App incompatibility with R-Studio

JEFworks commented 9 years ago

Deploying Rook app appears to have issues from RStudio:

> show.app(app, "pollen", browse = TRUE, port = 1468)
Error in paste("http://", listenAddr, ":", listenPort, appList[[i]]$path,  : 
  cannot coerce type 'closure' to vector of type 'character'

Error does not appear for same commands run in R on command line.

JEFworks commented 9 years ago

RStudio's IDE is known to affect default R web server

stla commented 7 years ago

The fix is here: https://github.com/jeffreyhorner/Rook/pull/31/files (I've just tested it and it works fine). It's just waiting for a merge since two years ^^

JEFworks commented 6 years ago

Is there something already running on port 1468? Can you try specifying another port?

Another thing to try: Explicitly remove the “___scde.server” object, which may be hogging up port 1468. Then try relaunching the app:

run("___scde.server”) scde::show.app(app, 'cll’)

On Aug 19, 2018, at 8:39 AM, petrsha notifications@github.com<mailto:notifications@github.com> wrote:

Hi, today I reopened a project after two months and wanted to browse the results (show.app(app, "CLL", browse = TRUE, port = 1468)), however, I got the following error: ERROR: port is already being used. The PAGODA app is currently incompatible with RStudio. Please try running the interactive app in the R console.Error in paste("http://", listenAddr, ":", listenPort, appList[[i]]$path, : cannot coerce type 'closure' to vector of type 'character'

sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] Rook_1.1-1 scde_2.6.0 flexmix_2.3-14 lattice_0.20-35

loaded via a namespace (and not attached): [1] zip_1.0.0 Rcpp_0.12.18 cellranger_1.1.0 pillar_1.3.0 [5] compiler_3.4.4 RColorBrewer_1.1-2 forcats_0.3.0 Lmoments_1.2-3 [9] tools_3.4.4 nlme_3.1-137 tibble_1.4.2 mgcv_1.8-24 [13] pkgconfig_2.0.2 rlang_0.2.2 Matrix_1.2-14 openxlsx_4.1.0 [17] rstudioapi_0.7 curl_3.2 yaml_2.2.0 parallel_3.4.4 [21] SparseM_1.77 haven_1.1.2 RcppArmadillo_0.9.100.5.0 rio_0.5.10 [25] MatrixModels_0.4-1 extRemes_2.0-9 hms_0.4.2 stats4_3.4.4 [29] nnet_7.3-12 locfit_1.5-9.1 grid_3.4.4 Biobase_2.38.0 [33] data.table_1.11.4 distillery_1.0-4 readxl_1.1.0 BiocParallel_1.12.0 [37] foreign_0.8-71 limma_3.34.9 carData_3.0-1 car_3.0-0 [41] magrittr_1.5 edgeR_3.20.9 modeltools_0.2-22 BiocGenerics_0.24.0 [45] pcaMethods_1.70.0 MASS_7.3-50 RMTstat_0.3 abind_1.4-5 [49] brew_1.0-6 quantreg_5.36 crayon_1.3.4 rjson_0.2.20 [53] Cairo_1.5-9

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hms-dbmi / scde

App incompatibility with R-Studio #4