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Question: Error using gCMAP and gCMAPWeb
0
3.2 years ago by
afshinmh0
United States
afshinmh0 wrote:

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()
modified 3.2 years ago • written 3.2 years ago by afshinmh0
1
3.2 years ago by
USA
Thomas Sandmann60 wrote:

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

0
3.2 years ago by
afshinmh0
United States
afshinmh0 wrote:

Thank you very much Thomas! This was very helpful.