R Error ... R language backend failed!

[polaris-bioit]

stderr:
Oct 04, 2015 12:12:29 AM com.twosigma.beaker.r.utils.RServerEvaluator$workerThread startRserve
SEVERE: exception starting RServe
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused
at org.rosuda.REngine.Rserve.RConnection.(RConnection.java:88)
at org.rosuda.REngine.Rserve.RConnection.(RConnection.java:60)
at com.twosigma.beaker.r.utils.RServerEvaluator$workerThread.startRserve(RServerEvaluator.java:421)
at com.twosigma.beaker.r.utils.RServerEvaluator$workerThread.run(RServerEvaluator.java:472)
Oct 04, 2015 12:21:13 AM com.twosigma.beaker.r.utils.RServerEvaluator$workerThread startRserve
SEVERE: exception starting RServe
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused
at org.rosuda.REngine.Rserve.RConnection.(RConnection.java:88)
at org.rosuda.REngine.Rserve.RConnection.(RConnection.java:60)
at com.twosigma.beaker.r.utils.RServerEvaluator$workerThread.startRserve(RServerEvaluator.java:421)
at com.twosigma.beaker.r.utils.RServerEvaluator$workerThread.run(RServerEvaluator.java:472)
Oct 04, 2015 12:29:52 AM com.twosigma.beaker.r.utils.RServerEvaluator$workerThread startRserve
SEVERE: exception starting RServe
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused
at org.rosuda.REngine.Rserve.RConnection.(RConnection.java:88)
at org.rosuda.REngine.Rserve.RConnection.(RConnection.java:60)
at com.twosigma.beaker.r.utils.RServerEvaluator$workerThread.startRserve(RServerEvaluator.java:421)
at com.twosigma.beaker.r.utils.RServerEvaluator$workerThread.run(RServerEvaluator.java:472)

[scottdraves]

Hi, thanks for the report. What is your Operating System? What version of Beaker are you running?
If you run base R (open a terminal and run R), not RStudio) and give the command

installed.packages()

what is the output?

[jslmann]

Hello!

preliminaries:
os: OSX 10.11
beaker: 1.4.1 (1)

i get the same error, before I show the installed.packages() result, a bit of context:
I use brew and anaconda, not because I'm smart just cause that's how things happened
bouncing from one hack to another...
that said, 'which r' gives the anaconda path.
when I open r from a bash shell and try: "install.package('Rserve')"
I will get the following after compiling all the required files with some warnings:

...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/jlatmann/anaconda/lib/R/library/Rserve/libs/Rserve.so':
dlopen(/Users/jlatmann/anaconda/lib/R/library/Rserve/libs/Rserve.so, 6): Library not loaded: libssl.1.0.0.dylib
Referenced from: /Users/jlatmann/anaconda/lib/R/library/Rserve/libs/Rserve.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘/Users/jlatmann/anaconda/lib/R/library/Rserve’
• restoring previous ‘/Users/jlatmann/anaconda/lib/R/library/Rserve’

I did, however, install all the required libraries by pulling them off of the anaconda cloud.

context done.
here is installed.packages():

and thank-you in advance for any help you can provide!

installed.packages()
Package LibPath Version
base "base" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
base64enc "base64enc" "/Users/jlatmann/anaconda/lib/R/library" "0.1-3"
BH "BH" "/Users/jlatmann/anaconda/lib/R/library" "1.58.0-1"
bitops "bitops" "/Users/jlatmann/anaconda/lib/R/library" "1.0-6"
boot "boot" "/Users/jlatmann/anaconda/lib/R/library" "1.3-17"
brew "brew" "/Users/jlatmann/anaconda/lib/R/library" "1.0-6"
class "class" "/Users/jlatmann/anaconda/lib/R/library" "7.3-14"
cluster "cluster" "/Users/jlatmann/anaconda/lib/R/library" "2.0.3"
codetools "codetools" "/Users/jlatmann/anaconda/lib/R/library" "0.2-14"
colorspace "colorspace" "/Users/jlatmann/anaconda/lib/R/library" "1.2-6"
compiler "compiler" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
curl "curl" "/Users/jlatmann/anaconda/lib/R/library" "0.9.3"
datasets "datasets" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
devtools "devtools" "/Users/jlatmann/anaconda/lib/R/library" "1.9.1"
dichromat "dichromat" "/Users/jlatmann/anaconda/lib/R/library" "2.0-0"
digest "digest" "/Users/jlatmann/anaconda/lib/R/library" "0.6.8"
evaluate "evaluate" "/Users/jlatmann/anaconda/lib/R/library" "0.8"
foreign "foreign" "/Users/jlatmann/anaconda/lib/R/library" "0.8-66"
ggplot2 "ggplot2" "/Users/jlatmann/anaconda/lib/R/library" "1.0.1"
git2r "git2r" "/Users/jlatmann/anaconda/lib/R/library" "0.11.0"
graphics "graphics" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
grDevices "grDevices" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
grid "grid" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
gtable "gtable" "/Users/jlatmann/anaconda/lib/R/library" "0.1.2"
httr "httr" "/Users/jlatmann/anaconda/lib/R/library" "1.0.0"
IRdisplay "IRdisplay" "/Users/jlatmann/anaconda/lib/R/library" "0.3"
IRkernel "IRkernel" "/Users/jlatmann/anaconda/lib/R/library" "0.4"
jpeg "jpeg" "/Users/jlatmann/anaconda/lib/R/library" "0.1-8"
jsonlite "jsonlite" "/Users/jlatmann/anaconda/lib/R/library" "0.9.17"
KernSmooth "KernSmooth" "/Users/jlatmann/anaconda/lib/R/library" "2.23-15"
labeling "labeling" "/Users/jlatmann/anaconda/lib/R/library" "0.3"
lattice "lattice" "/Users/jlatmann/anaconda/lib/R/library" "0.20-33"
magrittr "magrittr" "/Users/jlatmann/anaconda/lib/R/library" "1.5"
MASS "MASS" "/Users/jlatmann/anaconda/lib/R/library" "7.3-44"
Matrix "Matrix" "/Users/jlatmann/anaconda/lib/R/library" "1.2-2"
memoise "memoise" "/Users/jlatmann/anaconda/lib/R/library" "0.2.1"
methods "methods" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
mgcv "mgcv" "/Users/jlatmann/anaconda/lib/R/library" "1.8-7"
mime "mime" "/Users/jlatmann/anaconda/lib/R/library" "0.4"
munsell "munsell" "/Users/jlatmann/anaconda/lib/R/library" "0.4.2"
nlme "nlme" "/Users/jlatmann/anaconda/lib/R/library" "3.1-122"
nnet "nnet" "/Users/jlatmann/anaconda/lib/R/library" "7.3-11"
parallel "parallel" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
plyr "plyr" "/Users/jlatmann/anaconda/lib/R/library" "1.8.3"
proto "proto" "/Users/jlatmann/anaconda/lib/R/library" "0.3-10"
R6 "R6" "/Users/jlatmann/anaconda/lib/R/library" "2.1.1"
RColorBrewer "RColorBrewer" "/Users/jlatmann/anaconda/lib/R/library" "1.1-2"
Rcpp "Rcpp" "/Users/jlatmann/anaconda/lib/R/library" "0.12.1"
repr "repr" "/Users/jlatmann/anaconda/lib/R/library" "0.3"
reshape2 "reshape2" "/Users/jlatmann/anaconda/lib/R/library" "1.4.1"
RJSONIO "RJSONIO" "/Users/jlatmann/anaconda/lib/R/library" "1.3-0"
roxygen2 "roxygen2" "/Users/jlatmann/anaconda/lib/R/library" "4.1.1"
rpart "rpart" "/Users/jlatmann/anaconda/lib/R/library" "4.1-10"
Rserve "Rserve" "/Users/jlatmann/anaconda/lib/R/library" "1.7-3"
rstudioapi "rstudioapi" "/Users/jlatmann/anaconda/lib/R/library" "0.3.1"
rversions "rversions" "/Users/jlatmann/anaconda/lib/R/library" "1.0.2"
rzmq "rzmq" "/Users/jlatmann/anaconda/lib/R/library" "0.7.7"
scales "scales" "/Users/jlatmann/anaconda/lib/R/library" "0.3.0"
spatial "spatial" "/Users/jlatmann/anaconda/lib/R/library" "7.3-11"
splines "splines" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
stats "stats" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
stats4 "stats4" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
stringi "stringi" "/Users/jlatmann/anaconda/lib/R/library" "0.5-5"
stringr "stringr" "/Users/jlatmann/anaconda/lib/R/library" "1.0.0"
survival "survival" "/Users/jlatmann/anaconda/lib/R/library" "2.38-3"
tcltk "tcltk" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
tools "tools" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
utils "utils" "/Users/jlatmann/anaconda/lib/R/library" "3.2.2"
uuid "uuid" "/Users/jlatmann/anaconda/lib/R/library" "0.1-2"
whisker "whisker" "/Users/jlatmann/anaconda/lib/R/library" "0.3-2"
xml2 "xml2" "/Users/jlatmann/anaconda/lib/R/library" "0.1.2"
Priority Depends
base "base" NA
base64enc NA "R (>= 2.9.0)"
BH NA NA
bitops NA NA
boot NA "R (>= 3.0.0), graphics, stats"
brew NA NA
class NA "R (>= 3.0.0), stats, utils"
cluster NA "R (>= 2.15.0), utils"
codetools NA "R (>= 2.1)"
colorspace NA "R (>= 2.13.0), methods"
compiler "base" NA
curl NA "R (>= 2.10.0)"
datasets "base" NA
devtools NA "R (>= 3.0.2)"
dichromat NA "R (>= 2.10), stats"
digest NA "R (>= 2.4.1)"
evaluate NA "R (>= 3.0.2)"
foreign NA "R (>= 3.0.0)"
ggplot2 NA "R (>= 2.14), stats, methods"
git2r NA "R (>= 3.0.2)"
graphics "base" NA
grDevices "base" NA
grid "base" NA
gtable NA "R (>= 2.14), grid"
httr NA "R (>= 3.0.0)"
IRdisplay NA "\nR (>= 3.0.1)"
IRkernel NA "\nR (>= 3.0.1)"
jpeg NA "R (>= 2.9.0)"
jsonlite NA "methods"
KernSmooth NA "R (>= 2.5.0), stats"
labeling NA NA
lattice NA "R (>= 3.0.0)"
magrittr NA NA
MASS NA "R (>= 3.1.0), grDevices, graphics, stats, utils"
Matrix NA "R (>= 3.0.1)"
memoise NA NA
methods "base" NA
mgcv NA "R (>= 2.14.0), nlme (>= 3.1-64)"
mime NA NA
munsell NA NA
nlme NA "graphics, stats, R (>= 3.0.0)"
nnet NA "R (>= 2.14.0), stats, utils"
parallel "base" NA
plyr NA "R (>= 3.1.0)"
proto NA NA
R6 NA "R (>= 3.0)"
RColorBrewer NA "R (>= 2.0.0)"
Rcpp NA "R (>= 3.0.0)"
repr NA "\nR (>= 3.0.1)"
reshape2 NA NA
RJSONIO NA NA
roxygen2 NA "R (>= 3.0.2)"
rpart NA "R (>= 2.15.0), graphics, stats, grDevices"
Rserve NA "R (>= 1.5.0)"
rstudioapi NA NA
rversions NA NA
rzmq NA NA
scales NA "R (>= 2.13)"
spatial NA "R (>= 3.0.0), graphics, stats, utils"
splines "base" NA
stats "base" NA
stats4 "base" NA
stringi NA "R (>= 2.13.1)"
stringr NA "R (>= 2.14)"
survival NA "R (>= 2.13.0), graphics, stats"
tcltk "base" NA
tools "base" NA
utils "base" NA
uuid NA "R (>= 2.9.0)"
whisker NA NA
xml2 NA "R (>= 3.1.0)"
Imports
base NA
base64enc NA
BH NA
bitops NA
boot NA
brew NA
class "MASS"
cluster "graphics, grDevices, stats"
codetools NA
colorspace "graphics"
compiler NA
curl NA
datasets NA
devtools "httr (>= 0.4), curl (>= 0.9), utils, tools, methods, memoise,\nwhisker, evaluate, digest, rstudioapi (>= 0.2.0), jsonlite,\nroxygen2 (>= 4.1.0), rversions, stats, git2r (>= 0.11.0)"
dichromat NA
digest NA
evaluate "methods, stringr (>= 0.6.2)"
foreign "methods, utils, stats"
ggplot2 "plyr (>= 1.7.1), digest, grid, gtable (>= 0.1.1), reshape2,\nscales (>= 0.2.3), proto, MASS"
git2r "graphics, methods, utils"
graphics "grDevices"
grDevices NA
grid "grDevices"
gtable NA
httr "digest, jsonlite, mime, curl (>= 0.6), R6, stringr (>= 0.6.1)"
IRdisplay "\nrepr,\nbase64enc"
IRkernel "\nrepr,\nmethods,\nevaluate (>= 0.5.4),\nIRdisplay,\nrzmq (>= 0.7.0),\njsonlite (>= 0.9.6),\nuuid,\ndigest"
jpeg NA
jsonlite NA
KernSmooth NA
labeling NA
lattice "grid, grDevices, graphics, stats, utils"
magrittr NA
MASS "methods"
Matrix "methods, graphics, grid, stats, utils, lattice"
memoise "digest"
methods "utils"
mgcv "methods, stats, graphics, Matrix"
mime "tools"
munsell "colorspace"
nlme "lattice"
nnet NA
parallel "tools"
plyr "Rcpp (>= 0.11.0)"
proto NA
R6 NA
RColorBrewer NA
Rcpp "methods, utils"
repr NA
reshape2 "plyr (>= 1.8.1), stringr, Rcpp"
RJSONIO "methods"
roxygen2 "stringr (>= 0.5), brew, digest, methods, Rcpp (>= 0.11.0)"
rpart NA
Rserve NA
rstudioapi NA
rversions "curl, xml2, utils"
rzmq NA
scales "RColorBrewer, dichromat, plyr, munsell (>= 0.2), labeling,\nmethods, Rcpp"
spatial NA
splines "graphics, stats"
stats NA
stats4 "graphics, methods, stats"
stringi "tools, utils, stats"
stringr "stringi (>= 0.4.1), magrittr"
survival "splines, methods"
tcltk "utils"
tools NA
utils NA
uuid NA
whisker NA
xml2 "Rcpp"
LinkingTo
base NA
base64enc NA
BH NA
bitops NA
boot NA
brew NA
class NA
cluster NA
codetools NA
colorspace NA
compiler NA
curl NA
datasets NA
devtools NA
dichromat NA
digest NA
evaluate NA
foreign NA
ggplot2 NA
git2r NA
graphics NA
grDevices NA
grid NA
gtable NA
httr NA
IRdisplay NA
IRkernel NA
jpeg NA
jsonlite NA
KernSmooth NA
labeling NA
lattice NA
magrittr NA
MASS NA
Matrix NA
memoise NA
methods NA
mgcv NA
mime NA
munsell NA
nlme NA
nnet NA
parallel NA
plyr "Rcpp"
proto NA
R6 NA
RColorBrewer NA
Rcpp NA
repr NA
reshape2 "Rcpp"
RJSONIO NA
roxygen2 "Rcpp"
rpart NA
Rserve NA
rstudioapi NA
rversions NA
rzmq NA
scales "Rcpp"
spatial NA
splines NA
stats NA
stats4 NA
stringi NA
stringr NA
survival NA
tcltk NA
tools NA
utils NA
uuid NA
whisker NA
xml2 "Rcpp (>= 0.11.4.6), BH"
Suggests
base NA
base64enc NA
BH NA
bitops NA
boot "MASS, survival"
brew NA
class NA
cluster "MASS"
codetools NA
colorspace "KernSmooth, MASS, kernlab, mvtnorm, vcd, dichromat, tcltk"
compiler NA
curl "testthat, knitr, jsonlite, rmarkdown, magrittr"
datasets NA
devtools "testthat (>= 0.7), BiocInstaller, Rcpp (>= 0.10.0), MASS,\nrmarkdown, knitr, lintr (>= 0.2.1), bitops"
dichromat NA
digest NA
evaluate "testthat, lattice, ggplot2"
foreign NA
ggplot2 "quantreg, Hmisc, mapproj, maps, hexbin, maptools, multcomp,\nnlme, testthat, knitr, mgcv"
git2r NA
graphics NA
grDevices NA
grid "lattice"
gtable "testthat, plyr"
httr "base64enc, httpuv, jpeg, knitr, PKI (>= 0.1-2), png, testthat\n(>= 0.8.0), XML"
IRdisplay NA
IRkernel NA
jpeg NA
jsonlite "curl (>= 0.5), plyr, testthat, knitr, rmarkdown, R.rsp"
KernSmooth "MASS"
labeling NA
lattice "KernSmooth, MASS"
magrittr "testthat, knitr"
MASS "lattice, nlme, nnet, survival"
Matrix "expm, MASS"
memoise NA
methods NA
mgcv "splines, parallel, survival, MASS"
mime NA
munsell "ggplot2 (>= 0.9.2)"
nlme "Hmisc, MASS"
nnet "MASS"
parallel NA
plyr "abind, testthat, tcltk, foreach, doParallel, itertools,\niterators"
proto "graph, Rgraphviz"
R6 "knitr, microbenchmark, pryr, testthat, ggplot2, scales"
RColorBrewer NA
Rcpp "RUnit, inline, rbenchmark, highlight, pkgKitten (>= 0.1.2)"
repr "\nhighr"
reshape2 "testthat (>= 0.8.0), lattice"
RJSONIO NA
roxygen2 "testthat (>= 0.8.0), knitr"
rpart "survival"
Rserve "RSclient"
rstudioapi NA
rversions NA
rzmq NA
scales "testthat (>= 0.8)"
spatial "MASS"
splines NA
stats NA
stats4 NA
stringi NA
stringr "testthat, knitr"
survival "cmprsk"
tcltk NA
tools "XML"
utils NA
uuid NA
whisker "markdown"
xml2 "testthat, curl"
Enhances
base NA
base64enc "png"
BH NA
bitops NA
boot NA
brew NA
class NA
cluster NA
codetools NA
colorspace NA
compiler NA
curl NA
datasets NA
devtools NA
dichromat NA
digest NA
evaluate NA
foreign NA
ggplot2 "sp"
git2r NA
graphics NA
grDevices NA
grid NA
gtable NA
httr NA
IRdisplay NA
IRkernel NA
jpeg NA
jsonlite NA
KernSmooth NA
labeling NA
lattice "chron"
magrittr NA
MASS NA
Matrix "MatrixModels, graph, SparseM, sfsmisc"
memoise NA
methods NA
mgcv NA
mime NA
munsell NA
nlme NA
nnet NA
parallel "snow, nws, Rmpi"
plyr NA
proto NA
R6 NA
RColorBrewer NA
Rcpp NA
repr NA
reshape2 NA
RJSONIO NA
roxygen2 NA
rpart NA
Rserve NA
rstudioapi NA
rversions NA
rzmq NA
scales NA
spatial NA
splines NA
stats NA
stats4 NA
stringi NA
stringr NA
survival NA
tcltk NA
tools NA
utils NA
uuid NA
whisker NA
xml2 NA
License License_is_FOSS
base "Part of R 3.2.2" NA
base64enc "GPL-2 | GPL-3" NA
BH "BSL-1.0" NA
bitops "GPL (>= 2)" NA
boot "Unlimited" NA
brew "GPL-2" NA
class "GPL-2 | GPL-3" NA
cluster "GPL (>= 2)" NA
codetools "GPL" NA
colorspace "BSD_3_clause + file LICENSE" NA
compiler "Part of R 3.2.2" NA
curl "MIT + file LICENSE" NA
datasets "Part of R 3.2.2" NA
devtools "GPL (>= 2)" NA
dichromat "GPL-2" NA
digest "GPL-2" NA
evaluate "MIT + file LICENSE" NA
foreign "GPL (>= 2)" NA
ggplot2 "GPL-2" NA
git2r "GPL-2" NA
graphics "Part of R 3.2.2" NA
grDevices "Part of R 3.2.2" NA
grid "Part of R 3.2.2" NA
gtable "GPL-2" NA
httr "MIT + file LICENSE" NA
IRdisplay "MIT + file LICENSE" NA
IRkernel "MIT + file LICENSE" NA
jpeg "GPL-2 | GPL-3" NA
jsonlite "MIT + file LICENSE" NA
KernSmooth "Unlimited" NA
labeling "MIT + file LICENSE | Unlimited" NA
lattice "GPL (>= 2)" NA
magrittr "MIT + file LICENSE" NA
MASS "GPL-2 | GPL-3" NA
Matrix "GPL (>= 2)" NA
memoise "MIT + file LICENSE" NA
methods "Part of R 3.2.2" NA
mgcv "GPL (>= 2)" NA
mime "GPL-2" NA
munsell "MIT + file LICENSE" NA
nlme "GPL (>= 2)" NA
nnet "GPL-2 | GPL-3" NA
parallel "Part of R 3.2.2" NA
plyr "MIT + file LICENSE" NA
proto "GPL-2" NA
R6 "MIT + file LICENSE" NA
RColorBrewer "Apache License 2.0" NA
Rcpp "GPL (>= 2)" NA
repr "GPL-3" NA
reshape2 "MIT + file LICENSE" NA
RJSONIO "BSD_3_clause + file LICENSE" NA
roxygen2 "GPL (>= 2)" NA
rpart "GPL-2 | GPL-3" NA
Rserve "GPL-2 | file LICENSE" NA
rstudioapi "MIT + file LICENSE" NA
rversions "MIT + file LICENSE" NA
rzmq "GPL-3" NA
scales "MIT + file LICENSE" NA
spatial "GPL-2 | GPL-3" NA
splines "Part of R 3.2.2" NA
stats "Part of R 3.2.2" NA
stats4 "Part of R 3.2.2" NA
stringi "file LICENSE" "yes"
stringr "GPL-2" NA
survival "LGPL (>= 2)" NA
tcltk "Part of R 3.2.2" NA
tools "Part of R 3.2.2" NA
utils "Part of R 3.2.2" NA
uuid "MIT + file LICENSE" NA
whisker "GPL-3" NA
xml2 "GPL (>= 2)" NA
License_restricts_use OS_type MD5sum NeedsCompilation Built
base NA NA NA NA "3.2.2"
base64enc NA NA NA "yes" "3.2.1"
BH NA NA NA "no" "3.2.2"
bitops NA NA NA "yes" "3.2.1"
boot NA NA NA "no" "3.2.2"
brew NA NA NA NA "3.2.2"
class NA NA NA "yes" "3.2.1"
cluster NA NA NA "yes" "3.2.2"
codetools NA NA NA "no" "3.2.2"
colorspace NA NA NA "yes" "3.2.2"
compiler NA NA NA NA "3.2.2"
curl NA NA NA "yes" "3.2.2"
datasets NA NA NA NA "3.2.2"
devtools NA NA NA "yes" "3.2.2"
dichromat NA NA NA NA "3.2.2"
digest NA NA NA "yes" "3.2.2"
evaluate NA NA NA "no" "3.2.2"
foreign NA NA NA "yes" "3.2.2"
ggplot2 NA NA NA "no" "3.2.2"
git2r NA NA NA "yes" "3.2.2"
graphics NA NA NA NA "3.2.2"
grDevices NA NA NA NA "3.2.2"
grid NA NA NA NA "3.2.2"
gtable NA NA NA NA "3.2.2"
httr NA NA NA "no" "3.2.2"
IRdisplay NA NA NA NA "3.2.1"
IRkernel NA NA NA NA "3.2.1"
jpeg NA NA NA "yes" "3.2.2"
jsonlite NA NA NA "yes" "3.2.2"
KernSmooth NA NA NA "yes" "3.2.2"
labeling NA NA NA "no" "3.2.2"
lattice NA NA NA "yes" "3.2.2"
magrittr NA NA NA "no" "3.2.2"
MASS NA NA NA "yes" "3.2.2"
Matrix NA NA NA "yes" "3.2.1"
memoise NA NA NA "no" "3.2.2"
methods NA NA NA NA "3.2.2"
mgcv NA NA NA "yes" "3.2.1"
mime NA NA NA "yes" "3.2.2"
munsell NA NA NA "no" "3.2.2"
nlme NA NA NA "yes" "3.2.1"
nnet NA NA NA "yes" "3.2.2"
parallel NA NA NA NA "3.2.2"
plyr NA NA NA "yes" "3.2.2"
proto NA NA NA NA "3.2.2"
R6 NA NA NA "no" "3.2.2"
RColorBrewer NA NA NA "no" "3.2.2"
Rcpp NA NA NA "yes" "3.2.2"
repr NA NA NA NA "3.2.1"
reshape2 NA NA NA "yes" "3.2.2"
RJSONIO NA NA NA "yes" "3.2.2"
roxygen2 NA NA NA "yes" "3.2.2"
rpart NA NA NA "yes" "3.2.2"
Rserve NA NA NA "yes" "3.2.2"
rstudioapi NA NA NA "no" "3.2.2"
rversions NA NA NA "no" "3.2.2"
rzmq NA NA NA "yes" "3.2.1"
scales NA NA NA "yes" "3.2.2"
spatial NA NA NA "yes" "3.2.2"
splines NA NA NA NA "3.2.2"
stats NA NA NA NA "3.2.2"
stats4 NA NA NA NA "3.2.2"
stringi NA NA NA "yes" "3.2.2"
stringr NA NA NA "no" "3.2.2"
survival NA NA NA "yes" "3.2.2"
tcltk NA NA NA NA "3.2.2"
tools NA NA NA NA "3.2.2"
utils NA NA NA NA "3.2.2"
uuid NA NA NA "yes" "3.2.1"
whisker NA NA NA "no" "3.2.2"
xml2 NA NA NA "yes" "3.2.2"

[filipstachura]

Same for me. Two days ago everything worked fine!

OS: Win 8.1
Beaker: beaker-notebook-1.4.2-0-ge55c059-windows
installed.packages: https://gist.github.com/filipstachura/b168e6838853ec618d42

Edit: For me reinstalling required R packages under current user has solved the problem.

[vascoosx]

I am working on Win 7 and did @filipstachura suggestion but it did not work

[ArthurZ]

Hmm on Win 7 Pro.
Can't overcome this error.
IPython starts, not R.
Points to issues with Rserve
I went to the base non-gui R of each bitness and did install.packages('Rserve')
Restarted Beaker, same error:
stderr: [Thread-11] INFO com.twosigma.beaker.r.module.ErrorGobbler - Error line not captured: 'Error in library(Rserve) : there is no package called 'Rserve''

[scottdraves]

Hi Arthur, perhaps you have more than one version of R installed and the one you that's running in Beaker is different from the one where you are installing the package.

On Windows Beaker uses the registry to find the executable:
https://github.com/twosigma/beaker-notebook/blob/master/plugin/r/src/dist/rPlugin#L30
but the PATH has precedence.

[ArthurZ]

Hi @scottdraves,
you are right, I also have MS R Open, too:

I guess the top entry wins as the code stops at the 1st match.
But I would like Beaker to work under this setup. Is that possible?

[ArthurZ]

Attempting to answer my own question:
I saw there is an option of adding a preference for a language in .beaker\v1\config\beaker.pref.json
So I did for R as:
"R" : { "path" : "C:\\Program Files\\R\\R-3.3.2\\bin" }
Alas, I see R is starting, but the same error referencing RServe persists:

'Error in library(Rserve) : there is no package called 'Rserve''

I created a Gist with more details preceding and after it occurs taken from the Beaker console (web server) output in hopes it will help resolving the issue.
Thank you!

[RoccoDAnt]

Dear ArthurZ, I had the same problem. I solved it:

1. checking that "RServe" was installed in the used version of R (in this case "R-3.3.2").
2. removing \\bin at the end of the path set in the file .beaker\v1\config\beaker.pref.json.
   Best,
   Rocco