I'm used to R but I'm a complete beginner in C++. I'm having a hard time installing GSL to use it with RcppGSL in R in order to refine a package comprising C++ code. I downloaded the latest GSL version, unpacked it to C:/GSL, set the environmental variable LIB_GSL to C:/GSL and the PATHtoC:/GSL/bin.
Like I said, I want to refine an existing package. I've forked and pulled the latest version of the package in question from github. My primary goal is simply to be able to use and refine the package. However, when I'm trying to make a source package out of the source files I get the following Error:
Installing to library 'C:/Users/Simon/Documents/R/win-library/3.1'
* installing *source* package 'Rflim' ...
** libs
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/Simon/Documents/R/win-library/3.1/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -IC:/Users/Simon/Documents/R/win-library/3.1/Rcpp/include -I/usr/local/include -I C:/Users/Simon/Documents/R/win-library/3.1/RcppGSL/include -O2 -Wall -mtune=core2 -c flim.cpp -o flim.o
In file included from C:/Users/Simon/Documents/R/win-library/3.1/RcppGSL/include/RcppGSL.h:23:0,
from flim.cpp:1:
C:/Users/Simon/Documents/R/win-library/3.1/RcppGSL/include/RcppGSLForward.h:26:29: fatal error: gsl/gsl_vector.h: No such file or directory
compilation terminated.
make: *** [flim.o] Error 1
Warnung: Ausf�hrung von Kommando 'make -f "Makevars" -f "C:/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-31~1.2/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="Rflim.dll" WIN=64 TCLBIN=64 OBJECTS="flim.o"' ergab Status 2
ERROR: compilation failed for package 'Rflim'
* removing 'C:/Users/Simon/Documents/R/win-library/3.1/Rflim'
Exited with status 1.
Sorry, there are a couple of german words in there:
Warnung: Ausf�hrung von Kommando==Warning:executing command
What I realize is that R is trying to access the GSL library via the RcppGSL path. Is that correct? Shouldn't it go directly to C:/GSL instead? I also realized that R is trying to go to paths from both Rcpp as well as RcppGSL and I don't see why...
I would appreciate any clarification or suggestions on how to solve the problem.
Thank you!!!
Please install the prebuild GSL version for R on Windows from the support site provided by Prof Ripley and then set these values accordingly in src/Makevars.win
## This assumes that the LIB_GSL variable points to working GSL libraries
PKG_CPPFLAGS=-I$(LIB_GSL)/include -I../inst/include
PKG_LIBS=-L$(LIB_GSL)/lib -lgsl -lgslcblas
either directly, or set LIB_GSL accordingly.
This is how CRAN builds the package, and it evidently works.
Related
I'm trying to use packages that require Rcpp in R on my M1 Mac, which I was never able to get up and running after purchasing this computer. I updated it to Monterey in the hope that this would fix some installation issues but it hasn't. I tried running the Rcpp check from this page but I get the following error:
> Rcpp::sourceCpp("~/github/helloworld.cpp")
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_4.so] Error 1
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppArmadillo/include" -I"/Users/afredston/github" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helloworld.cpp -o helloworld.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sourceCpp_4.so helloworld.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in Rcpp::sourceCpp("~/github/helloworld.cpp") :
Error 1 occurred building shared library.
I get that it can't "find" gfortran. I installed this release of gfortran for Monterey. When I type which gfortran into Terminal, it returns /opt/homebrew/bin/gfortran. (Maybe this version of gfortran requires Xcode tools that are too new—it says something about 13.2 and when I run clang --version it says 13.0—but I don't see another release of gfortran for Monterey?)
I also appended /opt/homebrew/bin: to PATH in R so it looks like this now:
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Applications/RStudio.app/Contents/MacOS/postback"
Other things I checked:
Xcode command line tools is installed (which clang returns /usr/bin/clang).
Files ~/.R/Makevars and ~/.Renviron don't exist.
Here's my session info:
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1 RcppArmadillo_0.10.7.5.0
[4] Rcpp_1.0.7
Background
Currently (2023-02-20), CRAN builds R 4.2 binaries for Apple silicon using Apple Clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.
If you obtain R from CRAN (i.e., here), then you need to replicate CRAN's compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.
A further complication is the fact that Apple Clang doesn't support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself, all R packages, and all external libraries from sources with LLVM Clang, which does support OpenMP, but that approach is onerous and "for experts only".
There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also "for experts only", but it works on my machine and is much simpler than learning to build R and other libraries yourself.
Instructions for obtaining a working toolchain
Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.
I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you've already taken, though you might find a fresh start helpful.
I've tested these instructions on a machine running Big Sur, but they should also work on Monterey and Ventura.
Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.
Run
$ sudo xcode-select --install
in Terminal to install the latest release version of Apple's Command Line Tools for Xcode, which includes Apple Clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.
Download the GNU Fortran binary provided here and install by unpacking to root:
$ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK
The last command updates a symlink inside of the installation so that it points to the SDK inside of your Command Line Tools installation.
Download an OpenMP runtime suitable for your Apple Clang version here and install by unpacking to root. You can query your Apple Clang version with clang --version. For example, I have version 1300.0.29.3, so I did:
$ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /
After unpacking, you should find these files on your system:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
Test that you are able to use R to compile a C or C++ program with OpenMP support while linking relevant libraries from the GNU Fortran installation (indicated by the -l flags in the output of R CMD CONFIG FLIBS).
The most transparent approach is to use R CMD SHLIB directly. In a temporary directory, create an empty source file omp_test.c and add the following lines:
#ifdef _OPENMP
# include <omp.h>
#endif
#include <Rinternals.h>
SEXP omp_test(void)
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\n");
#endif
return R_NilValue;
}
Compile it:
$ R CMD SHLIB omp_test.c $(R CMD CONFIG FLIBS)
Then call the compiled C function from R:
$ R -e 'dyn.load("omp_test.so"); invisible(.Call("omp_test"))'
OpenMP threads available: 8
If the compiler or linker throws an error, or if you find that OpenMP is still not supported, then one of us has made a mistake. Please report any issues.
Note that you can implement the same test using Rcpp, if you don't mind installing it:
library(Rcpp)
registerPlugin("flibs", Rcpp.plugin.maker(libs = "$(FLIBS)"))
sourceCpp(code = '
#ifdef _OPENMP
# include <omp.h>
#endif
#include <Rcpp.h>
// [[Rcpp::plugins(flibs)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\\n");
#endif
return;
}
')
omp_test()
OpenMP threads available: 8
References
Everything is a bit scattered:
R Installation and Administration manual [link]
Writing R Extensions manual [link]
R for macOS Developers web page [link]
I resolved this issue by adding a path to the homebrew installation of gfortran to my ~/.R/Makevars following these instructions: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran
I just avoided the issue until MacOS had things working more smoothly. so I either Windows Developer Virtual Machine (VM) or run my code development in another environment. I'm not too impressed with the updated and "faster" chipset, but that it doesn't work with much. Slow to implement and work-a-rounds often are a must.
Tested the following process for making multithread data.table work in a M2 MacBook Pro (macOS Monterey)
Steps are mostly the same with this answer by the user inferator.
Download and install R from CRAN
Download and install RStudio with developer tools
Run the following commands in terminal to install OpenMP
curl -O https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
sudo tar fvxz openmp-12.0.1-darwin20-Release.tar.gz -C /
Add compiler flags to connect clan w/ OpenMP. In terminal, write the following:
cd ~
mkdir .R
nano .R/Makevars
Inside the opened Makevars file paste the following lines. Once finished, hit command+O and then Enter to save. Do a command+X to close the editor.
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Download and run the installer for gfortran by downloading gfortran-ARM-12.1-Monterey.dmg from the respective GitHub repo
This concludes the steps regarding enabling OpenMP and (hopefully) Rcpp in R under a M2 chip system.
Now, for testing that everything works with data.table I did the following
Open RStudio and run
install.packages("data.table", type = "source")
If everything is done correctly, the package should compile without any errors and return the following when running getDTthreads(verbose = TRUE):
OpenMP version (_OPENMP) 201811
omp_get_num_procs() 8
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 8
OMP_THREAD_LIMIT unset
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 4 threads with throttle==1024. See ?setDTthreads.
[1] 4
To be precise, I'm attempting to run this excellent project: https://github.com/ppwwyyxx/panorama
I'm using a modern mac.
The issue is that I can't seem to get my computer to properly include the MTL library. I'm stuck with the endless error of:
$ make
[cc] matrix.cc ...
matrix.cc:5:10: fatal error: 'boost/numeric/mtl/mtl.hpp' file not found
#include <boost/numeric/mtl/mtl.hpp>
^
1 error generated.
make: *** [obj/matrix.o] Error 1
I've tried cmake. I've downloaded both the boost and mtl4 libraries. I've put them in my /usr/local/include directory. Nothing seems to be working.
Any advice would be excellent, thank you!
Try to modify the Makefile in src and add this on the line 7 of the Makefile:
-I/usr/local/include
I've built opencv 3.0 from source and can run a few sample apps, build against the headers ok so I presume it's installed successfully.
I'm also using python3 and I now go to install and build caffe. I set a few variables in Makefile.config as I'm using the CPU due to having an AMD GPU and also Anaconda.
When I run make all I get this error:
$ make all
CXX/LD -o .build_release/examples/cpp_classification/classification.bin
/usr/bin/ld: .build_release/examples/cpp_classification/classification.o: undefined reference to symbol '_ZN2cv6imreadERKNS_6StringEi'
//usr/local/lib/libopencv_imgcodecs.so.3.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:565: recipe for target '.build_release/examples/cpp_classification/classification.bin' failed
make: *** [.build_release/examples/cpp_classification/classification.bin] Error 1
from searching I think this is something to do with using openCV 3 but I'm not sure where to start looking for a solution. Any help?
And yes I'm one of the horde of inexperienced users looking to fiddle with the Google Inception learning technique.
You can also add the opencv_imgcodecs to the MakeFile in line 187, see this pull.
It could be that you are using OpenCV version 3. If yes just uncomment the following line in your Makefile.config:
# OPENCV_VERSION := 3
So it will look like
OPENCV_VERSION := 3
You could verify the version currently in use by doing:
$ python
>>> import cv2
>>> cv2.__version__
'3.1.0-dev'
The problem report is very clear. There is a problem with linking library libraries.The reason may be the difference between 3.0 and 2.x.
You need to add
opencv_core opencv_highgui opencv_imgproc opencv_imgcodecs
into LIBRARIES +=.
I used cmake instead with the -DBUILD_TIFF=ON flag and got a successful build.
You can edit Makefile.config with the following 2 lines like this and it worked for me. Note that your opencv path must be set before default path!
INCLUDE_DIRS := $(PYTHON_INCLUDE) /home/young/Soft/openCV-3.3.1/include \
/usr/local/include /usr/include/hdf5/serial
LIBRARY_DIRS := $(PYTHON_LIB) /home/young/Soft/openCV-3.3.1/lib \
/usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/hdf5/serial
A quick workaround is to add -lopencv_imgcodecs flag when you're compiling your code.
This worked for me:
g++ test.cpp -o test <Some flags> -lopencv_imgcodecs
I am trying to build a user package that has been building fine on my colleague's windows box which has R 2.15.1 installed. My config is:
R 2.15.3, RTools 3.0, Rcpp 0.10.4, RcppArmadillo 0.3.920.1, RStudio 0.97.551
This is the first compilation instance when I run "R CMD INSTALL mypackage". indfunForecast.cpp is one of the source files within the package.
>g++ -m32 -I"D:/PROGRA~1/R/R-215~1.3/include" -DNDEBUG
-I"D:/R/win-library/2.15/Rcpp/include" -I"D:/R/win-library/2.15/RcppArmadillo/include"
-I"d:/RCompile/CRANpkg/extralibs64/local/include"
-O2 -Wall -mtune=core2
-c indfunForecast.cpp -o indfunForecast.o
The error messages that follow are:
In file included from D:/R/win-library/2.15/RcppArmadillo/include/RcppArmadillo.h:30:0,
from indfunForecast.cpp:16:
D:/R/win-library/2.15/RcppArmadillo/include/RcppArmadilloForward.h:99:33:
error: 'ConstReferenceInputParameter' is not a template
D:/R/win-library/2.15/RcppArmadillo/include/RcppArmadilloForward.h:100:33:
error: 'ReferenceInputParameter' is not a template
D:/R/win-library/2.15/RcppArmadillo/include/RcppArmadilloForward.h:101:33:
error: 'ConstInputParameter' is not a template
Any idea what's going on???
Appreciate your help.
Sachko
You have the newest RcppArmadillo which needs the newest Rcpp, which you don't have (and I won't bore you with the details, but it is CRAN-related).
Install Rcpp 0.10.5 from source, and things should work.
I'm trying to call R from c++ on linux via RInside, I compiled R-2.15.1 from source with gcc version 4.5.3 (Debian 4.5.3-1) , I don't have sudo rights to use apt-get install. I'm using OpenBlas and a system optimized lapack. The blas and lapack libraries work fine for many scalapack applications
I installed R with
./configure --with-blas="-I/lib/OpenBLAS-v0.2.3-0/xianyi-OpenBLAS-48f075c/install/include -L/lib/OpenBLAS-v0.2.3-0/xianyi-OpenBLAS-48f075c/install/lib -lopenblas -lgfortran" --with-lapack="/usr/lib/liblapack.so -lgfortran" --enable-BLAS-shlib=yes --enable-R-shlib --enable-R-static-lib --prefix= .
which installed and runs fine,I ran make check with no errors, also all the packages (Rcpp and RInside) installed fine..
however when i use the given RInside makefile , the basic hello world example from /standard/rinside_sample0.cpp compiles! but it does not run and i get the following error
./rinside_sample0: error while loading shared libraries: libRblas.so: cannot open shared object file: No such file or directory
the file libRblas.so exists and is in the R/lib folder,
when i try to link it manually with the g++ command the make file creates or linking as follows i get a segmentation fault
/R/lib/libRblas.so ./hello_world
Segmentation fault
EDIT: heres how the example make file tries to compile an example, (which compiles fine) but won't run with the above missing libRblas.so error
g++ -I/nfs/user03/jimmie21/libs/lib64/R/include -I/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/include -I/nfs/user03/jimmie21/libs/lib64/R/library/RInside/include -g -O2 -Wall -I/usr/local/include hello_world.cpp -L/nfs/user03/jimmie21/libs/lib64/R/lib -lR -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRblas -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRlapack -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRblas -L/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/lib -L/nfs/user03/jimmie21/libs/lib64/R/library/RInside/lib -lRInside -Wl,-rpath,/nfs/user03/jimmie21/libs/lib64/R/library/RInside/lib -o hello_world
Couple of things:
Reproducible examples, please
You have a non-standard setup
With the script from 1), try it on a standard setting as that is how Rcpp / RInside get developed and tested (on Ubuntu / Debian)
The Rcpp test suite now contains almost 800 unit tests from around 350 unit test functions. These do not seg.fault, so the issue is at your end. Similarly, RInside has dozens of examples in the four examples/ subdirectories. This also works.
It may be as easy as tweaking the Makefile / Makevars files to make sure you get your libraries in all cases. But we can't tell as there is nothing reproducible here.
Edit If you want to link with libRblas.so then you have a completely non-standard setup as the R packages for Debian / Ubuntu as use the external BLAS. Again, not an RInside issue.
I fixed the problem by adding the R install path lib ../R/lib: to the beginning of LD_LIBRARY_PATH after that all the examples compiled and run fine