[BioC] Error in clusterProfiler package with function \"setReadable<-\"
Martin Morgan
mtmorgan at fhcrc.org
Tue Jul 9 00:26:44 CEST 2013
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, Frédéric 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 Tells me that DOSE 1.6.0 is out of date...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]
> > Envoyé : lundi 8 juillet 2013 03:28
> > À : 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.
> >>>
> >>> _______________________________________________
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> >
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>
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