Hi,

I've been following the example for using GOstats at its manual at https://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf. Unfortunately I have an error

Error in initialize(value, ...) :
  invalid names for slots of class “GOHyperGResult”: pvalues, oddsRatios, expectedCounts, catToGeneId, organism

These are the commands. The error appears after "Over <- hyperGTest(params)"

Thanks in advance,

Carlos

(BTW, the version in Bioconductor 3.2.4 works well)

source("https://bioconductor.org/biocLite.R")
biocLite(c("GSEABase","GO.db","AnnotationForge","GO.db","org.Hs.eg.db","GOstats"))

library("org.Hs.eg.db")
library("AnnotationForge")
library("GO.db")
available.dbschemas()

frame = toTable(org.Hs.egGO)
goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id)
head

goFrame=GOFrame(goframeData,organism="Homo sapiens")
goAllFrame=GOAllFrame(goFrame)

library("GSEABase")
gsc <- GeneSetCollection(goAllFrame, setType = GOCollection())
library("GOstats")
universe = Lkeys(org.Hs.egGO)
genes = universe[1:500]
params <- GSEAGOHyperGParams(name="My Custom GSEA based annot Params",
                              geneSetCollection=gsc,
                              geneIds = genes,
                              universeGeneIds = universe,
                              ontology = "MF",
                              pvalueCutoff = 0.05,
                              conditional = FALSE,
                              testDirection = "over")
Over <- hyperGTest(params)
head(summary(Over))

----------

sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin15.5.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

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  stats4    stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
 [1] GOstats_2.38.0         Category_2.38.0       
 [3] Matrix_1.2-6           RSQLite_1.0.0         
 [5] DBI_0.4-1              org.Hs.eg.db_3.3.0    
 [7] GO.db_3.3.0            AnnotationForge_1.14.2
 [9] BiocInstaller_1.22.2   GSEABase_1.34.0       
[11] graph_1.50.0           annotate_1.50.0       
[13] XML_3.98-1.4           AnnotationDbi_1.34.3  
[15] IRanges_2.6.0          S4Vectors_0.10.1      
[17] Biobase_2.32.0         BiocGenerics_0.18.0   

loaded via a namespace (and not attached):
[1] lattice_0.20-33   RBGL_1.48.1       grid_3.3.0       
[4] xtable_1.8-2      genefilter_1.54.2 splines_3.3.0    
[7] tools_3.3.0       survival_2.39-4