issue with sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""

[João Carlos]

Hello,

I am not able to properly install the shiny package Cento OS VPS server.

First I got the error > there is no package called 'shiny' at  http://192.254.199.202:3838/ap1/

Then I tried to follow almost all the posts on "there is no package called 'shiny'," but when I try the most recommend solution "su - c" and R-\ "install.packages ('shiny' repos = 'http://cran.rstudio.com/') \ "" "I realized that there is an error occurring at the end.

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Date.cpp -o Date.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Module.cpp -o Module.o
{standard input}: Assembler messages:
{standard input}:12724: Warning: end of file not at end of a line; newline inserted
{standard input}:14573: Warning: zero assumed for missing expression
{standard input}:14533: Error: undefined symbol `.LLSDATT11072' in operation
{standard input}:14536: Error: undefined symbol `.LLSDACSE11072' in operation
g++: Internal error: Killed (program cc1plus)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make: *** [Module.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/usr/lib64/R/library/Rcpp’
ERROR: dependency ‘Rcpp’ is not available for package ‘httpuv’
* removing ‘/usr/lib64/R/library/httpuv’
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/usr/lib64/R/library/shiny’

The downloaded source packages are in
    ‘/tmp/Rtmp40EIcN/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
  installation of package ‘Rcpp’ had non-zero exit status
2: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
  installation of package ‘httpuv’ had non-zero exit status
3: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
  installation of package ‘shiny’ had non-zero exit status

Thanks for any help for a non-linux user.

Regards

Joao Carlos

[João Carlos]

I tried just to install Rcpp package alone changing the repository with no success 

> install.packages('Rcpp', repos='http://cran.fhcrc.org/')
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.fhcrc.org/src/contrib/Rcpp_0.10.6.tar.gz'
Content type 'application/x-gzip' length 1985569 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Date.cpp -o Date.o
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Module.cpp -o Module.o
{standard input}: Assembler messages:

{standard input}:21309: Warning: end of file not at end of a line; newline inserted
{standard input}:22141: Error: no such instruction: `c'
{standard input}:22141: Error: open CFI at the end of file; missing .cfi_endproc directive

g++: Internal error: Killed (program cc1plus)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make: *** [Module.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/usr/lib64/R/library/Rcpp’

The downloaded source packages are in

    ‘/tmp/RtmpAu3WeP/downloaded_packages’

Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

Warning message:
In install.packages("Rcpp", repos = "http://cran.fhcrc.org/") :

  installation of package ‘Rcpp’ had non-zero exit status

[Narbeh Yousefian]

Hi Joao, 

Did you manage to resolve this issue? I just tried to install and ran into the same problem. 

thanks, 

[Gustavo Ribeiro]

I had the same problem installing shiny, but updating all packages installed solved the problem!

Try run the followng command to update them all (it takes a while but it works):
 
update.packages(checkBuilt = TRUE, ask = FALSE)


Regards
Gustavo

[Narbeh Yousefian]

Hey Gustavo, 

Managed to sort it out by installing the dependency packages individually. It was kind of annoying nut ended up running 

wget http://cran.r-project.org/src/contrib/Rcpp_0.11.1.tar.gz

sudo R CMD INSTALL --build Rcpp_0.11.1.tar.gz

wget http://cran.r-project.org/src/contrib/httpuv_1.2.3.tar.gz

sudo R CMD INSTALL --build httpuv_1.2.3.tar.gz

then I installed shiny and it worked fine. 

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