I am trying to setup an R interface to access Broad's connectivity map database. gCMAP and gCMAPWeb seem like the right tool. However, I didn't get far with either. I have installed the latest version of R and bioconductor installer. Running the following:

library( gCMAPWeb )
gCMAPWeb()

I get:

Error in paste("http://", listenAddr, ":", listenPort, appList[[i]]$path,  : 
  cannot coerce type 'closure' to vector of type 'character'

Any help will be much appreciated. Below are additional info on my setting.

Here is the output of sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.18.2 brew_1.0-6           gCMAPWeb_1.8.0       Rook_1.1-1           gCMAP_1.12.0        
 [6] limma_3.24.4         GSEABase_1.30.1      graph_1.46.0         annotate_1.46.0      XML_3.98-1.1        
[11] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0      Biobase_2.28.0      
[16] BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
 [1] splines_3.2.0      GSEAlm_1.28.0      xtable_1.7-4       lattice_0.20-31    Category_2.34.2    DESeq_1.20.0      
 [7] hwriter_1.3.2      tools_3.2.0        grid_3.2.0         DBI_0.3.1          genefilter_1.50.0  yaml_2.1.13       
[13] survival_2.38-1    RBGL_1.44.0        Matrix_1.2-0       geneplotter_1.46.0 RColorBrewer_1.1-2 RSQLite_1.0.0     

Here is the output of traceback()

> traceback()
5: paste("http://", listenAddr, ":", listenPort, appList[[i]]$path, 
       sep = "")
4: full_url(which(appName == names(appList)))
3: browseURL(full_url(which(appName == names(appList))))
2: .e$s$launch(name = "gcmap", app = gcmap)
1: gCMAPWeb()

Hi Afshin,

Are you by any chance using the RStudio IDE ? gCMAPWeb doesn't work with RStudio, so in case that's your environment, please try again using the standard R IDE.

Also, just to be clear: the gCMAP / gCMAPWeb package do not provide access to the Broad's data. You will need to download and preprocess the data yourself; the packages just provide some software infrastructure to analyze the data, not the data itself.

Best,

Thomas

Thank you very much Thomas! This was very helpful.