Question: Error in clusterProfiler package with function \"setReadable<-\"
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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<-" 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.
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ADD COMMENTlink modified 6.2 years ago by Dan Tenenbaum8.2k • written 6.2 years ago by Guest User12k
Answer: Error in clusterProfiler package with function \"setReadable<-\"
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gravatar for Dan Tenenbaum
6.2 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k 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. 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
ADD COMMENTlink written 6.2 years ago by Dan Tenenbaum8.2k
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
ADD REPLYlink written 6.2 years ago by Dan Tenenbaum8.2k
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
ADD REPLYlink written 6.2 years ago by Frédéric Bertrand10
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