[Bioc-devel] GOstats won't load with BioC 2.0
Mark W Kimpel
mwkimpel at gmail.com
Sat Feb 10 20:32:05 CET 2007
Robert and Seth,
I hope you made it safely to New Zealand, a beautiful country from what
I've seen of it in movies and TV shows.
I will try to provide you a little better debugging info than I did
yesterday, when for some reason I didn't copy the whole thing.
Today I downloaded the latest R-devel and updated all R and BioC devel
packages. Still have the same error output. I started with a fresh boot
of R and tried both require and library for GOstats. Everything is below.
Thanks,
Mark
R version 2.5.0 Under development (unstable) (2007-02-09 r40677)
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ISBN 3-900051-07-0
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There were 16 warnings (use warnings() to see them)
Loading required package: tools
Loading required package: utils
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Warning: unable to access index for repository
http://bioconductor.org/packages/2.0/monograph/bin/windows/contrib/2.5
Loading required package: affy
Loading required package: affyio
[1] TRUE
Loading required package: limma
[1] TRUE
> options(error=recover)
> require(GOstats)
Loading required package: GOstats
Loading required package: graph
Loading required package: GO
Loading required package: annotate
Loading required package: RBGL
Loading required package: Category
Loading required package: KEGG
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Error in expMethods[[i]] <- allMethodLists[ii] :
more elements supplied than there are to replace
Enter a frame number, or 0 to exit
1: require(GOstats)
2: library(package, lib.loc = lib.loc, character.only = TRUE, logical =
TRUE, warn.conflicts = warn.conflicts, keep.source = keep.source,
version = version)
3: try({
4: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
Selection: 4
Called from: eval(expr, envir, enclos)
Browse[1]> expMethods
[1] ".__M__hyperGTest:Category" ".__M__getGoGraph:GOstats"
".__M__pvalues:Category" ".__M__isConditional:Category"
".__M__description:Biobase"
[6] ".__M__oddsRatios:Category" ".__M__expectedCounts:Category"
".__M__htmlReport:Category" ".__M__goDag:GOstats"
".__M__geneCounts:Category"
[11] ".__M__universeCounts:Category" ".__M__geneIds:Category"
"geneIdUniverse" "condGeneIdUniverse"
"universeMappedCount"
[16] "geneMappedCount" "annotation"
"testName" "summary" "$"
[21] "[[" "as.character"
"is.na" "length" "names"
Browse[1]> allMethodsLists
Error during wrapup: object "allMethodsLists" not found
Browse[1]> allMethodLists
[1] ".__M__condGeneIdUniverse:GOstats"
".__M__description:Biobase" ".__M__expectedCounts:Category"
".__M__geneCounts:Category"
[5] ".__M__geneIdUniverse:GOstats"
".__M__getGoGraph:GOstats" ".__M__goDag:GOstats"
".__M__htmlReport:Category"
[9] ".__M__hyperGTest:Category"
".__M__isConditional:Category" ".__M__oddsRatios:Category"
".__M__pvalues:Category"
[13] ".__M__summary:base"
".__M__universeCounts:Category"
".__M__universeMappedCount:Category" ".__M__$:base"
[17] ".__M__[[:base"
".__M__addNextMethod:methods" ".__M__annotation:Biobase"
".__M__Arith:base"
[21] ".__M__as.character:base" ".__M__body<-:base"
".__M__categoryName:Category"
".__M__categoryToEntrezBuilder:Category"
[25] ".__M__cbind2:methods" ".__M__chrGraph:Category"
".__M__coerce:methods"
".__M__coerce<-:methods"
[29] ".__M__Compare:methods" ".__M__Complex:base"
".__M__condGeneIdUniverse:Category"
".__M__conditional:Category"
[33] ".__M__conditional<-:Category" ".__M__geneIds:Category"
".__M__geneIds<-:Category"
".__M__geneIdUniverse:Category"
[37] ".__M__geneMappedCount:Category"
".__M__GO2AllProbes:Category" ".__M__ID2EntrezID:Category"
".__M__ID2GO:Category"
[41] ".__M__initialize:methods" ".__M__is.na:base"
".__M__length:base"
".__M__loadMethod:methods"
[45] ".__M__Logic:base"
".__M__makeValidParams:Category" ".__M__Math:base"
".__M__Math2:methods"
[49] ".__M__names:base" ".__M__ontology:Category"
".__M__ontology<-:Category"
".__M__Ops:base"
[53] ".__M__pvalueCutoff:Category"
".__M__pvalueCutoff<-:Category" ".__M__rbind2:methods"
".__M__show:methods"
[57] ".__M__Summary:base"
".__M__testDirection:Category"
".__M__testDirection<-:Category" ".__M__testName:Category"
[61] ".__M__universeBuilder:Category"
".__M__universeGeneIds:Category"
Browse[1]> c
Enter a frame number, or 0 to exit
1: require(GOstats)
2: library(package, lib.loc = lib.loc, character.only = TRUE, logical =
TRUE, warn.conflicts = warn.conflicts, keep.source = keep.source,
version = version)
3: try({
4: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
Selection: 0
[1] FALSE
> library(GOstats)
Error in expMethods[[i]] <- allMethodLists[ii] :
more elements supplied than there are to replace
Enter a frame number, or 0 to exit
1: library(GOstats)
2: try({
3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
Selection: 3
Called from: eval(expr, envir, enclos)
Browse[1]> expMethods
[1] ".__M__hyperGTest:Category" ".__M__getGoGraph:GOstats"
".__M__pvalues:Category" ".__M__isConditional:Category"
".__M__description:Biobase"
[6] ".__M__oddsRatios:Category" ".__M__expectedCounts:Category"
".__M__htmlReport:Category" ".__M__goDag:GOstats"
".__M__geneCounts:Category"
[11] ".__M__universeCounts:Category" ".__M__geneIds:Category"
"geneIdUniverse" "condGeneIdUniverse"
"universeMappedCount"
[16] "geneMappedCount" "annotation"
"testName" "summary" "$"
[21] "[[" "as.character"
"is.na" "length" "names"
Browse[1]> allMethodLists
[1] ".__M__condGeneIdUniverse:GOstats"
".__M__description:Biobase" ".__M__expectedCounts:Category"
".__M__geneCounts:Category"
[5] ".__M__geneIdUniverse:GOstats"
".__M__getGoGraph:GOstats" ".__M__goDag:GOstats"
".__M__htmlReport:Category"
[9] ".__M__hyperGTest:Category"
".__M__isConditional:Category" ".__M__oddsRatios:Category"
".__M__pvalues:Category"
[13] ".__M__summary:base"
".__M__universeCounts:Category"
".__M__universeMappedCount:Category" ".__M__$:base"
[17] ".__M__[[:base"
".__M__addNextMethod:methods" ".__M__annotation:Biobase"
".__M__Arith:base"
[21] ".__M__as.character:base" ".__M__body<-:base"
".__M__categoryName:Category"
".__M__categoryToEntrezBuilder:Category"
[25] ".__M__cbind2:methods" ".__M__chrGraph:Category"
".__M__coerce:methods"
".__M__coerce<-:methods"
[29] ".__M__Compare:methods" ".__M__Complex:base"
".__M__condGeneIdUniverse:Category"
".__M__conditional:Category"
[33] ".__M__conditional<-:Category" ".__M__geneIds:Category"
".__M__geneIds<-:Category"
".__M__geneIdUniverse:Category"
[37] ".__M__geneMappedCount:Category"
".__M__GO2AllProbes:Category" ".__M__ID2EntrezID:Category"
".__M__ID2GO:Category"
[41] ".__M__initialize:methods" ".__M__is.na:base"
".__M__length:base"
".__M__loadMethod:methods"
[45] ".__M__Logic:base"
".__M__makeValidParams:Category" ".__M__Math:base"
".__M__Math2:methods"
[49] ".__M__names:base" ".__M__ontology:Category"
".__M__ontology<-:Category"
".__M__Ops:base"
[53] ".__M__pvalueCutoff:Category"
".__M__pvalueCutoff<-:Category" ".__M__rbind2:methods"
".__M__show:methods"
[57] ".__M__Summary:base"
".__M__testDirection:Category"
".__M__testDirection<-:Category" ".__M__testName:Category"
[61] ".__M__universeBuilder:Category"
".__M__universeGeneIds:Category"
Browse[1]> c
Enter a frame number, or 0 to exit
1: library(GOstats)
2: try({
3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
Selection: 0
Error: package/namespace load failed for 'GOstats'
Enter a frame number, or 0 to exit
1: library(GOstats)
Selection: c
Enter an item from the menu, or 0 to exit
Selection: 0
> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-09 r40677)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "splines" "stats" "graphics" "grDevices" "datasets" "utils"
"tools" "methods" "base"
other attached packages:
Category genefilter survival KEGG RBGL annotate
GO graph limma affy affyio Biobase
"2.1.15" "1.13.8" "2.31" "1.15.1" "1.11.4" "1.13.6"
"1.15.1" "1.13.6" "2.9.9" "1.13.14" "1.3.3" "1.13.37"
>
Robert Gentleman wrote:
> Hi Mark,
> Yes, there does seem to be something wrong with GOstats right now -
> some of the code base has been moved around.
>
> Unfortunately I do not have a windows computer to try and build a new
> version. If you have the right set of build tools then I recommend
> building GOstats off of the subversion archive and seeing if that fixes
> the issue. It did for me today, but my error message was different.
> What happens if you just do
> library("GOstats")
> before doing anything else? Does it load then?
>
> Now the really bad news, most of the folks from here are enroute to
> New Zealand for the DSC and will be pretty much out of contact for at
> least a week (and more like two) so answers, help, fixes to the build
> process etc are going to be slow, and intermittent, over that time period.
>
> best wishes
> Robert
>
>
>
>
> Mark W Kimpel wrote:
>> I can't get GOstats to load in BioC 2.0. New and old versions load
>> with BioC 1.9, but neither will load with BioC1.9.
>>
>> Possibly a coincidence, but tonight I just installed the latest
>> Biobase version.
>>
>> Attached is error, some debugging info, and sessionInfo() Thanks, Mark
>>
>> Enter a frame number, or 0 to exit
>>
>> 1: limma.contrast.output.func(affy.object.preprocessed, fit2, rslt,
>> contrast.num = 1, pheno.trait = "Treatment", anal.pref, ap.cutoff =
>> 0.5, IQR.cutoff = 25, named.gene.filte
>> 2: GO.anal.func(t.tab.annot.obj, initialPValue, FDR_Threshold,
>> maxIterations, plateauIterations, pValueDecrementer, testDirection,
>> sig.gene.threshold, total.gene.min, total.g
>> 3: require(GOstats)
>> 4: library(package, lib.loc = lib.loc, character.only = TRUE, logical
>> = TRUE, warn.conflicts = warn.conflicts, keep.source = keep.source,
>> version = version)
>> 5: try({
>> 6: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
>> keep.source)
>>
>> Selection: 0
>> Loading required package: rat2302
>> [1] 1
>>
>>
>> > sessionInfo()
>> R version 2.5.0 Under development (unstable) (2007-01-31 r40628)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] "splines" "stats" "graphics" "grDevices" "datasets"
>> "utils" "tools" "methods" "base"
>>
>> other attached packages:
>> rat2302 Category KEGG RBGL
>> annotate GO graph xlsReadWritePro
>> qvalue rat2302cdf genefilter
>> "1.15.0" "2.1.14" "1.15.1" "1.11.4"
>> "1.13.6" "1.15.1" "1.13.6" "1.0.6"
>> "1.9.0" "1.15.0" "1.13.8"
>> survival limma affy affyio
>> Biobase
>> "2.31" "2.9.9" "1.13.14" "1.3.3"
>> "1.13.36"
>
--
Mark W. Kimpel MD
Neuroinformatics
Department of Psychiatry
Indiana University School of Medicine
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