To reproduce:
Follow the instructions in the README of https://github.com/yencarnacion/GCP-jupyter-notebook
open an R jupyter notebook and execute:
system("mkdir -p ~/anaconda3/lib/R/library", intern=TRUE)
system("echo R_LIBS=~/anaconda3/lib/R/library > ~/.Renviron", intern=TRUE)
* Then do a Kernel>Restart and in the first cell of your notebook put:
.libPaths("~/anaconda3/lib/R/library")
as user ubuntu do:
wget https://cran.rstudio.com/src/contrib/Rcpp_0.12.10.tar.gz
as user ubuntu do:
/usr/lib/anaconda/lib/R/bin/R CMD INSTALL --library=~/anaconda3/lib/R/library Rcpp_0.12.10.tar.gz
This is the output I get from /usr/lib/anaconda/lib/R/bin/R CMD INSTALL --library=~/anaconda3/lib/R/library Rcpp_0.12.10.tar.gz:
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/lib/anaconda/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/lib/anaconda/include -fpic -I/usr/lib/anaconda/include -c Date.cpp -o Date.o
g++ -I/usr/lib/anaconda/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/lib/anaconda/include -fpic -I/usr/lib/anaconda/include -c Module.cpp -o Module.o
g++ -I/usr/lib/anaconda/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/lib/anaconda/include -fpic -I/usr/lib/anaconda/include -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/lib/anaconda/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/lib/anaconda/include -fpic -I/usr/lib/anaconda/include -c api.cpp -o api.o
g++ -I/usr/lib/anaconda/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/lib/anaconda/include -fpic -I/usr/lib/anaconda/include -c attributes.cpp -o attributes.o
g++ -I/usr/lib/anaconda/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/lib/anaconda/include -fpic -I/usr/lib/anaconda/include -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/anaconda/lib/R/lib -L/usr/lib/anaconda/lib -lgfortran -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/anaconda/lib/R/lib -lR
installing to /home/ubuntu/anaconda3/lib/R/library/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/ubuntu/anaconda3/lib/R/library/Rcpp/libs/Rcpp.so':
/home/ubuntu/anaconda3/lib/R/library/Rcpp/libs/Rcpp.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEED1Ev
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/ubuntu/anaconda3/lib/R/library/Rcpp’
Because of the Rcpp problem, I am unable to devtools::install_github('rstudio/leaflet') among other things.
Note: This question may be related to Rcpp package in R not install ubuntu 14.04
You can install Rcpp through conda:
conda install r-rcpp
Fyi, you can create a Jupyter Notebook for R on GCP in seconds by using GCP's new AI Platform Notebooks.
In the GCP console go to AI Notebooks -> New Instance -> Select R. You should be able to install any R packages that you need
Related
I just updated my R packages packages in RStudio. For the RcppArmadillo package (version 0.11.4.3.1), RStudio warned me that no binary package is available for my system (x86_64, Windows 11) and asked if I wanted to install the source package instead. Since I have RTools installed for just this purpose, I said yes.
The installation succeeded, but a warning was issued that the package "has a configure script" and "probably needs manual configuration".
* installing *source* package 'RcppArmadillo' ...
** package 'RcppArmadillo' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I'C:/.../R/win-library/4.2/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -I../inst/include -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastLm.cpp -o fastLm.o
g++ -shared -s -static-libgcc -o RcppArmadillo.dll tmp.def RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.2/bin/x64 -lR
installing to C:/.../R/win-library/4.2/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
My questions are:
Should I be concerned?
How can I tell that the package is working correctly?
If manual configuration is needed, how do I do it?
An aside for the second of those: I'm not using this package directly, and presume that it was installed as a dependency of another package that I used in the past. Since I do not remember which package that may have been (or when I last used it), I can't just dig into my older code, find a script that uses this package, and see if it still works.
Is there such a thing in the R world as automated tests to ensure that a newly-compiled package actually works before it gets installed? I'm a little surprised that this is apparently not done by default.
I just started R. I am on a M1 BigSur Mac.
I have tried several packages, but I could not install anyone of them.
for example, swirl
> install.packages("swirl")
trying URL 'https://cran.rstudio.com/src/contrib/swirl_2.4.5.tar.gz'
Content type 'application/x-gzip' length 108847 bytes (106 KB)
==================================================
downloaded 106 KB
* installing *source* package ‘swirl’ ...
** package ‘swirl’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so':
dlopen(/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so, 6): no suitable image found. Did find:
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘swirl’
* removing ‘/opt/homebrew/Cellar/r/4.1.0/lib/R/library/swirl’
Warning in install.packages :
installation of package ‘swirl’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/t6/qy2rcbdx0g9_fv98q1g48v_h0000gn/T/RtmpDAcI28/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
tidyverse it has been repeating the following output but it does not complete a proper installation.
* installing *source* package ‘cpp11’ ...
** package ‘cpp11’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cpp11)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c api.cpp -o api.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c attributes.cpp -o attributes.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c barrier.cpp -o barrier.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c date.cpp -o date.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c module.cpp -o module.o
clang++ -std=gnu++14 -I"/opt/homebrew/Cellar/r/4.1.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include -fPIC -g -O2 -c rcpp_init.cpp -o rcpp_init.o
clang++ -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/homebrew/Cellar/r/4.1.0/lib/R/lib -L/opt/homebrew/opt/gettext/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/xz/lib -L/opt/homebrew/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/opt/homebrew/Cellar/r/4.1.0/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
I tried install.package('swirl', type='mac.binary').
It forces a successful installation but it gives the following error when I call library("swirl"):
Error: package or namespace load failed for ‘swirl’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so':
dlopen(/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so, 6): no suitable image found. Did find:
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
/opt/homebrew/Cellar/r/4.1.0/lib/R/library/stringi/libs/stringi.so: mach-o, but wrong architecture
I am very new to R language. Being an admin I am setting up an rserver and installing the required packages for my use of this R server with SAP HANA 1.0.
The fundamental problem here is when i am installing the rcpp.0.12.16 and getting the below error. g++ is 4.8-6.189.
Are there an incompatibilities witht the OS version R version and rccp package i am using? Please help resolving this issue.
> setwd("/Media/R/R_indep_pack")
> install.packages("Rcpp_0.12.16.tar.gz",repos = NULL, type="source")
* 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 -c Date.cpp -o Date.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -
I/usr/local/include -fPIC -c Module.cpp -o Module.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -
I/usr/local/include -fPIC -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -
I/usr/local/include -fPIC -c api.cpp -o api.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -
I/usr/local/include -fPIC -c attributes.cpp -o attributes.o
g++ -I/usr/local/lib64/R/include -DNDEBUG -I../inst/include/ -
I/usr/local/include -fPIC -c barrier.cpp -o barrier.o
g++ -L/usr/local/lib64/R/lib -L/usr/local/lib64 -o Rcpp.so Date.o Module.o
Rcpp_init.o api.o attributes.o barrier.o -L/usr/local/lib64/R/lib -lR
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o: In function
`_start':
/home/abuild/rpmbuild/BUILD/glibc-2.22/csu/../sysdeps/x86_64/start.S:114:
undefined reference to `main'
collect2: error: ld returned 1 exit status
/usr/local/lib64/R/share/make/shlib.mk:6: recipe for target 'Rcpp.so' failed
make: *** [Rcpp.so] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/usr/local/lib64/R/library/Rcpp’
Warning message:
In install.packages("Rcpp_0.12.16.tar.gz", repos = NULL, type = "source") :
installation of package ‘Rcpp_0.12.16.tar.gz’ had non-zero exit status
>
Your linker is looking for a main function since it is not told to build a shared library:
g++ -L/usr/local/lib64/R/lib -L/usr/local/lib64 -o Rcpp.so Date.o Module.o
Rcpp_init.o api.o attributes.o barrier.o -L/usr/local/lib64/R/lib -lR
Here a -shared is missing from the command line. The command line flags used here are defined via the Makevars file:
$ grep SHLIB.*LDFLAGS $(R RHOME)/etc/Makeconf
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LDFLAGS = -shared
SHLIB_FCLDFLAGS = -shared
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS)
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_CXX1XLDFLAGS = -shared
Either these are incorrectly set on your system or you are overriding them via ~/.R/Makevars.
In ubuntu, in such situation, I would search for
apt search rcpp # search in central repository for \
# packages for R packages
In this case, this leads to 'r-cran-rcpp' package which I then install with
sudo apt install r-cran-rcpp
(such packages from 'r-cran-' help, because they install for you the further dependencies in the system - which are often dependencies outside of R - automatically for you. E.g. some packages require java or some other system libraries.).
Similarly, you have to search in rpm or yast2 repos for rcpp packages.
I found googling http://rpmfind.net/linux/rpm2html/search.php?query=R-Rcpp
or http://rpm.pbone.net/index.php3/stat/4/idpl/33595438/dir/opensuse/com/R-RcppArmadillo-0.4.450.1.0-2.38.i586.rpm.html
Or: if you are using conda:
conda install -c r r-rcpp
would definitely help ...
If you don't know conda: This tutorial is super!
https://www.youtube.com/watch?v=YJC6ldI3hWk
Just spend 11 minutes and you will be able to use conda!
(With conda, you can install several R versions with all their packages in parallel in your system - sometimes you need that because some versions are not compativle with some R packages - conda creates for you different local environments within which you can install programs with all their specific dependencies. And you can switch between the environments.)
I definitely recommend you to use conda. Because this solves many package dependency problems.
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.