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

Tue May 29 18:21:19 CEST 2012

Hi,

No I have again another problem:

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'
Error in download.file(url, destfile, method, mode = "wb", ...) :
   cannot open URL 
'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/AnnotationDbi_1.18.0.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
   cannot open: HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
   download of package ‘AnnotationDbi’ failed

Would you please help me?

On 05/25/2012 06:36 PM, omranian wrote:
> 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 Hi Nooshin -- the AnnotationDbi package is slightly out of date with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
>
> _______________________________________________
> 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