/biocLite.R");
>> biocLite("human.db0");
>> biocLite("AnnotationDbi");
>> biocLite("AnnotationForge");
>> library(human.db0);
>> library(AnnotationDbi);
>> library(AnnotationForge);
>
> First, this isn't Perl, so adding in extraneous semi-colons isn't 
> necessary.
>
>>> available.chipdbschemas();
>>> dir.create("primeview");
>>>
>> populateDB("HUMANCHIP_DB",affy=F,prefix="primeview",fileName="primeviewHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM"="Homo 
>>
>> sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="PrimeView 
>>
>> Human Gene Expression 
>> Array","MANUFACTURERURL"="http://www.affymetrix.com
>> "),baseMapType="eg",outputDir="primeview");
>
> You are using arguments for makeDBPackage, but calling populateDB. 
> There is no reason that I can think of that you should be using 
> populateDB directly, unless you just want the sqlite database. I have 
> no idea why you are doing things this way - why not just follow the 
> vignette?
>
> In addition, about half of your arguments are all caps, and are 
> quoted. There are no all caps arguments for any of the functions you 
> are trying to use, nor are there any quoted arguments in R.
>
> I would recommend just following the vignette. Also, IIRC the 
> primeview chip is just a 3'-biased array, so you can probably also set 
> affy = TRUE and have the parsing of the file done automatically.
>
> Best,
>
> Jim
>
>
>
>>> seed<-new("AnnDbPkgSeed",Package =
>> "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPrefix="primeview"); 
>>
>> makeAnnDbPkg(seed,file.path("primeview","primeview.sqlite"),dest_dir="primeview"); 
>>
>> Error in match(x, table, nomatch = 0L) :
>> object 'doc_template_names' not found
>>> sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5
>> human.db0_2.9.0
>> [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0
>>
>>
>