[BioC] Error in .testGOFrame(x, organism)

Fri May 25 18:36:44 CEST 2012

On 05/25/2012 05:29 PM, Martin Morgan wrote:
> On 05/25/2012 06:33 AM, omranian wrote:
>> On 05/25/2012 03:20 PM, Martin Morgan wrote:
>>> On 05/25/2012 06:13 AM, omranian wrote:
>>>> On 05/25/2012 03:09 PM, Martin Morgan wrote:
>>>>> On 05/25/2012 02:35 AM, omranian wrote:
>>>>>> Hello,
>>>>>>
>>>>>> Can anybody help me to solve this error? I can not understand it :(
>>>>>>
>>>>>> library(org.Sc.sgd.db)
>>>>>> frame <- toTable(org.Sc.sgdGO)
>>>>>> goframeData <- data.frame(frame$go_id, frame$Evidence,
>>>>>> frame$systematic_name)
>>>>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces 
>>>>>> cerevisiae")
>>>>>> Loading required package: GO.db
>>>>>>
>>>>>> Error in .testGOFrame(x, organism) :
>>>>>> All of the Evidence codes in your data.frame object must be 
>>>>>> legitimate
>>>>>> Evidence Codes.
>>>>>
>>>>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with
>>>>> respect to Evidence codes it selects; this is fixed in AnnotationDbi
>>>>> 1.18.1, which will be available for download via biocLite in a day or
>>>>> so. A work-around is to drop the 13 'IRD' evidence codes,
>>>>>
>>>>> > idx = goframeData$frame.Evidence != "IRD"
>>>>> > table(idx)
>>>>> idx
>>>>> FALSE TRUE
>>>>> 13 73735
>>>>> > goframeData = goframeData[idx,]
>>>>>
>>>>> Martin
>>>>>
>>>>>>
>>>>>> Thanks a lot.
>>>>>> Nooshin
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>> Hi Martin,
>>>> Thanks for the reply!
>>>> I removed the package and reinstalled it many times, but doesn't 
>>>> help :(
>>>>
>>>> I used biocLite to install and hope it installed the latest version.
>>>> Now, I really don't know what should I do?!
>>>
>>> wait two days and try again; the package had a bug, the bug has been
>>> fixed (a few minutes ago); it takes a couple of days for the package
>>> to be checked and made available to you. When it is ready, using
>>> biocLite will download and install AnnotationDbi version 1.18.1. You
>>> must be using R version 2.15.0.
>>>
>>> Martin
>>>
>>>>
>>>> Best,
>>>> Nooshin
>>>
>>>
>> Thanks a lot.
>> So, you believe if I wait it would work!
>> I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even
>> when I uninstall and install it again.
>> So I'll wait for two days and try it again.
>> I hope it works by then.
>
> biocLite should not be installing AnnotationDbi 1.14.1 when using R 
> 2.15. If that is really the case, then please report (copy and paste) 
> the result of running the following commands in a new R session.
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("AnnotationDbi")
> sessionInfo()
>
> Martin
>
>>
>> Best,
>> Nooshin
>
>

I think I made a mistake by the version. But still is not working and I 
have to wait for another 2 days as you said!
Nooshin

 > source("http://bioconductor.org/biocLite.R")
 > biocLite("AnnotationDbi")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.4.
Installing package(s) 'AnnotationDbi'
trying URL 
'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/AnnotationDbi_1.18.0.tar.gz'
Content type 'application/x-gzip' length 4609048 bytes (4.4 Mb)
opened URL
==================================================
downloaded 4.4 Mb

* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘toString’ from package ‘base’ in 
package ‘AnnotationDbi’
Creating a generic function for ‘rev’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘subset’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘as.data.frame’ from package ‘base’ in 
package ‘AnnotationDbi’
Creating a generic function for ‘head’ from package ‘utils’ in package 
‘AnnotationDbi’
Creating a generic function for ‘tail’ from package ‘utils’ in package 
‘AnnotationDbi’
Creating a generic function for ‘as.list’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package 
‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package 
‘AnnotationDbi’
** help
*** installing help indices
converting help for package ‘AnnotationDbi’
finding HTML links ... done
AnnDbBimap-envirAPI html
AnnDbObj-class html
AnnDbPkg-checker html
AnnDbPkg-maker html
AnnotationDb-class html
AnnotationDbi-internals html
Bimap-direction html
Bimap-keys html
Bimap-toTable html
Bimap html
BimapFiltering html
BimapFormatting html
GOFrame html
GOTerms-class html
KEGGFrame html
NCBI_getters html
available.db0pkgs html
createSimpleBimap html
getProbeDataAffy html
getProbeData_1lq html
inpIDMapper html
makeOrgPackage html
makeProbePackage html
make_eg_to_go_map html
print.probetable html
sqlForge-makeCHIPDB html
sqlForge-popDB html
sqlForge-wrapDBPackages html
toSQLStringSet html
unlist2 html
** building package indices
** installing vignettes
‘AnnotationDbi.Rnw’
‘IntroToAnnotationPackages.Rnw’
‘NewSchema.Rnw’
‘SQLForge.Rnw’
‘makeProbePackage.Rnw’
** testing if installed package can be loaded

* DONE (AnnotationDbi)

The downloaded source packages are in
‘/tmp/RtmpGs7sqo/downloaded_packages’
 > sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)

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

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

other attached packages:
[1] feature_1.2.8 ks_1.8.7 misc3d_0.8-2 rgl_0.92.880 mvtnorm_0.9-9992 
KernSmooth_2.23-7
[7] limma_3.12.0 fields_6.6.3 spam_0.29-1 igraph_0.5.5-4 BiocInstaller_1.4.4

loaded via a namespace (and not attached):
[1] tools_2.15.0