CMake problem while installing ROpenCVLite

[jubelik]

Describe the bug
When I run ROpenCVLite::installOpenCV(), I have error about the path of CMake.
(following issues 36 on TrackR)

To Reproduce
Here is the code I'm using

if (!require("installr"))
install.packages("installr")
installr::install.Rtools()
installr::install.CMake()
remotes::install_github("swarm-lab/ROpenCVLite@85a94ef")
ROpenCVLite::installOpenCV()

OpenCV is not installed on this system. Would you like to install it now? This will take several minutes.

1: yes
2: no

Selection: yes
OpenCV will be installed in C:\Users\jbelik\AppData\Local\R\win-library\4.3\ROpenCV
Clearing install path.
trying URL 'https://github.com/opencv/opencv/archive/4.8.0.tar.gz'
downloaded 87.7 MB

trying URL 'https://github.com/opencv/opencv_contrib/archive/4.8.0.tar.gz'
downloaded 56.5 MB

CMake Warning:
Ignoring extra path from command line:

"C:/Program Files/Files/rtools43/x86_64-w64-mingw32.static.posix/bin/gcc.exe"

CMake Warning:
Ignoring extra path from command line:

"Files/rtools43/usr/bin/make.exe"

-- The CXX compiler identification is unknown
-- The C compiler identification is unknown
CMake Error at CMakeLists.txt:113 (enable_language):
The CMAKE_CXX_COMPILER:

C:/Program

is not a full path to an existing compiler tool.

Tell CMake where to find the compiler by setting either the environment
variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
to the compiler, or to the compiler name if it is in the PATH.

CMake Error at CMakeLists.txt:113 (enable_language):
The CMAKE_C_COMPILER:

C:/Program

is not a full path to an existing compiler tool.

Tell CMake where to find the compiler by setting either the environment
variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
the compiler, or to the compiler name if it is in the PATH.

-- Configuring incomplete, errors occurred!
See also "C:/Users/jbelik/AppData/Local/Temp/Rtmp8kV4Ls/opencv-4.8.0/build64/CMakeFiles/CMakeOutput.log".
See also "C:/Users/jbelik/AppData/Local/Temp/Rtmp8kV4Ls/opencv-4.8.0/build64/CMakeFiles/CMakeError.log".
[1] FALSE

Expected behavior

Computer (please complete the following information):

• Operating system: Windows
• Version 11

R (please complete the following information):

• R version: 4.3.2
• ROpenCVLite version: 4.80.1
• Cmake version: 3.28.1
• Rtools version (Windows only): 4.3

Additional context
I kown the error message is pretty self explanotory, but I can't figure out how to solve the issue. I've never code on Windows so it is kinda new.
Thanks a lot

[sjmgarnier]

@jubelik Can you try with the latest version that I pushed on the main branch last week? This is the version that should fix definitely the issue we were discussing on the trackR repo. You can install it with:

remotes::install_github("swarm-lab/ROpenCVLite")

Note that with this new version, the installation of Cmake is not required anymore for R >= 4.2 since it is included in Rtools now.

[jubelik]

I have the same error.

remotes::install_github("swarm-lab/ROpenCVLite")
Downloading GitHub repo swarm-lab/ROpenCVLite@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: cli (3.6.1 -> 3.6.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
cli (3.6.1 -> 3.6.2) [CRAN]
Installing 1 packages: cli
Installing package into ‘C:/Users/jbelik/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/cli_3.6.2.zip'
Content type 'application/zip' length 1340852 bytes (1.3 MB)
downloaded 1.3 MB

package ‘cli’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘cli’
Warning: restored ‘cli’

The downloaded binary packages are in
C:\Users\jbelik\AppData\Local\Temp\Rtmp8kV4Ls\downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\jbelik\AppData\Local\Temp\Rtmp8kV4Ls\remotes5af466ef7316\swarm-lab-ROpenCVLite-c83b8ef/DESCRIPTION' ...
─ preparing 'ROpenCVLite': (573ms)
✔ 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'
Omitted 'LazyData' from DESCRIPTION
─ building 'ROpenCVLite_4.90.0.tar.gz'
Warning: file 'ROpenCVLite/configure' did not have execute permissions: corrected

Warning: package ‘ROpenCVLite’ is in use and will not be installed
Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\jbelik\AppData\Local\R\win-library\4.3\00LOCK\cli\libs\x64\cli.dll to C:\Users\jbelik\AppData\Local\R\win-library\4.3\cli\libs\x64\cli.dll: Permission denied

ROpenCVLite::installOpenCV()
OpenCV is not installed on this system. Would you like to install it now? This will take several minutes.

1: yes
2: no

Selection: yes
OpenCV will be installed in C:\Users\jbelik\AppData\Local\R\win-library\4.3\ROpenCV
Clearing install path.
trying URL 'https://github.com/opencv/opencv/archive/4.8.0.tar.gz'
Content type 'application/x-gzip' length 91992565 bytes (87.7 MB)
downloaded 87.7 MB

trying URL 'https://github.com/opencv/opencv_contrib/archive/4.8.0.tar.gz'
downloaded 56.5 MB

CMake Warning:
Ignoring extra path from command line:

"C:/Program Files/Files/rtools43/x86_64-w64-mingw32.static.posix/bin/gcc.exe"

CMake Warning:
Ignoring extra path from command line:

"Files/rtools43/usr/bin/make.exe"

-- The CXX compiler identification is unknown
-- The C compiler identification is unknown
CMake Error at CMakeLists.txt:113 (enable_language):
The CMAKE_CXX_COMPILER:

C:/Program

is not a full path to an existing compiler tool.

Tell CMake where to find the compiler by setting either the environment
variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
to the compiler, or to the compiler name if it is in the PATH.

CMake Error at CMakeLists.txt:113 (enable_language):
The CMAKE_C_COMPILER:

C:/Program

is not a full path to an existing compiler tool.

Tell CMake where to find the compiler by setting either the environment
variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
the compiler, or to the compiler name if it is in the PATH.

-- Configuring incomplete, errors occurred!
See also "C:/Users/jbelik/AppData/Local/Temp/Rtmp8kV4Ls/opencv-4.8.0/build64/CMakeFiles/CMakeOutput.log".
See also "C:/Users/jbelik/AppData/Local/Temp/Rtmp8kV4Ls/opencv-4.8.0/build64/CMakeFiles/CMakeError.log".
[1] FALSE

[sjmgarnier]

@jubelik Actually, I see what the problem is now. You have installed Rtools in C:/Program Files/Files/rtools43/ instead of the recommended location C:/Rtools43/ as per CRAN's recommendation: https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html.

I can see if I can find a workaround for non-standard installation of Rtools but that may take me a few days before I get there.

[jubelik]

Even if I install RTools in C:, the installation still doesn't work.

remotes::install_github("swarm-lab/ROpenCVLite@85a94ef", force = TRUE)
Downloading GitHub repo 85a94ef
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: cli (3.6.1 -> 3.6.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\jbelik\AppData\Local\Temp\RtmpkTXKzf\remotes1e441662737f\swarm-lab-ROpenCVLite-85a94ef/DESCRIPTION' ...
─ preparing 'ROpenCVLite': (464ms)
✔ 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'
Omitted 'LazyData' from DESCRIPTION
─ building 'ROpenCVLite_4.80.1.tar.gz'
Warning: file 'ROpenCVLite/configure' did not have execute permissions: corrected

Installing package into ‘C:/Users/jbelik/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)

• installing source package 'ROpenCVLite' ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (ROpenCVLite)

ROpenCVLite::installOpenCV()
OpenCV is not installed on this system. Would you like to install it now? This will take several minutes.

1: yes
2: no

Selection: yes
OpenCV will be installed in C:\Users\jbelik\AppData\Local\R\win-library\4.3\ROpenCV
Clearing install path.
trying URL 'https://github.com/opencv/opencv/archive/4.8.0.tar.gz'
downloaded 87.7 MB

trying URL 'https://github.com/opencv/opencv_contrib/archive/4.8.0.tar.gz'
downloaded 56.5 MB

-- The CXX compiler identification is GNU 12.3.0
-- The C compiler identification is GNU 12.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - failed
-- Check for working CXX compiler: C:/rtools43/x86_64-w64-mingw32.static.posix/bin/g++.exe
-- Check for working CXX compiler: C:/rtools43/x86_64-w64-mingw32.static.posix/bin/g++.exe - works
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - failed
-- Check for working C compiler: C:/rtools43/x86_64-w64-mingw32.static.posix/bin/gcc.exe
-- Check for working C compiler: C:/rtools43/x86_64-w64-mingw32.static.posix/bin/gcc.exe - works
-- Detecting C compile features
-- Detecting C compile features - done
-- ocv_init_download: OpenCV source tree is not fetched as git repository. 3rdparty resources will be downloaded from github.com by default.
CMake Error at CMakeLists.txt:160 (message):
CMake fails to determine the bitness of the target platform.

Please check your CMake and compiler installation. If you are cross-compiling then ensure that your CMake toolchain file correctly sets the compiler details.

-- Configuring incomplete, errors occurred!
See also "C:/Users/jbelik/AppData/Local/Temp/RtmpkTXKzf/opencv-4.8.0/build64/CMakeFiles/CMakeOutput.log".
See also "C:/Users/jbelik/AppData/Local/Temp/RtmpkTXKzf/opencv-4.8.0/build64/CMakeFiles/CMakeError.log".
make: Entering directory '/c/Users/jbelik/AppData/Local/Temp/RtmpkTXKzf/opencv-4.8.0/build64'
make: *** No targets specified and no makefile found. Stop.
make: Leaving directory '/c/Users/jbelik/AppData/Local/Temp/RtmpkTXKzf/opencv-4.8.0/build64'
make: Entering directory '/c/Users/jbelik/AppData/Local/Temp/RtmpkTXKzf/opencv-4.8.0/build64'
make: *** No rule to make target 'install'. Stop.
make: Leaving directory '/c/Users/jbelik/AppData/Local/Temp/RtmpkTXKzf/opencv-4.8.0/build64'
[1] FALSE

[sjmgarnier]

@jubelik What's the output of version in the R console?

[jubelik]

platform x86_64-w64-mingw32
arch x86_64
os mingw32
crt ucrt
system x86_64, mingw32
status
major 4
minor 3.2
year 2023
month 10
day 31
svn rev 85441
language R
version.string R version 4.3.2 (2023-10-31 ucrt)
nickname Eye Holes

[sjmgarnier]

@jubelik By any chance, is your antivirus (Windows Defender or other) throwing a fit just before this happens?

[sjmgarnier]

BTW, I also pushed a quick and dirty fix for the non-standard installation path of Rtools. You should be able to test it with:

remotes::install_github("swarm-lab/ROpenCVLite@develop")

[jubelik]

No it is not, sorry.
Thanks, I'll try.

[jubelik]

remove.packages("ROpenCVLite")
Removing package from ‘C:/Users/jbelik/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)

remotes::install_github("swarm-lab/ROpenCVLite@develop")
Downloading GitHub repo swarm-lab/ROpenCVLite@develop
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: cli (3.6.1 -> 3.6.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1
cli (3.6.1 -> 3.6.2) [CRAN]
Installing 1 packages: cli
Installing package into ‘C:/Users/jbelik/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/cli_3.6.2.zip'
Content type 'application/zip' length 1340852 bytes (1.3 MB)
downloaded 1.3 MB

package ‘cli’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘cli’
Warning: restored ‘cli’

The downloaded binary packages are in
C:\Users\jbelik\AppData\Local\Temp\RtmpkTXKzf\downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\jbelik\AppData\Local\Temp\RtmpkTXKzf\remotes1e4438815069\swarm-lab-ROpenCVLite-5d00a06/DESCRIPTION' ...
─ preparing 'ROpenCVLite': (451ms)
✔ 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'
Omitted 'LazyData' from DESCRIPTION
─ building 'ROpenCVLite_4.90.0.tar.gz'
Warning: file 'ROpenCVLite/configure' did not have execute permissions: corrected

Warning: package ‘ROpenCVLite’ is in use and will not be installed
Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\jbelik\AppData\Local\R\win-library\4.3\00LOCK\cli\libs\x64\cli.dll to C:\Users\jbelik\AppData\Local\R\win-library\4.3\cli\libs\x64\cli.dll: Permission denied

[sjmgarnier]

@jubelik This looks like an issue with your running R session. Something is held up somewhere. You need to restart R.

[sjmgarnier]

@jubelik If that still doesn't work, you can contact me at [email protected] and I can jump on a quick call in the next 30 minutes or so. Might be easier to figure out the issue.

[jubelik]

I have to go to another meeting, but if it is still not working in the next few days I'll contact you.
Thanks a lot!!