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()
Error in paste("http://", listenAddr, ":", listenPort, appList[[i]]$path, : cannot coerce type 'closure' to vector of type 'character'
Any help will be much appreciated. Below are additional info on my setting.
Here is the output of sessionInfo()
R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252  LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.18.2 brew_1.0-6 gCMAPWeb_1.8.0 Rook_1.1-1 gCMAP_1.12.0  limma_3.24.4 GSEABase_1.30.1 graph_1.46.0 annotate_1.46.0 XML_3.98-1.1  AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0 IRanges_2.2.1 S4Vectors_0.6.0 Biobase_2.28.0  BiocGenerics_0.14.0 loaded via a namespace (and not attached):  splines_3.2.0 GSEAlm_1.28.0 xtable_1.7-4 lattice_0.20-31 Category_2.34.2 DESeq_1.20.0  hwriter_1.3.2 tools_3.2.0 grid_3.2.0 DBI_0.3.1 genefilter_1.50.0 yaml_2.1.13  survival_2.38-1 RBGL_1.44.0 Matrix_1.2-0 geneplotter_1.46.0 RColorBrewer_1.1-2 RSQLite_1.0.0
Here is the output of traceback()
> traceback() 5: paste("http://", listenAddr, ":", listenPort, appList[[i]]$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()