I'm getting this error when I run the hyperGTest function (GOstats package) for one list of gene IDs that I'm interested in.

Error in order(pvals) : argument 1 is not a vector

I have already checked the file and the list itself but I haven't been able to solve the problem, since it only happens for this specific list of genes when I have been able to run the test on other lists of genes generated the same way.

> modFile <- read.csv("../module_purple_listGenes.csv", header = FALSE)
>
> modFile$V1 %in% fpkm2_IDs #Check if Gene IDs are in the universe of genes
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[30] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[59] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
>
> biased_BP_over <- GSEAGOHyperGParams(name="My custom GSEA based annot params",
+                                                      geneSetCollection=gsc,
+                                                      geneIds=modFile,
+                                                      universeGeneIds=fpkm2_IDs,
+                                                      ontology="BP",
+                                                      pvalueCutoff=0.05,
+                                                      conditional=TRUE,
+                                                      testDirection="over")
Warning message:
In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist
> test_biased_BP_over <- hyperGTest(biased_BP_over)
Error in order(pvals) : argument 1 is not a vector

Can anyone help me solve this error?

Here's the sessionInfo() output:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

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=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GOstats_2.34.0         Category_2.34.2        Matrix_1.2-6           GSEABase_1.30.2        graph_1.46.0           annotate_1.46.1       
 [7] XML_3.98-1.4           GO.db_3.1.2            AnnotationForge_1.10.1 org.Hs.eg.db_3.1.2     AnnotationDbi_1.30.1   GenomeInfoDb_1.4.3    
[13] IRanges_2.2.9          S4Vectors_0.6.6        Biobase_2.28.0         BiocGenerics_0.14.0    gplots_3.0.1           WGCNA_1.51            
[19] RSQLite_1.0.0          DBI_0.4-1              fastcluster_1.1.20     dynamicTreeCut_1.63-1  RColorBrewer_1.1-2     VennDiagram_1.6.17    
[25] futile.logger_1.4.1   

loaded via a namespace (and not attached):
 [1] genefilter_1.50.0     gtools_3.5.0          splines_3.2.2         lattice_0.20-33       colorspace_1.2-6      RBGL_1.44.0          
 [7] chron_2.3-47          survival_2.39-4       foreign_0.8-66        lambda.r_1.1.7        matrixStats_0.50.2    foreach_1.4.3        
[13] plyr_1.8.3            munsell_0.4.3         gtable_0.2.0          caTools_1.17.1        codetools_0.2-14      latticeExtra_0.6-28  
[19] doParallel_1.0.10     preprocessCore_1.30.0 Rcpp_0.12.5           acepack_1.3-3.3       KernSmooth_2.23-15    xtable_1.8-2         
[25] scales_0.4.0          gdata_2.17.0          Hmisc_3.17-4          gridExtra_2.2.1       impute_1.42.0         ggplot2_2.1.0        
[31] tools_3.2.2           bitops_1.0-6          Formula_1.2-1         cluster_2.0.4         futile.options_1.0.0  data.table_1.9.6     
[37] iterators_1.0.8       rpart_4.1-10          nnet_7.3-12 

You are being unnecessarily vague about what you are doing, so it's actually impossible for anybody to help you.

Howeva, do note that you are first testing

modFile$V1 %in% fpkm2_IDs

But you then pass ALL of modFile to GSEGOHyperGParams, and it's being unlisted (that's what this warning means)

Warning message:
In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist

So if I were to hazard a guess, I would bet that there are other things in modFile that are not Gene IDs, and they are wreaking havoc.