Trouble installing

[twesleyb]

Hi Daniel, I really appreciate your efforts to make wholebrain as open source and accessible as possible. Thank you! I followed your tutorial to install on Windows, but on one of the final steps I run into an issue. In Rstudio I call the following to install your package from GitHub:

devtools::install_github("tractatus/wholebrain", args='--no-multiarch')

This generate the following message in which there is an error:

The downloaded binary packages are in
	C:\Users\tyler\AppData\Local\Temp\RtmpIl0P90\downloaded_packages
Downloading GitHub repo swarm-lab/ROpenCVLite@master
√  checking for file 'C:\Users\tyler\AppData\Local\Temp\RtmpIl0P90\remotes4da41f491205\swarm-lab-ROpenCVLite-e0dbc33/DESCRIPTION' ... 
-  preparing 'ROpenCVLite':
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
   Removed empty directory 'ROpenCVLite/man/figures'
-  building 'ROpenCVLite_0.2.40.1.tar.gz'
   Warning: file 'ROpenCVLite/cleanup' did not have execute permissions: corrected
   Warning: file 'ROpenCVLite/configure' did not have execute permissions: corrected
   
* installing *source* package 'ROpenCVLite' ...
+ set -e
+ cd ./src
+ D:/R-3.5.1/bin/Rscript.exe -e 'download.file('\''https://github.com/opencv/opencv/archive/4.0.1.tar.gz'\'', '\''opencv-4.0.1.tar.gz'\'')'
trying URL 'https://github.com/opencv/opencv/archive/4.0.1.tar.gz'
Content type 'application/x-gzip' length 87593916 bytes (83.5 MB)
==================================================
downloaded 83.5 MB

+ tar zxvf opencv-4.0.1.tar.gz
+ cp ../inst/cap_dshow.cpp opencv-4.0.1/modules/videoio/src/
+ cp ../inst/cap_dshow.hpp opencv-4.0.1/modules/videoio/src/
+ cd opencv-4.0.1
+ '[' '!' -d ../../inst/opencv ']'
+ mkdir ../../inst/opencv
+ '[' -d D:/R-3.5.1/bin/x64 ']'
+ ARCH=64
+ '[' '!' -d build64 ']'
+ mkdir build64
+ cd build64
+ cmake -G 'Unix Makefiles' -DCMAKE_C_COMPILER=C:/Rtools/mingw_64/bin/gcc.exe -DCMAKE_CXX_COMPILER=C:/Rtools/mingw_64/bin/g++.exe -DCMAKE_RC_COMPILER=C:/Rtools/mingw_64/bin/windres.exe -DCMAKE_MAKE_PROGRAM=C:/Rtools/bin/make.exe -DENABLE_PRECOMPILED_HEADERS=OFF -DENABLE_CXX11=ON -DBUILD_ZLIB=ON -DBUILD_opencv_world=OFF -DBUILD_opencv_contrib_world=OFF -DBUILD_matlab=OFF -DBUILD_opencv_java=OFF -DBUILD_opencv_python2=OFF -DBUILD_opencv_python3=OFF -DBUILD_PERF_TESTS=OFF -DBUILD_TESTS=OFF -DWITH_MSMF=OFF -DBUILD_PROTOBUF=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=../../../inst/opencv/ ../
-- The CXX compiler identification is GNU 4.9.3
-- The C compiler identification is GNU 4.9.3
-- Check for working CXX compiler: C:/Rtools/mingw_64/bin/g++.exe
-- Check for working CXX compiler: C:/Rtools/mingw_64/bin/g++.exe -- broken
CMake Error at C:/Program Files/CMake/share/cmake-3.8/Modules/CMakeTestCXXCompiler.cmake:44 (message):
  The C++ compiler "C:/Rtools/mingw_64/bin/g++.exe" is not able to compile a
  simple test program.

  It fails with the following output:

   Change Dir: C:/Users/tyler/AppData/Local/Temp/RtmpMB5Jjo/R.INSTALL520c2fa01373/ROpenCVLite/src/opencv-4.0.1/build64/CMakeFiles/CMakeTmp

   Run Build Command:"C:/Rtools/bin/make.exe" "cmTC_1391c/fast"

  /Rtools/bin/make -f CMakeFiles/cmTC_1391c.dir/build.make
  CMakeFiles/cmTC_1391c.dir/build

  make: /bin/sh: Command not found

  make: *** [Makefile:126: cmTC_1391c/fast] Error 127

    CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
  CMakeLists.txt:131 (project)


-- Configuring incomplete, errors occurred!
See also "C:/Users/tyler/AppData/Local/Temp/RtmpMB5Jjo/R.INSTALL520c2fa01373/ROpenCVLite/src/opencv-4.0.1/build64/CMakeFiles/CMakeOutput.log".
See also "C:/Users/tyler/AppData/Local/Temp/RtmpMB5Jjo/R.INSTALL520c2fa01373/ROpenCVLite/src/opencv-4.0.1/build64/CMakeFiles/CMakeError.log".
ERROR: configuration failed for package 'ROpenCVLite'
* removing 'D:/R-3.5.1/library/ROpenCVLite'
In R CMD INSTALL
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/tyler/AppData/Local/Temp/RtmpIl0P90/file4da44b633341/ROpenCVLite_0.2.40.1.tar.gz’ had non-zero exit status

I'm hoping your experienced eye can catch the underlying problem. I hope I have provided enough information, but I can provide more info if necessary.

Thanks, Tyler

[luckylara]

hi Tyler, I have just got the same problem with you. I wonder if you have found answers to solve this problem, if so, please let me know, thank you very much!

[twesleyb]

Hi luckylara, I'm sorry I have not found a solution. If you are able to overcome the install problem, please let me know!

[tractatus]

@twesleyb you havent set Rtools properly.
The C++ compiler "C:/Rtools/mingw_64/bin/g++.exe" is not able to compile a simple test program.

Is Cmake complaining that the compiler cant compile.

Later you have this error:

make: /bin/sh: Command not found

Which means that sh.exe cant be found by the Rtools your Rstudio/R is using. Check your paths.