[BioC] Error in clusterProfiler package with function \"setReadable<-\"

[Dan Tenenbaum]

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