R has been installing packages just fine, but suddenly – I can't think of anything relevant that I modified or uninstalled –
it can't find gcc when I run R CMD check in the command prompt, or devtools::check() in the R console; it delivers the following error:
* installing *source* package 'PkgName' ...
** libs
C:/MinGW/bin/gcc -I"C:/PROGRA~1/R/R-34~1.2/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c PkgName-init.c -o PkgName-init.o
C:/MinGW/bin/gcc: not found
I want R to find gcc in C:\Rtools-3.4\mingw_32\bin, which is the location specified in the system PATH; strsplit(Sys.getenv('PATH'), ';') gives
[...]
[4] "c:\\Rtools-3.4\\bin"
[5] "c:\\Rtools-3.4\\mingw_32\\bin"
[7] "C:\\Program Files\\R\\R-3.4.2\\bin\\i386"
[8] "C:\\Program Files\\R\\R-3.4.2\\bin"
[9] "C:\\Program Files\\MiKTeX 2.9\\miktex\\bin\\x64\\"
[...]
How can I tell R not to look in the non-existent directory C:\MinGW, and instead to follow the PATH?
I don't want to install a second copy of MinGW there, as this causes other issues.
R uses a BINPREF variable to locate executables:
the location of the gcc executable is given by CC = $(BINPREF)gcc $(M_ARCH)
In my case, BINPREF was being set by C:/Users/MYUSERNAME/Documents/.R/Makevars. Deleting the contents of this file removed the incorrect location.
It is also worth checking the file $RPATH/etc/i386/Makeconf, which will be re-created with each new installation of R. Note the line
BINPREF ?= c:/Rtools/mingw_32/bin/, which (via the ?= operator) will set the value of BINPREF if it is not already set, as it was in the Makevars file mentioned above.
Related
I followed these instructions to get R to use an alternative GCC compiler I have installed on my MacOS.
Building R Packages using Alternate GCC
As basic internet research will tell you (as it told me), the default compiler on the MacOS is clang / clang++, which doesn't work for my specific needs. I installed gcc-8.1 and dependencies in order to enable OpenMP on my machine. OpenMP works when I run gcc-8.1 with a standalone tmp.c file with pragma omp commands in it.
However, when I go back to R to try to run the same code using Rcpp R package, I run into some problems.
The below is what is in my Makevars file located at ~/.R/Makevars on my machine.
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CFLAGS)
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
CC=gcc-8.1
CXX=g++-8.1
CXX98=g++-8.1
CXX11=g++-8.1
CXX14=g++-8.1
CXX17=g++-8.1
This now correctly activates my alternative complier in lieu of clang++. I can install my package with OpenMP functionality by using a Terminal and using the R commands below.
cd /folder/where/package/is
R CMD build packageName
R CMD build packageName_1.0.tar.gz
However, I cannot install the package using devtools and roxygen2, which I would prefer. Specifically, the devtools function has_devel() fails.
has_devel()
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD SHLIB foo.c
gcc-8.1 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c foo.c -o foo.o
/bin/sh: gcc-8.1: command not found
make: *** [foo.o] Error 127
Error: Command failed (1)
Here is the code I use when trying to install updates using devtools / roxygen2.
require(Rcpp)
require(devtools)
require(roxygen2)
setwd("/folder/where/package/is")
compileAttributes(pkgdir = "/folder/where/package/is")
install("packageName/")
I suspect the pop up window I get from RStudio is directly related to has_devel() function failing to be TRUE. If I revert back to using the default compiler, clang++ (by deleting my Makevars at ~/.R/Makevars), has_devel() returns TRUE and RStudio doesn't ask if I want to install developer command line tools. How can I get around this hiccup with installing a package I am developing using devtools instead of installing from source each time?
RcppArmadillo 0.8.400.0.0 works just fine on my computer, both from sourceCpp and cxxfunction. Now I want to upgrade to 0.8.500.0, which requires compilation from source. Then I got the error
ccache /usr/local/clang6/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -I/Applications/CPLEX_Studio128/cplex/include -I/Applications/CPLEX_Studio128/concert/include -DIL_STD -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
RcppArmadillo.cpp:22:10: fatal error: 'RcppArmadillo.h' file not found
#include <RcppArmadillo.h>
^~~~~~~~~~~~~~~~~
1 error generated.
I got this error whether I ran install.packages("RcppArmadillo") in RStudio or in R console outside RStudio. My compiler is clang4, and I have no problem installing RcppParallel or compiling my own Rcpp code that uses RcppArmadillo and RcppParallel. R version: 3.5.0, MacOS High Sierra.
Edit: I looked at https://github.com/RcppCore/RcppArmadillo/issues/143, which is very relevant. I did install clang6 and gfortran 6.1, both downloaded from the CRAN website. I also changed the .R/Makevars file to reflect the changes to clang6. I have also installed ccache as suggested, to make compilation faster. Here's my Makevars:
F77 = /usr/local/gfortran/bin/gfortran
FC = $F77
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=ccache /usr/local/clang6/bin/clang
SHLIB_CXXLD=ccache /usr/local/clang6/bin/clang++
CXX= ccache /usr/local/clang6/bin/clang++ -Wall
CXX1X= ccache /usr/local/clang6/bin/clang++
CXX98= ccache /usr/local/clang6/bin/clang++
CXX11= ccache /usr/local/clang6/bin/clang++
CXX14= ccache /usr/local/clang6/bin/clang++
CXX17= ccache /usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib
From the outputs in the R console when I was installing the package (added to the error message above), I can tell that clang6 was used for compilation. I also found the downloaded RcppArmadillo tarball, unpacked it, and ran ./configure from the command line. Nothing seemed wrong there; no config.log file was generated. This doesn't seem to be a configuration problem. Then I still got the exact same error when trying to install the package in R, after configuration, in libs. I also didn't get any message about -fopenmp. It seems that my problem is a bit different from that in the GitHub ticket.
R 3.5.x requires clang6 and adding clang6 to your system PATH variable.
Steps:
x Download and install the clang-6.0.0.pkg official package from CRAN.
x Delete your ~/.R/Makevars as it is likely set to use clang4. To do this, open Terminal and type:
sudo rm ~/.R/Makevars
x Then add to your ~/.bash_profile the following:
if [ -d "/usr/local/clang6/bin" ] ; then
export PATH="/usr/local/clang6/bin:$PATH"
fi
Note: If you are using a shell other than bash you will need to add the above into the appropriate file, e.g. for zsh add to ~/.zshrc, as this was not implemented in the official installer.
I should have a few cycles to finish writing a new unofficial Rtools installer a bit later. See: https://github.com/coatless/r-macos-rtools/issues/7
Note: Alternatively, you can remove the paths individual with
sudo vi ~/.R/Makevars
Pressing I to enter insert mode, deleting lines with clang4 in the path, and then pressing ESC + :wq to write changes to file.
Never mind, this problem went away with version 0.8.600. Later, this problem appeared again when I upgraded to RcppArmadillo 0.9.100.5.0. Somehow I only got this error when building from source; I downloaded the binary manually from the CRAN website, and used R CMD INSTALL to install the prebuilt version, and it worked; somehow R doesn't seem to know that there is a binary available for the newest version.
I did install clang6 and modified .R/Makevars to use clang6, but the same problem persisted; probably something else caused the problem.
I was looking at the verbose=TRUE when I tried to sourceCpp a Rcpp file. The last output is:
DIR: C:/Users/xyz/AppData/Local/Temp/RtmpmielLn/sourcecpp_226416891d0e
C:/PROGRA~1/R/R-31~1.0/bin/x64/R CMD SHLIB -o "sourceCpp_22129.dll" --preclean "myfile.cpp"
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.0/include" -DNDEBUG -I"C:/Users/xyz/Documents/R/win-library/3.1/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c myfile.cpp -o myfile.o
g++ -m64 -shared -s -static-libgcc -o sourceCpp_22129.dll tmp.def myfile.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.0/bin/x64 -lR
I have a few questions regarding this:
the 1nd g++ command refers to -I"d:/RCompile/CRANpkg/extralibs64/local/include" and the 2nd command refers to -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 and -Ld:/RCompile/CRANpkg/extralibs64/local/lib . But I don't have a D: drive, or a RCompile folder anywhere. What do these things refer to?
I tried to manually run the 1st g++ which ran file and created myfun.o file, but when I tried to manually run the 2nd g++ it gave me an error saying that it couldn't find the tmp.def file. I couldn't find the tmp.def file anywhere on my drives. Where would this tmp.def file located?
I looked under the hood of sourceCpp function. if I directly run the definition of cmd in the sourceCpp function: C:/PROGRA~1/R/R-31~1.0/bin/x64/R CMD SHLIB -o "sourceCpp_22129.dll" --preclean "myfile.cpp" on Windows' command window , I noticed that it does not include -I"C:/Users/xyz/Documents/R/win-library/3.1/Rcpp/include" and the R CMD SHLIB gives me an error.
How does the system(cmd, ..) within the sourceCpp function include this? The value of the cmd variable in the sourceCpp didn't include -I"C:/Users/xyz/Documents/R/win-library/3.1/Rcpp/include"
the 1nd g++ command refers to -I"d:/RCompile/CRANpkg/extralibs64/local/include" and the 2nd command refers to -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 and -Ld:/RCompile/CRANpkg/extralibs64/local/lib . But I don't have a D: drive, or a RCompile folder anywhere. What do these things refer to?
AFAIK these are left in as part of the CRAN R Windows distribution; when R binaries are built on Windows they use something in these library paths on the build servers (but stay baked into R anyhow). You can safely ignore it, but it is a bit odd. Unused / non-existent directories passed through gcc / g++ are just ignored.
I tried to manually run the 1st g++ which ran file and created myfun.o file, but when I tried to manually run the 2nd g++ it gave me an error saying that it couldn't find the tmp.def file. I couldn't find the tmp.def file anywhere on my drives. Where would this tmp.def file located?
tmp.def, as it sounds, is a temporary definition file created by R CMD SHLIB on Windows. If you just re-run what you see it does not get generated, so I suppose R does something behind the curtains to generate it. If you are curious about where it's generated, see share/make/winshlib.mk in the R sources.
I looked under the hood of sourceCpp function. if I directly run the definition of cmd in the sourceCpp function: C:/PROGRA~1/R/R-31~1.0/bin/x64/R CMD SHLIB -o "sourceCpp_22129.dll" --preclean "myfile.cpp" on Windows' command window , I noticed that it does not include -I"C:/Users/xyz/Documents/R/win-library/3.1/Rcpp/include" and the R CMD SHLIB gives me an error.
This is because sourceCpp is setting the appropriate environment flags behind the scenes for you as well -- in this case, the CXXFLAGS environment variable. This gets automatically done on package installs as well when the LinkingTo: entry is specified in the DESCRIPTION file.
I had a very similar g++ compilation command as posted in the question, and the compilation of a very simple C function didn't work for me.
The reason it didn't work is the following option shown in the g++ command:
-I"d:/RCompile/CRANpkg/extralibs64/local/include"
which adds an include directory on a drive that does not exist on my computer. Apparently non-existent directories listed in the -I option are ignored by g++ (as stated by Kevin Ushey) but this seems not to be the case for non-existent drives.
The error message I received was that the sdtlib.h header file was not found:
C:/PROGRA~1/R/R-32~1.0/include/R.h:28:20: fatal error:
d:/RCompile/r-compiling/local/local320/include/stdlib.h: Input/output
error #include
In order to remove the offending -I option from the g++ command I had to edit the Makeconf file located in $(R_HOME}/etc$(R_ARCH) (in my case C:\Program Files\R\R-3.2.0\etc\x64) and comment out the line:
LOCAL_SOFT = d:/RCompile/r-compiling/local/local320
I am trying to create my first package using the instructions on the hadley devtools wiki. I am using Windows 7 Professional, I have loaded R-tools 3.1, and I am using R 3.0.2. I get the error below when I run the has_devel() command and I do no know why. Does anyone know how I can successfully install devtools given the error below.
has_devel()
"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" --vanilla CMD SHLIB foo.c
Error: Command failed (1)
> traceback()
6: stop("Command failed (", status, ")", call. = FALSE)
5: system_check(r_path, options, c(r_env_vars(), env_vars), ...)
4: force(code)
3: in_dir(path, system_check(r_path, options, c(r_env_vars(), env_vars),
...))
2: R("CMD SHLIB foo.c", tempdir())
1: has_devel()
There is an existing related question, except in that example R is run on MAC OSX (The check for successful devtools load (has_devel) fails).
My Rtools installation was not complete.
I re-installed the most recent version of Rtools from CRAN (http://cran.rstudio.com/). I re-installed devtools using the instructions supplied by Hadley Wickham (http://adv-r.had.co.nz/Philosophy.html) and the error was fixed, has_devel() returned TRUE.
has_devel()
"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" --vanilla CMD SHLIB foo.c
gcc -m64 -I"C:/PROGRA~1/R/R-30~1.2/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c foo.c -o foo.o
gcc -m64 -shared -s -static-libgcc -o foo.dll tmp.def foo.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-30~1.2/bin/x64 -lR
[1] TRUE
see here for the same issue https://github.com/hadley/devtools/issues/234
(solution provided by hadley, running the script in this gist https://gist.github.com/hadley/4506250)
I have installed first time to a directory C:\Apps\Rtools without checking the environmental variable add step during installation. But, I have manually added the path into the PATH variable. Then, I had the same problem.
Then I reinstalled to the default directory C:\Rtools and this time I checked the environmental variable add step during installation. Then it worked.
I've successfully build my own package with Rcpp in R-Studio. However, when building the package in the Windows console, there are some error messages complaining file missing of R.h.
I set the path and R_Home environments with
SET PATH=D:\RTools\gcc-4.6.3\bin;D:\R3\bin;D:\RTools\bin;
SET R_HOME=D:\R3\
And the build command is
R CMD INSTALL --byte-compile --build mypkg
Below are the compiling error messages:
g++ -m32 -I"/include" -DNDEBUG -I"D:/R3/library/Rcpp/include" -I"d:
/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c Rcpp
Exports.cpp -o RcppExports.o
In file included from D:/R3/library/Rcpp/include/Rcpp.h:27:0,
from RcppExports.cpp:4:
D:/R3/library/Rcpp/include/RcppCommon.h:35:15: fatal error: R.h: No su
ch file or directory
compilation terminated.
You are missing an include for R.h, as the error says.
And if you look at your compile line, the statement
-I"/include"
is wrong relative to your stated R_HOME in D:/R3
You need to check your setup, somehow you confused R from using the correct include directory.
Rcpp builds just fine on Windows, you can even check by submitting your package to the win-builder service.