rstudio-help — This area is for all your questions related to help with installing/using.

[Rstudio-help] launch shiny app through RStudio

[Karim M. <kme...@gm...>]

Dear All,
Rstudio is required to save report generated by shiny app to doc and pdf.
For this reason, currently  I need to start the shiny app through rstudio.

I developer launcher desktop to facilitate the use of the shiny app. It
works well when I use R.exe but can't set it with rstudio.exe.
The structure of the folder is:

/R-3.3.2/bin/R.exe
/radiant.dose/inst/app/
/rstudio/bin/rstudio.exe

The launcher file (run.vbs ):

Randomize
CreateObject("Wscript.Shell").Run "R-3.3.2\bin\R.exe CMD BATCH --vanilla
--slave runShinyApp.R" & " " & RND & " ", 0, False

runShinyApp.R file:

.libPaths("./R-3.3.2/library")
shiny::runApp("./radiant.dose/inst/app/",launch.browser=TRUE)

How can I replace R.exe by rstudio.exe?

Thanks

Best Regards
Karim

[Rstudio-help] Circos + Shiny

[Karim M. <kme...@gm...>]

Dear all,
Can I have the code source of this app?

https://gallery.shinyapps.io/genome_browser/

Thanks
Karim

[Rstudio-help] Build rstudio 0.99 R link errors

[jupiter <jup...@gm...>]

Hi,

I am building RStudio 0.99.486 on CentOS 6. I
added-DLIBR_INCLUDE_DIRS=${R_INC}  -DLIBR_LIBRARIES=${R_LIB} where R_LIB
poing to the R 3.2.2 lib directory which contains libRblas.so,
libRlapack.so and libR.so, and ${R_INC} pointing to the R 3.2.2 include
directory, but I still got the R link errors:

....
RSearchPath.cpp:(.text+0xcf4): undefined reference to `R_GlobalEnv'
RSearchPath.cpp:(.text+0xd43): undefined reference to `ENCLOS'
RSearchPath.cpp:(.text+0xde4): undefined reference to `ENCLOS'
RSearchPath.cpp:(.text+0xdee): undefined reference to `R_BaseEnv'
RSearchPath.cpp:(.text+0xe33): undefined reference to `Rf_install'
RSearchPath.cpp:(.text+0xe3e): undefined reference to `Rf_getAttrib'

.......

I have checked, there are no issues with R 3.2.2 libraries, what I could be
missing?

Thank you.

- ju

[Rstudio-help] Fwd: Rstudio R-devel libR.so

[Karim M. <kme...@gm...>]

---------- Forwarded message ----------
From: Karim Mezhoud <kme...@gm...>
Date: Mon, Mar 9, 2015 at 10:41 AM
Subject: Rstudio R-devel libR.so
To: "r-...@r-..." <R-...@r-...>


Dear All,
I am actually on R-devel using shell consol. When I run RStudio, it can't
find libR.so in the new /lib folder where is libRblas.so  libRlapack.so.
At first step I configure R-devel to share library with ./configure
--enable-R-shlib.

when I copied libR.so from  /usr/lib/R/lib/libR.so (stable version R 3.1)
to /usr/local/R-devel/lib/libR.so (R-devel version), That doesn't work.

please find the detail  at below.
Karim mezhoud




$which R
/usr/bin/R
$R
> R.Version()[13]
$version.string
[1] "R version 3.1.2 (2014-10-31)

> Sys.getenv("R_HOME")
[1] "/usr/lib/R"

> .Library
[1] "/usr/lib/R/library"
> .libPaths()
[1] "/home/mezhoud/R/x86_64-pc-linux-gnu-library/3.1"
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"
"


$sudo apt-get build-dep r-base
$sudo apt-get install subversion ccache
$mkdir ~/svn/
$cd ~/svn/
$svn co https://svn.r-project.org/R/trunk r-devel/R

$cd /svn/r-devel/R
$./configure --enable-R-shlib
$make
$make check
$sudo make install rhome=/usr/local/R-devel

$which R
/usr/local/bin/R

$cd /usr/local/bin
$R

>R.Version()[13]
$version.string
[1] "R Under development (unstable) (2015-03-07 r67951)"

> .libPaths()
[1] "/usr/local/R-devel/library"
> .Library
[1] "/usr/local/R-devel/library"

> Sys.getenv("R_HOME")
[1] "/usr/local/R-devel"

$rstudio
R shared library (/usr/local/R-devel/lib/libR.so) not found.
If this is a custom build of R, was it built with the --enable-R-shlib
option?

$export RSTUDIO_WHICH_R=/usr/local/bin/R
$rstudio
R shared library (/usr/local/R-devel/lib/libR.so) not found.
If this is a custom build of R, was it built with the --enable-R-shlib
option?

$export RSTUDIO_WHICH_R=/usr/local/R-devel/bin/R
$rstudio
R shared library (/usr/local/R-devel/lib/libR.so) not found.
If this is a custom build of R, was it built with the --enable-R-shlib
option?

$sudo locate libR.so
/usr/lib/libR.so
/usr/lib/R/lib/libR.so

When I get a symbolic link with:

 sudo ln -s  /usr/lib/R/lib/libR.so /usr/local/R-devel//lib/libR.so


The R session had a fatal error.


ERROR r error 4 (R code execution error) [errormsg=Error in
.Internal(getOption(x)) :

there is no .Internal function 'getOption'

]; OCCURRED AT: core::Error r::exec::evaluateString(const std::string&,
SEXPREC**, r::sexp::Protect*) /home/ubuntu/rstudio/src/cpp/r/RExec.cpp: