Hi all, I am trying to build a small package that contains some specific functions to perform GO annotation and have encountered an error when running 'R CMD check' on the package I (try to) build. Specifically: [1] "S4" Length Class Mode 25369 GOTermsAnnDbBimap S4 TERM map for GO (object of class "GOTermsAnnDbBimap") Error in eapply(GOTERM, function(x) { : argument must be an environment Calls: WriteGoAnnotationToCsv -> AnnotateClusters -> unlist -> eapply Execution halted The relevant code in my package (that generates the above) is: print(mode(GOTERM)) print(summary(GOTERM)) print(GOTERM) print(is.environment(GOTERM)) goTermMaster <- unlist(eapply(GOTERM, function(x) {x at Term})); These functions work fine when I just 'source' them and run them via a script. The example in my package that 'check' is testing also runs fine when I cut-and-paste it into R (having sourced the relevant functions). Then problem only occurs with the package version. My concern is that I might not be importing something properly into my package. My NAMESPACE file looks like this: export(WriteGoAnnotationToCsv) export(WriteGoAnnotationToLatex) import(GO.db) import(GOstats) import(ath1121501.db) (both the exports are my own functions) Finally, I've also noticed that when I use the above print statements in R on GOTERM, I get different info. Compare: CODE ---- print(mode(GOTERM)) print(summary(GOTERM)) print(GOTERM) PACKAGE-BUILDING ---------------- [1] "S4" Length Class Mode 25369 GOTermsAnnDbBimap S4 TERM map for GO (object of class "GOTermsAnnDbBimap") IN R ITSELF ----------- > print(mode(GOTERM)) [1] "S4" > print(summary(GOTERM)) TERM map for GO (object of class "GOTermsAnnDbBimap") | | Lkeyname: go_id (Ltablename: go_term) | Lkeys: "GO:0000001", "GO:0000002", ... (total=25369/mapped=25369) | | Rkeyname: go_id (Rtablename: go_term) | Rkeys: "GO:0000001", "GO:0000002", ... (total=25369/mapped=25369) | | direction: L --> R NULL > print(GOTERM) TERM map for GO (object of class "GOTermsAnnDbBimap") SESSION INFO R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] BHC.GoAnnotation_1.2 ath1121501.db_2.2.7 GOstats_2.8.0 Category_2.8.0 [5] genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0 annotate_1.20.0 [9] xtable_1.5-4 graph_1.20.0 GO.db_2.2.5 RSQLite_0.7-0 [13] DBI_0.2-4 AnnotationDbi_1.4.0 Biobase_2.2.0 BHC_1.2.0 loaded via a namespace (and not attached): [1] GSEABase_1.4.0 XML_1.98-1 cluster_1.11.11 Thanks very much for any help you can offer! Rich -- ------------------------------------------------------------------ Dr. Richard Savage Tel: +44 (0)24 765 50243 Systems Biology Centre University of Warwick Coventry CV4 7AL United Kingdom Web: http://www.programming4scientists.com/ http://wsbc.warwick.ac.uk/~richsavage/