I am setting up R with Hadoop. I am getting the following error on installing package "rhbase": (other packages[see below] and their dependencies have been installed successfully)
bash-3.2$ ls
plyrmr_0.4.0.tar rhbase_1.2.1.tar rhdfs_1.0.8.tar rmr2_3.2.0.tar
ERROR:
> install.packages("/Users/raunak/Downloads/rlibs/rhbase_1.2.1.tar", repos = NULL, type="source")
* installing *source* package ‘rhbase’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -g -DHAVE_UINTPTR_T -DHAVE_NETDB_H=1 -fpermissive -DHAVE_INTTYPES_H -DHAVE_NETINET_IN_H -I./gen_cpp `pkg-config --cflags thrift` -Wall -fPIC -Wall -mtune=core2 -g -O2 -c Hbase.cpp -o Hbase.o
/bin/sh: pkg-config: command not found
In file included from Hbase.cpp:7:
./Hbase.h:10:10: fatal error: 'TProcessor.h' file not found
\#include <TProcessor.h>
^
1 error generated.
make: *** [Hbase.o] Error 1
ERROR: compilation failed for package ‘rhbase’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rhbase’
Warning in install.packages :
installation of package ‘/Users/raunak/Downloads/rlibs/rhbase_1.2.1.tar’ had non-zero exit status
bash-3.2$ which pkg-config
/usr/local/bin/pkg-config
What could be the cause?
Related
I've been trying to install an older version of stringi using renv and am getting the following error. I've had a few earlier errors using restore, but a few restarts have been able to move things through. I tried removing and reinstalling stringi, but still end up with the same error when trying to load the appropriate version.
Installing stringi [1.4.3] ...
FAILED
Error installing package 'stringi':
===================================
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0 -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stri_ICU_settings.cpp -o stri_ICU_settings.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0 -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stri_TODO_justify.cpp -o stri_TODO_justify.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0 -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stri_TODO_splitpos.cpp -o stri_TODO_splitpos.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0 -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stri_TODO_uchar.cpp -o stri_TODO_uchar.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I. -Iicu61/ -Iicu61/unicode -Iicu61/common -Iicu61/i18n -DU_STATIC_IMPLEMENTATION -DU_COMMON_IMPLEMENTATION -DU_I18N_IMPLEMENTATION -DUCONFIG_USE_LOCAL -DU_TOOLUTIL_IMPLEMENTATION -DNDEBUG -DWINVER=0x0600 -D_WIN32_WINNT=0x0600 -DU_USE_STRTOD_L=0 -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stri_brkiter.cpp -o stri_brkiter.o
stri_brkiter.cpp: In member function 'void StriBrkIterOptions::setType(SEXP, const char*)':
stri_brkiter.cpp:60:8: error: 'isNull' was not declared in this scope; did you mean 'Rf_isNull'?
60 | if (isNull(opts_brkiter)) {
| ^~~~~~
| Rf_isNull
stri_brkiter.cpp: In member function 'void StriBrkIterOptions::setLocale(SEXP)':
stri_brkiter.cpp:130:8: error: 'isNull' was not declared in this scope; did you mean 'Rf_isNull'?
130 | if (isNull(opts_brkiter)) {
| ^~~~~~
| Rf_isNull
stri_brkiter.cpp: In member function 'void StriBrkIterOptions::setSkipRuleStatus(SEXP)':
stri_brkiter.cpp:171:8: error: 'isNull' was not declared in this scope; did you mean 'Rf_isNull'?
171 | if (isNull(opts_brkiter)) {
| ^~~~~~
| Rf_isNull
make: *** [C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf:259: stri_brkiter.o] Error 1
ERROR: compilation failed for package 'stringi'
* removing 'D:/Projects/project1/renv/staging/1/stringi'
Error: install of package 'stringi' failed [error code 1]
When I try to load the version directly using devtools it conflicts with renv
require(devtools)
install_version("stringi", version = "1.4.3", repos = "http://cran.us.r-project.org")
require(devtools)
Loading required package: devtools
Loading required package: usethis
Warning messages:
1: package ‘devtools’ was built under R version 4.2.2
2: package ‘usethis’ was built under R version 4.2.2
> install_version("stringi", version = "1.4.3", repos = "http://cran.us.r-project.org")
Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/stringi/stringi_1.4.3.tar.gz
Installing package into ‘D:/Projects/project1/renv/library/R-4.2/x86_64-w64-mingw32’
(as ‘lib’ is unspecified)
ℹ Using R 4.2.0 (lockfile was generated with R 4.0.3)
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: cannot remove earlier installation, is it in use?
* removing 'D:/Projects/project1/renv/library/R-4.2/x86_64-w64-mingw32/stringi'
* restoring previous 'D:/Projects/project1/renv/library/R-4.2/x86_64-w64-mingw32/stringi'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
problem copying D:\Projects\project1\renv\library\R-4.2\x86_64-w64-mingw32\00LOCK-stringi\stringi\libs\icudt69l.dat to D:\Projects\project1\renv\library\R-4.2\x86_64-w64-mingw32\stringi\libs\icudt69l.dat: Invalid argument
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
problem copying D:\Projects\project1\renv\library\R-4.2\x86_64-w64-mingw32\00LOCK-stringi\stringi\libs\x64\stringi.dll to D:\Projects\project1\renv\library\R-4.2\x86_64-w64-mingw32\stringi\libs\x64\stringi.dll: Permission denied
Warning message:
In i.p(...) :
installation of package ‘C:/Users/user/AppData/Local/Temp/RtmpK41CGy/remotesce6857a77e39/stringi’ had non-zero exit status
>
The OS/platform by jay.sf made me check over my setup and I realized that I was working with different versions of R. I installed the earlier version, called renv::restore() and the packages successfully installed.
I've already installed the CplexApi package using the following guide: https://www.r-bloggers.com/using-cplex-in-r-installing-cplexapi-in-windows-10/
I'm now trying to install the Rcplex package in a simillar way. I've edited the makevars.win file to the following:
ifeq "$(WIN)" "64"
PKG_LIBS = -L"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/x64_win64" -lcplex1280 -lm
PKG_CPPFLAGS = -D_LP64 -I"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/include"
else
PKG_LIBS = -L"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/bin/x86_win32" -lcplex1280 -lm
PKG_CPPFLAGS = -I"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/include"
endif
I then entered the following in CMD:
C:\Users\A>R CMD build --no-build-vignettes --no-manual --md5 C:\Users\A\Downloads\cPlex\Rcplex_0.3-3.tar\Rcplex_0.3-3\Rcplex
And this was the output:
* checking for file 'C:\Users\A\Downloads\cPlex\Rcplex_0.3-3.tar\Rcplex_0.3-3\Rcplex/DESCRIPTION' ... OK
* preparing 'Rcplex':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* adding MD5 file
* building 'Rcplex_0.3-3.tar.gz'
Warning: file 'Rcplex/cleanup' did not have execute permissions: corrected
Warning: file 'Rcplex/configure' did not have execute permissions: corrected`
Then I entered the following:
C:\Users\A>R CMD INSTALL --build --no-multiarch .\Rcplex_0.3-3.tar.gz
And I got this as the output:
In R CMD INSTALL
* installing to library 'C:/Users/A/Documents/R/win-library/3.5'
* installing *source* package 'Rcplex' ...
** package 'Rcplex' successfully unpacked and MD5 sums checked
** libs
c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -D_LP64 -I"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rcplex.c -o Rcplex.o
c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -D_LP64 -I"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rcplex_QCP.c -o Rcplex_QCP.o
Rcplex_QCP.c: In function 'Rcplex_QCP':
Rcplex_QCP.c:37:7: warning: unused variable 'trace' [-Wunused-variable]
int trace = INTEGER(getListElement(control,"trace"))[0];
^
c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -D_LP64 -I"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rcplex_params.c -o Rcplex_params.o
c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-35~1.0/include" -DNDEBUG -D_LP64 -I"C:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rcplex_utils.c -o Rcplex_utils.o
c:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rcplex.dll tmp.def Rcplex.o Rcplex_QCP.o Rcplex_params.o Rcplex_utils.o -LC:/Program Files/IBM/ILOG/CPLEX_Studio128/cplex/x64_win64 -lcplex1280 -lm -LC:/PROGRA~1/R/R-35~1.0/bin/x64 -lR
C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lcplex1280
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'Rcplex'
* removing 'C:/Users/A/Documents/R/win-library/3.5/Rcplex'
I'm wondering what exactly I did wrong?
R version: 3.1.1
I want to install this package. I downloaded the source and put it under my home directory. After that I ran install.packages("~/rEDM/",repos=NULL,type="source") to install from source. The error message I got is:
Installing package into ‘/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package ‘rEDM’ ...
** libs
I/usr/include/R -DNDEBUG -I/usr/local/include -I"/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I../inst/include -c RcppExports.cpp -o RcppExports.o
/bin/sh: I/usr/include/R: No such file or directory
make: [RcppExports.o] Error 127 (ignored)
I/usr/include/R -DNDEBUG -I/usr/local/include -I"/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I../inst/include -c block_lnlp.cpp -o block_lnlp.o
/bin/sh: I/usr/include/R: No such file or directory
make: [block_lnlp.o] Error 127 (ignored)
I/usr/include/R -DNDEBUG -I/usr/local/include -I"/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I../inst/include -c forecast_machine.cpp -o forecast_machine.o
/bin/sh: I/usr/include/R: No such file or directory
make: [forecast_machine.o] Error 127 (ignored)
I/usr/include/R -DNDEBUG -I/usr/local/include -I"/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I../inst/include -c lnlp.cpp -o lnlp.o
/bin/sh: I/usr/include/R: No such file or directory
make: [lnlp.o] Error 127 (ignored)
I/usr/include/R -DNDEBUG -I/usr/local/include -I"/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/include" -I../inst/include -c xmap.cpp -o xmap.o
/bin/sh: I/usr/include/R: No such file or directory
make: [xmap.o] Error 127 (ignored)
-L/usr/local/lib64 -o rEDM.so RcppExports.o block_lnlp.o forecast_machine.o lnlp.o xmap.o -L/usr/lib64/R/lib -lR
/bin/sh: line 2: -L/usr/local/lib64: No such file or directory
make: *** [rEDM.so] Error 127
ERROR: compilation failed for package ‘rEDM’
* removing ‘/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1/rEDM’
Warning message:
In install.packages("~/rEDM/", repos = NULL, type = "source") :
installation of package ‘/ghome/dwuab/rEDM/’ had non-zero exit status
Something is very wrong here, as R did not call the compiler at all.
The author of the package said this is due to R and/or GCC being misconfigured.
My question: is there anyone who knows what the problem is? Or how to troubleshoot the problem?
Edit 1: installing the package through zip file using command install.packages("./master.zip",repos=NULL,type="source") led to the following error message:
Installing package into ‘/d1/dwuab/R/x86_64-redhat-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
Error in rawToChar(block[seq_len(ns)]) :
embedded nul in string: 'PK\003\004\n\0\0\0\0\0\x83h,H\0\0\0\0\0\0\0\0\0\0\0\0\f\0\t\0rEDM-master/UT\005\0\001Fj\x95VPK\003\004\n\0\0\0\b\0\x83h,H\x8ewq\xa1\030\0\0\0\034\0\0\0\031\0\t\0rEDM-master/.Rbuild'
Warning message:
In install.packages("./master.zip", repos = NULL, type = "source") :
installation of package ‘./master.zip’ had non-zero exit status
Edit 2: I have no root privilege on the machine.
As a workaround, I used EasyBuild to compile and install R 3.2.1 with GCC 4.9.3. The whole compiling and installing process took me several days ... Now it works.
You can try the following link...
http://www.cyberciti.biz/faq/centos-linux-install-gcc-c-c-compiler/
I want to install Rcpp using install.packages("Rcpp"), but it failed.
The error message:
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Date.cpp -o Date.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Module.cpp -o Module.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c api.cpp -o api.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c attributes.cpp -o attributes.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c barrier.cpp -o barrier.o
g++ -shared -L/usr/local/lib64 -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o
installing to /home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/libs/Rcpp.so':
/home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp/libs/Rcpp.so: undefined symbol: _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/sethbrin/R/x86_64-redhat-linux-gnu-library/3.1/Rcpp’
The downloaded source packages are in
‘/tmp/Rtmp6PKB8N/downloaded_packages’
Warning message:
In install.packages("Rcpp") :
installation of package ‘Rcpp’ had non-zero exit status
Then I use
c++fit _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode
std::basic_streambuf<char, std::char_traits<char> >::seekoff(long long, std::_Ios_Seekdir, std::_Ios_Openmode)
I have searched for some solutions for that. It seems that it is because of the gcc version. But I don't know how to change the gcc version that R uses to compile Rcpp package.
CRAN tests Rcpp just like any other of the (by now) 6700+ package.
You can see the aggregate test report and the test setups includes two Fedora-based machines:
one fedora setup using clang and
one fedora setup using g++.
As such your problems are possibly local, or simply due to using an older setup. In which case the Archive section gives you access to an older version.
I've encountered a similar problem.
And after some searches, here are the solutions to alter the compiler:
1. If you have the root privilege:
I found that the Makeconf file in R directory actually sets all the information that is needed for compilation.
To find the path to it, echo which R in the command line.
e.g. I got like:
/data/apps/R/3.1.2/bin/R
And then the file is in:
/data/apps/R/3.1.2/lib64/R/etc/Makeconf
then sudo edit the file on line CC = XXX and maybe more relative lines.
Problem solved!
2. If you only have local user privilege.
Add your own configurations to ~/.R/Makevars
However, #Dirk is probably right.
For me, I finally solved my problem by adding -Doff_t=__off_t to CFLAGS (My problem was error: unknown type name 'off_t'). And I got the halted error when I manually altered parts of the compilers...
I am trying to install an R shiny server on my local Ubuntu 12.04 machine, and I followed the instructions here https://github.com/rstudio/shiny-server/wiki/Ubuntu-step-by-step-install-instructions:
When trying to do a:
install.packages('shiny', repos='http://cran.rstudio.com/')
It goes through the dependencies, but fails to install Rcpp. See error log below:
* installing *source* package 'Rcpp' ...
* package 'Rcpp' successfully unpacked and MD5 sums checked
* libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Module.cpp -o Module.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Rcpp_init.c -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Timer.cpp -o Timer.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c barrier.cpp -o barrier.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c exceptions.cpp -o exceptions.o
g++ -shared -o Rcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o -L/usr/lib/R/lib -lR
g++ -o libRcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o -shared -L/usr/lib/R/lib -lR
ar qc libRcpp.a Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o
cp libRcpp.so ../inst/lib
cp libRcpp.a ../inst/lib
rm libRcpp.so libRcpp.a
installing to /usr/local/lib/R/site-library/Rcpp/libs
* R
* inst
* preparing package for lazy loading
Error : package 'codetools' was built before R 3.0.0: please re-install it
Error : unable to load R code in package 'Rcpp'
ERROR: lazy loading failed for package 'Rcpp'
* removing '/usr/local/lib/R/site-library/Rcpp'
* installing *source* package 'httpuv' ...
* package 'httpuv' successfully unpacked and MD5 sums checked
* libs
g++ -I/usr/share/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -I"/usr/lib/R/site-library/Rcpp/include" -fpic -O3 -pipe -g -c RcppExports.cpp -o RcppExports.o
RcppExports.cpp:75:10: error: 'uint32_t' was not declared in this scope
RcppExports.cpp: In function 'SEXPREC* httpuv_run(SEXP)':
RcppExports.cpp:79:5: error: 'uint32_t' was not declared in this scope
RcppExports.cpp:79:14: error: expected ';' before 'timeoutMillis'
RcppExports.cpp:80:25: error: 'timeoutMillis' was not declared in this scope
RcppExports.cpp:80:38: error: 'run' cannot be used as a function
make: * [RcppExports.o] Error 1
ERROR: compilation failed for package 'httpuv'
* removing '/usr/local/lib/R/site-library/httpuv'
ERROR: dependency 'httpuv' is not available for package 'shiny'
* removing '/usr/local/lib/R/site-library/shiny'
EDITED:
Manually downloading and installing Rcpp gives me:
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Error : package 'codetools' was built before R 3.0.0: please re-install it
So I manually downloaded and installed codetools and re-tried Rcpp:
sudo R CMD INSTALL codetools_0.2-8.tar.gz
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Then followed the instructions again from the Shiny webpage from "Install R" and "Install shiny" and got a similar error but now with caTools, bitops and xtable, so I did the manual installation of each of them. The shiny was installed correctly.
Then followed the next steps in the instructions.
Any ideas why I got this 'was built before R 3.0.0' errors?
Ubuntu 12.04 is a pre-R 3.0.0 release. You have to decide whether you want its long-term support and stability "as is", or if you want newer software.
You can mix and match. Read the CRAN Ubuntu README, adjust your apt settings and enjoy updated r-cran-* packages. With those you can then install shiny and its dependencies.
Manually downloading and installing Rcpp gives me:
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Error : package 'codetools' was built before R 3.0.0: please re-install it
So I manually downloaded and installed codetools and re-tried Rcpp:
sudo R CMD INSTALL codetools_0.2-8.tar.gz
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Then followed the instructions again from the Shiny webpage from "Install R" and "Install shiny" and got a similar error but now with caTools, bitops and xtable, so I did the manual installation of each of them. The shiny was installed correctly.
Then followed the next steps in the instructions. All went well from there. Not sure why I was getting these was built before 3.0.0 errors.