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

[Dan Tenenbaum]

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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