Question: Error in clusterProfiler package with function \"setReadable<-\"
6.4 years ago by
Guest User • 12k
Guest User • 12k wrote:
Greetings, It seems that clusterProfiler no longer works with bioC 2.13, yet it works perfectly well for bioC 2.11 and 2.12. Has anyone else got this issue ? It seems to be due to a failed method importation from package DOSE. I am aware that this was an issue that was reported in the past but was corrected at least in bioC 2.11 and 2.12. Here is the log of a minimal non working example (the package example itself). R version 3.0.1 (2013-05-16) -- "Good Sport" [..] > library(clusterProfiler) [..] No methods found in "DOSE" for requests: setReadable<- Example for groupGO function fails: data(gcSample) yy <- groupGO(gcSample[], organism="human", ont="BP", level=2) Loading required package: org.Hs.eg.db Error in setReadable(x) <- readable : could not find function "setReadable<-" Thanks for your help, Best regards, Frederic Bertrand Assistant professor University of Strasbourg, France. -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252  LC_MONETARY=French_France.1252 LC_NUMERIC=C  LC_TIME=French_France.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  org.Hs.eg.db_2.9.0 clusterProfiler_1.9.1 AnnotationDbi_1.23.16  Biobase_2.21.6 BiocGenerics_0.7.2 RSQLite_0.11.4  DBI_0.2-7 ggplot2_0.9.3.1 loaded via a namespace (and not attached):  colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 DO.db_2.6.0  DOSE_1.99.1 GO.db_2.9.0 GOSemSim_1.19.1 grid_3.0.1  gtable_0.1.2 igraph_0.6.5-2 IRanges_1.19.15 KEGG.db_2.9.1  labeling_0.2 MASS_7.3-26 munsell_0.4 plyr_1.8  proto_0.3-10 qvalue_1.35.0 RColorBrewer_1.0-5 reshape2_1.2.2  scales_0.2.3 stats4_3.0.1 stringr_0.6.2 tcltk_3.0.1  tools_3.0.1 > -- Sent via the guest posting facility at bioconductor.org.
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