windows 10 install

[lidan99]

Hi Daniel,

Thanks for all your hard work on developing wholebrain!
I'm coming across and issue where opencv is not being installed correctly during the first stage of the wholebrain install. So of course I cannot then add opencv to system path bc it is not there.
Thanks in advance for any insight you could provide on this!

devtools::install_github("tractatus/wholebrain", args="--no-multiarch")
Downloading GitHub repo tractatus/wholebrain@master
Downloading GitHub repo swarm-lab/ROpenCVLite@master
√ checking for file 'C:\Users\GourleyLab\AppData\Local\Temp\RtmpoN6G8o\remotesce83a607ca2\swarm-lab-ROpenCVLite-3a5ef7f/DESCRIPTION' (631ms)

• preparing 'ROpenCVLite': (355ms)
  √ checking DESCRIPTION meta-information ...
• 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_0.3.410.tar.gz'
  Warning: file 'ROpenCVLite/configure' did not have execute permissions: corrected

Installing package into ‘C:/Users/GourleyLab/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)

• installing source package 'ROpenCVLite' ...

• set -e
• hash cmake
• exit 0
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  converting help for package 'ROpenCVLite'
  finding HTML links ... done
  ROpenCVLite-package html
  installOpenCV html
  isOpenCVInstalled html
  opencvConfig html
  opencvVersion html
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded
  Warning in installOpenCV() :
  OpenCV can only be installed in interactive mode.
  OpenCV was not installed at this time. You can install it at any time by using the installOpenCV() function in interactive mode.

• DONE (ROpenCVLite)
  In R CMD INSTALL
  Installing 14 packages: png, grImport, sp, rgl, misc3d, XML, knitr, manipulateWidget, highr, markdown, xfun, miniUI, base64enc, webshot
  Installing packages into ‘C:/Users/GourleyLab/Documents/R/win-library/3.5’
  (as ‘lib’ is unspecified)
  trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/png_0.1-7.zip'
  Content type 'application/zip' length 292639 bytes (285 KB)
  downloaded 285 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/grImport_0.9-2.zip'
Content type 'application/zip' length 825059 bytes (805 KB)
downloaded 805 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/sp_1.3-1.zip'
Content type 'application/zip' length 1868805 bytes (1.8 MB)
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rgl_0.100.30.zip'
Content type 'application/zip' length 4242560 bytes (4.0 MB)
downloaded 4.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/misc3d_0.8-4.zip'
Content type 'application/zip' length 237276 bytes (231 KB)
downloaded 231 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/XML_3.98-1.20.zip'
Content type 'application/zip' length 4601568 bytes (4.4 MB)
downloaded 4.4 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/knitr_1.25.zip'
Content type 'application/zip' length 1418726 bytes (1.4 MB)
downloaded 1.4 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/manipulateWidget_0.10.0.zip'
Content type 'application/zip' length 1858300 bytes (1.8 MB)
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/highr_0.8.zip'
Content type 'application/zip' length 48182 bytes (47 KB)
downloaded 47 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/markdown_1.1.zip'
Content type 'application/zip' length 189550 bytes (185 KB)
downloaded 185 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/xfun_0.10.zip'
Content type 'application/zip' length 178361 bytes (174 KB)
downloaded 174 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/miniUI_0.1.1.1.zip'
Content type 'application/zip' length 36168 bytes (35 KB)
downloaded 35 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/base64enc_0.1-3.zip'
Content type 'application/zip' length 43316 bytes (42 KB)
downloaded 42 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/webshot_0.5.1.zip'
Content type 'application/zip' length 140937 bytes (137 KB)
downloaded 137 KB

package ‘png’ successfully unpacked and MD5 sums checked
package ‘grImport’ successfully unpacked and MD5 sums checked
package ‘sp’ successfully unpacked and MD5 sums checked
package ‘rgl’ successfully unpacked and MD5 sums checked
package ‘misc3d’ successfully unpacked and MD5 sums checked
package ‘XML’ successfully unpacked and MD5 sums checked
package ‘knitr’ successfully unpacked and MD5 sums checked
package ‘manipulateWidget’ successfully unpacked and MD5 sums checked
package ‘highr’ successfully unpacked and MD5 sums checked
package ‘markdown’ successfully unpacked and MD5 sums checked
package ‘xfun’ successfully unpacked and MD5 sums checked
package ‘miniUI’ successfully unpacked and MD5 sums checked
package ‘base64enc’ successfully unpacked and MD5 sums checked
package ‘webshot’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\GourleyLab\AppData\Local\Temp\RtmpoN6G8o\downloaded_packages
Skipping install of 'ROpenCVLite' from a github remote, the SHA1 (3a5ef7f9) has not changed since last install.
Use force = TRUE to force installation
√ checking for file 'C:\Users\GourleyLab\AppData\Local\Temp\RtmpoN6G8o\remotesce829747816\tractatus-wholebrain-8e12757/DESCRIPTION' (447ms)

• preparing 'wholebrain': (2.1s)
  √ 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 (1s)
• looking to see if a 'data/datalist' file should be added
• building 'wholebrain_0.1.1.tar.gz' (2.5s)

Installing package into ‘C:/Users/GourleyLab/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)

• installing source package 'wholebrain' ...
  ** libs
  Error in ROpenCVLite::opencvConfig("cflags", arch = Sys.getenv("R_ARCH")) :
  OpenCV is not installed on this system. Please use installOpenCV() to install it.
  Execution halted
  c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-3.5.1/include" -DNDEBUG -I"C:\fftw/" -I../inst/include -I"C:/Users/GourleyLab/Documents/R/win-library/3.5/Rcpp/include" -IC:/Users/GourleyLab/Documents/R/win-library/3.5/Rcpp/include -O2 -Wall -mtune=generic -c CThinPlateSpline.cpp -o CThinPlateSpline.o
  CThinPlateSpline.cpp:9:30: fatal error: opencv2/opencv.hpp: No such file or directory
  #include "opencv2/opencv.hpp"
  ^
  compilation terminated.
  make: *** [CThinPlateSpline.o] Error 1
  ERROR: compilation failed for package 'wholebrain'
• removing 'C:/Users/GourleyLab/Documents/R/win-library/3.5/wholebrain'
  In R CMD INSTALL
  Error: Failed to install 'wholebrain' from GitHub:
  (converted from warning) installation of package ‘C:/Users/GourleyLab/AppData/Local/Temp/RtmpoN6G8o/filece87d08793a/wholebrain_0.1.1.tar.gz’ had non-zero exit status

[GxHam]

Try installing RopenCV first before reinstalling wholebrain:
devtools::install_github("swarm-lab/ROpenCVLite")
library(ROpenCVLite)