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

Tue May 29 21:29:10 CEST 2012

On 05/29/2012 09:21 AM, omranian wrote:
>
> 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

try in a new R session; it looks like the list of available packages is 
old. Martin
]
>
>
> 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 Hi Nooshin -- the AnnotationDbi package is slightly out of date with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
>
>


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