Link error installing Rcpp "library not found for -lintl" - r

I just stumbled over a linker error when trying to install some R packages which have Rcpp as a dependency. My setup is Mac OS X 10.9.1 (Mavericks), R 3.0.2 installed by Homebrew. Here's the error output:
> install.packages('Rcpp')
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
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Date.cpp -o Date.o
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Module.cpp -o Module.o
clang -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -c Rcpp_init.c -o Rcpp_init.o
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Timer.cpp -o Timer.o
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c api.cpp -o api.o
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c attributes.cpp -o attributes.o
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c barrier.cpp -o barrier.o
clang++ -I/usr/local/Cellar/r/3.0.2/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c exceptions.cpp -o exceptions.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o -F/usr/local/Cellar/r/3.0.2/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation
ld: library not found for -lintl
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Apparently, libintl is part of the gettext package. I did the following, possibly redundant reinstall to make sure my copy was up-to-date:
$ brew install gettext
Warning: gettext-0.18.3.2 already installed
$ brew reinstall gettext
==> Reinstalling gettext
==> Downloading http://ftpmirror.gnu.org/gettext/gettext-0.18.3.2.tar.gz
Already downloaded: /Library/Caches/Homebrew/gettext-0.18.3.2.tar.gz
==> ./configure --prefix=/usr/local/Cellar/gettext/0.18.3.2 --with-included-gettext --with-included-glib --with-included-libcroco --with-included-libunistring --with-emac
==> make
==> make install
==> Caveats
This formula is keg-only, so it was not symlinked into /usr/local.
OS X provides the BSD gettext library and some software gets confused if both are in the library path.
Generally there are no consequences of this for you. If you build your
own software and it requires this formula, you'll need to add to your
build variables:
LDFLAGS: -L/usr/local/opt/gettext/lib
CPPFLAGS: -I/usr/local/opt/gettext/include
It says in the above output that brew doesn't symlink the library, which might explain why install.packages can't find it. What did the trick was adding a library path into ~/.R/Makevars like so:
PKG_LIBS=-L/usr/local/Cellar/gettext/0.18.3.2/lib

This answer is to modify Giupo's answer as it contains a typo but I believe it is important enough to be more prominent than a comment. The solution is a very effective way to install the Rserve package from Homebrew without causing broader problems on OSX:
flags="CPPFLAGS=-I/usr/local/opt/gettext/lib LDFLAGS=-L/usr/local/opt/gettext/include"
install.packages('Rserve', configure.args=flags)
To reduce namespace pollution even more can wrap in local:
local({
flags="CPPFLAGS=-I/usr/local/opt/gettext/lib LDFLAGS=-L/usr/local/opt/gettext/include"
install.packages('Rserve', configure.args=flags)})

I wanna add my 2 cents to the quest by suggesting a less intrusive (meaning: no files/env changes for the user bringing unwanted side-effects in the future)
Take note of LDFLAGS and CPPFLAGS by reinstalling gettext as #cbare did and pass them to install.packages (inside R) with the configure.args param:
flags="LDFLAGS=-L/usr/local/opt/gettext/lib CPPFLAGS=-I/usr/local/opt/gettext/include"
install.packages('Rcpp', configure.args=flags)
This should do the trick (it worked for me while struggling with the same problem installing Rserve).

This worked fine for me:
brew link gettext --force

Related

Unable to install a package on R

I'm getting an issue when I try to install Bioconductor for R. I've searched everywhere for solutions however nothing is really working for me. Please, any advice?
The downloaded binary packages are in
/var/folders/74/y92tqhzj0l98l6syjjl7vtcr0000gn/T//RtmpNYOkbZ/downloaded_packages
Old packages: 'nlme'
Update all/some/none? [a/s/n]:
a
Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6:
cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘nlme’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘nlme’
trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-144.tar.gz'
Content type 'application/x-gzip' length 778660 bytes (760 KB)
==================================================
downloaded 760 KB
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fPIC -Wall -g -O2 -c chol.f -o chol.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c corStruct.c -o corStruct.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c gnls.c -o gnls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c matrix.c -o matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nlOptimizer.c -o nlOptimizer.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nlme.c -o nlme.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nlmefit.c -o nlmefit.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pdMat.c -o pdMat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pythag.c -o pythag.o
gfortran -fPIC -Wall -g -O2 -c rs.f -o rs.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [nlme.so] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nlme’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nlme’
The downloaded source packages are in
‘/private/var/folders/74/y92tqhzj0l98l6syjjl7vtcr0000gn/T/RtmpNYOkbZ/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘nlme’ had non-zero exit status
I've tried to reinstall R and it didn't work.
The code I am using to install bioconductor is:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.10")
I had the same problem. This happens since I updated to R4.0. I've seen that in Mac (and maybe Windows) can be related to missing Rtools. In Linux, I tried to install the package from other mirrors (this solved my problem in the past), but no success. Finally, I realized that the initial error is "make: gfortran: No such file or directory"
Therefore, I installed gcc & gcc-fortran and that solved it!
In Manjaro, Arch linux:
pacman -S gcc
pacman -S gcc-fortran
In Debian or Ubuntu should be:
sudo apt update
sudo apt install build-essential
sudo apt-get install manpages-dev
gcc --version
Check here for more information:
https://linuxize.com/post/how-to-install-gcc-compiler-on-debian-10/
https://linuxize.com/post/how-to-install-gcc-compiler-on-ubuntu-18-04/
https://linuxhostsupport.com/blog/how-to-install-gcc-on-ubuntu-18-04/
Because now the new version of Bioconductor is BiocManager, try to use this one: install.packages("BiocManager")
Apparently, it is trying to install package nlme as a dependency and fails doing that. Did you try installing that one manually before installing Bioconductor ? That could give us more info on the issue.
Just as a heads up for someone who encounters similar issue. I was presented with a choice of installing a binary or compiling from scratch. As I chose compilation option, it was failing to install nlme. However, installation of binary was successful and there was a minor version difference between the source and the binary.

Error when installing xml2 package on Mavericks

I'm trying to install devtools package in R, and as its dependency xml2 needs to be installed, but I'm getting the following error message.
> install.packages("xml2")
Installing package into ‘/Users/xlong3/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/xml2_0.1.2.tar.gz'
Content type 'application/x-gzip' length 74808 bytes (73 KB)
==================================================
downloaded 73 KB
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/Users/xlong3/anaconda/include/libxml2
Using PKG_LIBS=-L/Users/xlong3/anaconda/lib -lxml2 -lz -liconv -lm
** libs
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c connection.cpp -o connection.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml2_doc.cpp -o xml2_doc.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml2_init.cpp -o xml2_init.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml2_namespace.cpp -o xml2_namespace.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml2_node.cpp -o xml2_node.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml2_url.cpp -o xml2_url.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml2_xpath.cpp -o xml2_xpath.o
clang++ -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/Users/xlong3/anaconda/include/libxml2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I"/Users/xlong3/Library/R/3.2/library/Rcpp/include" -I"/usr/local/lib/R/3.2/site-library/BH/include" -fPIC -g -O2 -c xml_push.cpp -o xml_push.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -o xml2.so RcppExports.o connection.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_url.o xml2_xpath.o xml_push.o -L/Users/xlong3/anaconda/lib -lxml2 -lz -liconv -lm -F/usr/local/Cellar/r/3.2.2_1/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation
installing to /Users/xlong3/Library/R/3.2/library/xml2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/xlong3/Library/R/3.2/library/xml2/libs/xml2.so':
dlopen(/Users/xlong3/Library/R/3.2/library/xml2/libs/xml2.so, 6): Library not loaded: libxml2.2.dylib
Referenced from: /Users/xlong3/Library/R/3.2/library/xml2/libs/xml2.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/xlong3/Library/R/3.2/library/xml2’
The downloaded source packages are in
‘/private/tmp/RtmpJc4WKq/downloaded_packages’
Warning message:
In install.packages("xml2") :
installation of package ‘xml2’ had non-zero exit status
>
> version
_
platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
version.string R version 3.2.2 (2015-08-14)
nickname Fire Safety
The problem is that 'pkg-config' is looking specifically for 'libxml2.pc' and the file that you have installed is named, "libxml-2.0.pc". If you manually create a symbolic link between the existing file and the one pkg-config expects, it should resolve that error.
Something like this (done in the same directory as the file) should work
$ ln -s libxml-2.0.pc libxml2.pc
I'm not sure how should I proceed from the following situation:
pkg-config --libs --cflags libxml2
Package libxml2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml2' found
brew ls libxml2
/usr/local/Cellar/libxml2/2.9.2/bin/xml2-config
/usr/local/Cellar/libxml2/2.9.2/bin/xmlcatalog
/usr/local/Cellar/libxml2/2.9.2/bin/xmllint
/usr/local/Cellar/libxml2/2.9.2/include/libxml2/ (47 files)
/usr/local/Cellar/libxml2/2.9.2/lib/libxml2.2.dylib
/usr/local/Cellar/libxml2/2.9.2/lib/cmake/libxml2/libxml2-config.cmake
/usr/local/Cellar/libxml2/2.9.2/lib/pkgconfig/libxml-2.0.pc
/usr/local/Cellar/libxml2/2.9.2/lib/ (3 other files)
/usr/local/Cellar/libxml2/2.9.2/share/aclocal/libxml.m4
/usr/local/Cellar/libxml2/2.9.2/share/doc/ (153 files)
/usr/local/Cellar/libxml2/2.9.2/share/gtk-doc/ (55 files)
/usr/local/Cellar/libxml2/2.9.2/share/man/ (4 files)
Try to change your CRAN mirror

R Rcpp install error in R 3.1.0

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...

Package install error: compilation failed

I recently updated R to 3.1.0. I tried to move my packages over to 3.1 inside the R.Framework (I'm running OSX Mavericks) and somehow made a mess of it, so did a complete uninstall of everything before a clean install.
When reinstalling packages I had no issues until I hit the forecast package which yields the following error:
package ‘forecast’ is available as a source package but not as a binary
Warning in install.packages :
package ‘forecast’ is not available (for R version 3.1.0)
I actually had R 3.1.0 and both forecast and hts working together prior to the reinstall so I suspect the problem stems from something I've done, rather than a compatibility problem.
I ran the following to see if I could unearth some more details about the install fail: install.packages("forecast", type = "source", verbose = T, quiet = F)
The output of which is a little beyond me, but may be of help in diagnosis:
system (cmd0): /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL
trying URL 'http://cran.rstudio.com/src/contrib/forecast_5.3.tar.gz'
Content type 'application/x-gzip' length 150395 bytes (146 Kb)
opened URL
==================================================
downloaded 146 Kb
foundpkgs: forecast, /var/folders/0y/_13fkvws0tn5xh4m8wsymkdh0000gp/T//RtmpzTzSpG/downloaded_packages/forecast_5.3.tar.gz
files: /var/folders/0y/_13fkvws0tn5xh4m8wsymkdh0000gp/T//RtmpzTzSpG/downloaded_packages/forecast_5.3.tar.gz
* installing *source* package ‘forecast’ ...
** package ‘forecast’ successfully unpacked and MD5 sums checked
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c calcBATS.cpp -o calcBATS.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c calcTBATS.cpp -o calcTBATS.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c etsTargetFunction.cpp -o etsTargetFunction.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c etsTargetFunctionWrapper.cpp -o etsTargetFunctionWrapper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c etscalc.c -o etscalc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c etspolyroot.c -o etspolyroot.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c makeBATSMatrices.cpp -o makeBATSMatrices.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c makeTBATSMatrices.cpp -o makeTBATSMatrices.o
makeTBATSMatrices.cpp:11:6: warning: unused variable 'lengthSeasonal' [-Wunused-variable]
int lengthSeasonal = 0;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c updateMatrices.cpp -o updateMatrices.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c updateTBATSMatrices.cpp -o updateTBATSMatrices.o
updateTBATSMatrices.cpp:38:10: warning: unused variable 'gammaVector' [-Wunused-variable]
double *gammaVector;
^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o forecast.so calcBATS.o calcTBATS.o etsTargetFunction.o etsTargetFunctionWrapper.o etscalc.o etspolyroot.o makeBATSMatrices.o makeTBATSMatrices.o updateMatrices.o updateTBATSMatrices.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [forecast.so] Error 1
ERROR: compilation failed for package ‘forecast’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/forecast’
Warning in install.packages :
installation of package ‘forecast’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/0y/_13fkvws0tn5xh4m8wsymkdh0000gp/T/RtmpzTzSpG/downloaded_packages’
I'd really appreciate some help here. Much of the code I've been working on lately relies on functions in forecast.
Here is what I did (RcppArmadillo Compile Errors on OS X Mavericks)
Install gfortran from brew (if you don't have brew, Google it. Installation is straightforward):
brew install gfortran
If it's installed, upgrade to latest with:
brew upgrade gfortran
Then do one of the following:
ln -s /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.* /usr/local/lib/
or add this line to the ~/.R/Makevars file:
FLIBS=-L/usr/local/Cellar/gfortran/4.8.2/gfortran
I did the second option.
Now run install.packages("forecast", type = "source") again and it should work.
In my case, I was trying to install the latest version of {forecast} package with devtools::install_github("robjhyndman/forecast") and had the similar error.
Then, although I am not sure if what I did is right, following mchangun's answer I did as follows and the error was resolved:
brew upgrade gcc
Error: gcc 5.2.0 already installed
gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1
Apple LLVM version 7.0.0 (clang-700.1.76)
Target: x86_64-apple-darwin15.0.0
Thread model: posix
ls /usr/local/Cellar/gcc
4.9.2 4.9.2_1 5.2.0
Add the line FLIBS=-L/usr/local/Cellar/gcc/5.2.0 to the ~/.R/Makevars file
Run devtools::install_github("robjhyndman/forecast") and it worked.
Terminal
brew install gcc
gcc --version
ls /usr/local/Cellar/gcc
6.3.0_1
sudo vi /Library/Frameworks/R.framework/Resources/etc/Makeconf
Add the line FLIBS=-L/usr/local/Cellar/gcc/6.3.0_1
Rstudio:
install.packages("forecast"
Download gfortran from https://gcc.gnu.org/wiki/GFortranBinariesMacOS
sudo rm -r /usr/local/gfortran /usr/local/bin/gfortran
Then install gfortran
sudo vi /Library/Frameworks/R.framework/Resources/etc/Makeconf
change all gfortran-4.8 to gfortran
FC = gfortran
FCFLAGS = -Wall -g -O2 $(LTO)
FCLIBS =
F77 = gfortran
F77_VISIBILITY =
FFLAGS = -g -O2 $(LTO)
FLIBS = -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm
change above FLIBS to the below
FLIBS = -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
To install gfortran, use
brew cask install gfortran

R shiny Ubuntu 12.04 installation instructions fail when installing Rcpp needed by R shiny library in R 3.0.2

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.

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