Hi! I am trying to use the package goseq, but when I try running the function supportedOrganisms() R says it cannot find it. Does anyone know what might be the reason?

Thanks!

sessionInfo()

R version 3.2.4 Revised (2016-03-16 r70336) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] KEGG.db_3.2.2 goseq_1.22.0
[3] geneLenDataBase_1.6.0 BiasedUrn_1.07
[5] GOstats_2.36.0 graph_1.48.0
[7] Category_2.36.0 GO.db_3.2.2
[9] Matrix_1.2-4 org.Bt.eg.db_3.2.3
[11] AnnotationDbi_1.32.3 edgeR_3.12.0
[13] limma_3.26.9 affycoretools_1.42.0 [15] Biobase_2.30.0 WGCNA_1.51
[17] RSQLite_1.0.0 DBI_0.3.1
[19] fastcluster_1.1.16 dynamicTreeCut_1.63-1 [21] rtracklayer_1.30.4 GenomicRanges_1.22.4 [23] GenomeInfoDb_1.6.3 IRanges_2.4.8
[25] S4Vectors_0.8.11 BiocGenerics_0.16.1

loaded via a namespace (and not attached): [1] nlme_3.1-126 bitops_1.0-6
[3] matrixStats_0.50.1 doParallel_1.0.10
[5] RColorBrewer_1.1-2 gcrma_2.42.0
[7] tools_3.2.4 affyio_1.40.0
[9] KernSmooth_2.23-15 rpart_4.1-10
[11] mgcv_1.8-12 Hmisc_3.17-2
[13] colorspace_1.2-6 nnet_7.3-12
[15] gridExtra_2.2.1 GGally_1.0.1
[17] DESeq2_1.10.1 bit_1.1-12
[19] preprocessCore_1.32.0 ggbio_1.18.5
[21] caTools_1.17.1 scales_0.4.0
[23] genefilter_1.52.1 affy_1.48.0
[25] RBGL_1.46.0 stringr_1.0.0
[27] Rsamtools_1.22.0 foreign_0.8-66
[29] R.utils_2.2.0 AnnotationForge_1.12.2
[31] XVector_0.10.0 dichromat_2.0-0
[33] BSgenome_1.38.0 PFAM.db_3.2.2
[35] impute_1.44.0 BiocInstaller_1.20.1
[37] hwriter_1.3.2 gtools_3.5.0
[39] BiocParallel_1.4.3 acepack_1.3-3.3
[41] R.oo_1.20.0 VariantAnnotation_1.16.4
[43] RCurl_1.95-4.8 magrittr_1.5
[45] Formula_1.2-1 oligoClasses_1.32.0
[47] futile.logger_1.4.1 Rcpp_0.12.4
[49] munsell_0.4.3 R.methodsS3_1.7.1
[51] stringi_1.0-1 SummarizedExperiment_1.0.2 [53] zlibbioc_1.16.0 gplots_3.0.1
[55] plyr_1.8.3 grid_3.2.4
[57] gdata_2.17.0 ReportingTools_2.10.0
[59] lattice_0.20-33 Biostrings_2.38.4
[61] splines_3.2.4 GenomicFeatures_1.22.13
[63] annotate_1.48.0 locfit_1.5-9.1
[65] knitr_1.12.3 geneplotter_1.48.0
[67] reshape2_1.4.1 codetools_0.2-14
[69] biomaRt_2.26.1 futile.options_1.0.0
[71] XML_3.98-1.4 RcppArmadillo_0.6.600.4.0 [73] biovizBase_1.18.0 latticeExtra_0.6-28
[75] lambda.r_1.1.7 foreach_1.4.3
[77] gtable_0.2.0 reshape_0.8.5
[79] ggplot2_2.1.0 xtable_1.8-2
[81] ff_2.2-13 survival_2.38-3
[83] OrganismDbi_1.12.1 iterators_1.0.8
[85] GenomicAlignments_1.6.3 cluster_2.0.3
[87] GSEABase_1.32.0

You can use supportedGenomes() and supportedGeneIDs() instead with your version. They give similar information. There's an example in the goseq vignette which matches your version of goseq. The new supportedOrganisms() function is just a bit easier to interpret and proved information about the GO terms support, not just the gene lengths.

That function is in the devel version, not release.