rjulia on Windows/RStudio
dgromer opened this issue · 16 comments
Building rjulia on Windows 7 64-bit with R 3.2.0 and Julia 0.3.9 (using devtools::install_github("armgong/RJulia", args = "--no-multiarch") fails with the following error:
* installing *source* package 'rjulia' ...
** libs
gcc -m64 -I"C:/R/R-32~1.0/include" -DNDEBUG -I"C:\\Julia-0.3.9\\bin"/../../src -I"C:\\Julia-0.3.9\\bin"/../../src/support -I"C:\\Julia-0.3.9\\bin"/../include -I"C:\\Julia-0.3.9\\bin"/../include/julia -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Julia_R.c -o Julia_R.o
In file included from C:\Julia-0.3.9\bin/../include/julia/uv.h:59:0,
from C:\Julia-0.3.9\bin/../include/julia/ios.h:5,
from C:\Julia-0.3.9\bin/../include/julia/libsupport.h:11,
from C:\Julia-0.3.9\bin/../include/julia/julia.h:10,
from Julia_R.c:11:
C:\Julia-0.3.9\bin/../include/julia/uv-win.h:241:3: error: unknown type name 'SRWLOCK'
make: *** [Julia_R.o] Error 1
Warning: Ausführung von Kommando 'make -f "Makevars" -f "C:/R/R-32~1.0/etc/x64/Makeconf" -f "C:/R/R-32~1.0/share/make/winshlib.mk" SHLIB="rjulia.dll" WIN=64 TCLBIN=64 OBJECTS="Julia_R.o R_Julia.o dataframe.o embedding.o"' ergab Status 2
ERROR: compilation failed for package 'rjulia'
* removing 'C:/R/R-3.2.0/library/rjulia'
* restoring previous 'C:/R/R-3.2.0/library/rjulia'
Error: Command failed (1)
However, after adding a Makevars.win with the contents of the Makevars plus PKG_CPPFLAGS+= -D_WIN32_WINNT=0x0600 (see JuliaLang/julia#9973) solved this problem.
Now when loading the package from within RStudio, the R session crashes. When loading rjulia in a R session in cmd.exe everything works fine. Any ideas?
could you enable RStudio log (https://support.rstudio.com/hc/en-us/articles/200554756-RStudio-Application-Logs ) and see what happend?
recently I am not test on windows , so didn't konw SRWLOCK problem, you can create pull request, I will merge it.
RStudio writes neither to rdesktop.log nor rsession-USER.log upon crash. Maybe that's due to the fact that RStudio does currently not support crash reports on Windows (https://support.rstudio.com/hc/en-us/articles/200488518).
I guess I will write an issue to RStudio Support.
tested on my PC, found these
1 SRWLOCK issue is caused by Rtools have too old winnt.h (I use msys2+mingwbuild gcc 4.9.2 which have the define)
2 julia 0.39 and rjulia crash RStudio 0.99.442 (but run ok on RStudio-0.98.1103 ). this is RStudio 0.99.442 bug, to verify this just run following code ,it will crash rsession
dyn.load('e:/julia/64/bin/libjulia.dll')3 julia 0.4 and rjulia run on rstudio
to solve this problem,there two way
1 when use julia 0.39 and rjulia stay at RStudio-0.98.1103
2 when use RStudio 0.99.442 , need julia 0.4 and rjulia 0.4 branch
RStudio 0.99.442 still crashes on my machine when using Julia 0.4 nightly build and rjulia 0.4 branch atdyn.load of libjulia.dll
Don't load rjulia just run dyn.load('e:/julia/64/bin/libjulia.dll') on rstudio see what happens ,or try rstudio nightly build 99.591
dyn.load("C:/Julia-0.4.0-dev/bin/libjulia.dll") crashes on both RStudio 0.99.442 and 0.99.591.
on my PC both julia 0.3 and 0.4 run ok on RStudio-0.98.1103,so please stay on this version,don't use 0.99.
or somebody can summit a issue to rstudio,wait rstudio to solve it.
btw your julia 0.4 is own build or download from julialang.org? mine is own build and it can run on rstudio 0.99.591
I use a 0.4 nightly build from julialang.org.
It works in RStudio 0.98.1103, so it seems to be a problem with either RStudio 0.99 or the nightly build from julialang.org. I will file an issue to RStudio.
thanks a lot
I tried to install rjulia on Windows 7 64-bit with R-3.2.0 and julia-0.3.9. The latest version fixed the SRWLOCK issue. However, I am still stuck at the final linking step.
> devtools::install_github("armgong/RJulia")
Downloading github repo armgong/RJulia@master
Installing rjulia
"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" --no-site-file --no-environ \
--no-save --no-restore CMD INSTALL \
"C:/Users/yanll/AppData/Local/Temp/RtmpsTNVnH/devtoolse8c6db6341d/armgong-RJulia-288964e" \
--library="C:/Users/yanll/Documents/R/win-library/3.2" \
--install-tests
* installing *source* package 'rjulia' ...
** libs
*** arch - i386
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.0/include" -DNDEBUG -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src/support -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include/julia -D_WIN32_WINNT=0x0600 -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Julia_R.c -o Julia_R.o
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.0/include" -DNDEBUG -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src/support -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include/julia -D_WIN32_WINNT=0x0600 -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_Julia.c -o R_Julia.o
R_Julia.c: In function 'R_Julia_MD':
R_Julia.c:120:11: warning: assignment from incompatible pointer type [enabled by default]
R_Julia.c:134:10: warning: assignment from incompatible pointer type [enabled by default]
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.0/include" -DNDEBUG -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src/support -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include/julia -D_WIN32_WINNT=0x0600 -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dataframe.c -o dataframe.o
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.0/include" -DNDEBUG -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../../src/support -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include -I"C:\\Users\\yanll\\AppData\\Local\\Julia-0.3.9\\bin"/../include/julia -D_WIN32_WINNT=0x0600 -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c embedding.c -o embedding.o
gcc -m32 -shared -s -static-libgcc -o rjulia.dll tmp.def Julia_R.o R_Julia.o dataframe.o embedding.o -ljulia -LC:\Users\yanll\AppData\Local\Julia-0.3.9\bin -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/PROGRA~1/R/R-32~1.0/bin/i386 -lR
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: skipping incompatible C:\Users\yanll\AppData\Local\Julia-0.3.9\bin/libjulia.dll when searching for -ljulia
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: skipping incompatible C:\Users\yanll\AppData\Local\Julia-0.3.9\bin/libjulia.dll when searching for -ljulia
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -ljulia
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'rjulia'
* removing 'C:/Users/yanll/Documents/R/win-library/3.2/rjulia'
Error: Command failed (1)
I installed julia-0.3.9 with the (Windows Self-Extracting Archive (.exe)) binary package from http://julialang.org/downloads/. I wonder if it is necessary to build julia from scratch.
1 try add C:\Users\yanll\AppData\Local\Julia-0.3.9\bin to you system PATH
if 1 don't work
2 try modify Makevar.win latest line:
PKG_LIBS=-L$(libjuliapath) -ljulia
I had already added the directory to PATH, otherwise R won't be able to find the correct julia path. The second method does not help either.
I searched in my julia installation directory, and found that there is no any '.lib' or '.a' file. I tried also the Nightly build, but the same error exists.
Therefore, I guess it is necessary to build julia from scratch. I will try this way.
basically dynamic link on windows don't need .lib or .a file , just need libjulia.dll. build julia from scratch will not help.
according you compile output, it is R package compile problem,normally R try to compile both 32 and 64 bit package,but your julia in system path is only 32bit or 64 bit, so need use this like @dgromer to compile rjulia
devtools::install_github("armgong/RJulia", args = "--no-multiarch")Thanks! It works now.