Question: Error in clusterProfiler package with function \"setReadable<-\"
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gravatar for Martin Morgan
6.2 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
Looks like the maintainer made changes but forgot to bump the version (svn revision 77544 and 76958; all svn check-ins should be accompanied by version bumps). Should be fixed when 1.9.2 appears. Martin ----- Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 07/08/2013 09:32 AM, Fr?d?ric Bertrand wrote: > > Hi, > > > > Thanks for your help. I upgraded MASS with latest version available on CRAN > > and used --vanilla R, yet I experience the same issue. > > I checked the tarball on Bioc 2.13 and the namespace of DOSE does export the > > method... yet it doesn't work. > > > I made a little test. I installed R 3.0.1, on another (Windows based) > > computer of my lab where it was not yet upgraded from 2.15.3, then Bioc > > 2.12. clusterProfiler works fine with vanilla Bioc 2.12. I upgraded to Bioc > > 2.13 and it stopped working. I manually reinstalled DOSE 1.6.0 from the > > Bioconductor 2.12 .zip windows binary and the issue is solved... > > > > library(BiocInstaller) > > biocValid() > > > > Tells me that DOSE 1.6.0 is out of date... and if upgrade again to DOSE > > 1.99.1, clusterProfiler stops working... > > > > Even with --vanilla, there is still a difference between my sessionInfo and > > yours (which is the same with the working version of clusterProfiler using > > 1.6 version of DOSE): > > > >> sessionInfo() > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C > > [5] LC_TIME=French_France.1252 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] org.Hs.eg.db_2.9.0 clusterProfiler_1.9.1 AnnotationDbi_1.23.16 > > [4] Biobase_2.21.6 BiocGenerics_0.7.2 RSQLite_0.11.4 > > [7] DBI_0.2-7 ggplot2_0.9.3.1 > > > > loaded via a namespace (and not attached): > > [1] colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 DO.db_2.6.0 > > > > [5] DOSE_1.99.1 GO.db_2.9.0 GOSemSim_1.19.1 grid_3.0.1 > > > > [9] gtable_0.1.2 igraph_0.6.5-2 IRanges_1.19.15 KEGG.db_2.9.1 > > > > [13] labeling_0.2 MASS_7.3-27 munsell_0.4 plyr_1.8 > > > > [17] proto_0.3-10 qvalue_1.35.0 RColorBrewer_1.0-5 reshape2_1.2.2 > > > > [21] scales_0.2.3 stats4_3.0.1 stringr_0.6.2 tcltk_3.0.1 > > > > [25] tools_3.0.1 > > > > Well, I will use DOSE 1.6 for the moment, but would be interested in an > > explanation. > > Best, > > Frederic. > > > > > > -----Message d'origine----- > > De : Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > > Envoy? : lundi 8 juillet 2013 03:28 > > ? : Frederic Bertrand [guest] > > Cc : bioconductor at r-project.org; fbertran at math.unistra.fr; clusterProfiler > > Maintainer > > Objet : Re: [BioC] Error in clusterProfiler package with function > > \"setReadable<-\" > > > > On Sun, Jul 7, 2013 at 6:27 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > >> On Sun, Jul 7, 2013 at 2:31 PM, Frederic Bertrand [guest] > >> <guest at="" bioconductor.org=""> 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[[1]], organism="human", ont="BP", level=2) > >>> Loading required package: org.Hs.eg.db > >>> > >>> Error in setReadable(x) <- readable : > >>> could not find function "setReadable<-" > >>> > >> > >> It works for me on a similar system, but my sessionInfo() is a bit > > different: > >> > >> R version 3.0.1 (2013-05-16) > >> Platform: x86_64-w64-mingw32/x64 (64-bit) > >> > >> 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] parallel stats graphics grDevices utils datasets methods > >> [8] base > >> > >> other attached packages: > >> [1] org.Hs.eg.db_2.9.0 clusterProfiler_1.9.1 AnnotationDbi_1.23.16 > >> [4] Biobase_2.21.6 BiocGenerics_0.7.2 RSQLite_0.11.4 > >> [7] DBI_0.2-7 ggplot2_0.9.3.1 > >> > >> loaded via a namespace (and not attached): > >> [1] colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 DO.db_2.6.0 > >> [5] DOSE_1.99.1 GO.db_2.9.0 GOSemSim_1.19.1 graph_1.39.2 > >> [9] grid_3.0.1 gtable_0.1.2 igraph_0.6.5-2 > > IRanges_1.19.15 > >> [13] KEGG.db_2.9.1 KEGGgraph_1.17.0 labeling_0.2 MASS_7.3-27 > >> [17] munsell_0.4 pathview_1.1.4 plyr_1.8 png_0.1-5 > >> [21] proto_0.3-10 qvalue_1.35.0 RColorBrewer_1.0-5 > > reshape2_1.2.2 > >> [25] Rgraphviz_2.5.4 scales_0.2.3 stats4_3.0.1 > > stringr_0.6.2 > >> [29] tcltk_3.0.1 tools_3.0.1 XML_3.98-1.1 > >> > >> The package versions are all the same (except for MASS which is > >> newer); however, I have some packages loaded that you do not have > >> loaded (and this is a vanilla session in which I've only run the > >> commands you've run), such as Rgraphviz, png, etc. > >> > > > > PS, just out of curiosity, you might try: > > > > library(BiocInstaller) > > biocValid() > > > > And see if it tells you anything.... > > > > Dan > > > > > >> Dan > >> > >> > >> > >>> 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: > >>> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] > >>> LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] > >>> LC_TIME=French_France.1252 > >>> > >>> attached base packages: > >>> [1] parallel stats graphics grDevices utils datasets methods > >>> [8] base > >>> > >>> other attached packages: > >>> [1] org.Hs.eg.db_2.9.0 clusterProfiler_1.9.1 AnnotationDbi_1.23.16 > >>> [4] Biobase_2.21.6 BiocGenerics_0.7.2 RSQLite_0.11.4 > >>> [7] DBI_0.2-7 ggplot2_0.9.3.1 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 DO.db_2.6.0 > >>> [5] DOSE_1.99.1 GO.db_2.9.0 GOSemSim_1.19.1 grid_3.0.1 > >>> [9] gtable_0.1.2 igraph_0.6.5-2 IRanges_1.19.15 > > KEGG.db_2.9.1 > >>> [13] labeling_0.2 MASS_7.3-26 munsell_0.4 plyr_1.8 > >>> [17] proto_0.3-10 qvalue_1.35.0 RColorBrewer_1.0-5 > > reshape2_1.2.2 > >>> [21] scales_0.2.3 stats4_3.0.1 stringr_0.6.2 tcltk_3.0.1 > >>> [25] tools_3.0.1 > >>>> > >>> > >>> -- > >>> Sent via the guest posting facility at bioconductor.org. > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793
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