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Published 20 hours ago • verified publisher icon dmurdoch

Install issue of rgl v0.105.22 on macOS in Homebrew

Open mjsteinbaugh opened this issue 3 years ago • 15 comments

Hi, I'm having trouble getting rgl to install on one of my Macs running macOS 10.15.7. I tested this on another computer running Big Sur 11.2.2 and rgl installs sucessfully.

install.packages("rgl", type = "source")

This runs through and looks good until the very end:

** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
sh: line 1:  8026 Abort trap: 6           R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T//RtmpJCkLFl/file1bbf1a8ba577'
ERROR: loading failed

Here's my session info:

> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] AcidDevTools_0.3.1

loaded via a namespace (and not attached):
[1] compiler_4.0.4 magrittr_2.0.1 tools_4.0.4

I use Homebrew and have the recommended macOS R developer tools, including gfortran installed.

mjsteinbaugh avatar Mar 05 '21 16:03 mjsteinbaugh

See related:

  • https://github.com/dmurdoch/rgl/issues/44
  • https://github.com/tylermorganwall/rayshader/issues/139
  • https://github.com/joey711/phyloseq/issues/1390
  • https://stackoverflow.com/questions/62961034/

Could be an X11 / XQuartz issue?

mjsteinbaugh avatar Mar 05 '21 16:03 mjsteinbaugh

This is likely a Homebrew issue. See the suggestions for debugging it in issue #44.

dmurdoch avatar Mar 05 '21 16:03 dmurdoch

I can confirm this works:

install.packages("rgl", type = "source", configure.args = "--disable-opengl")

Thanks, I'll take a look. Usually this gets installed as the binary, so I figured I'd post in case somebody else hits this.

mjsteinbaugh avatar Mar 05 '21 16:03 mjsteinbaugh

Let's leave this open, in case some other Homebrew users want to try to debug it properly.

dmurdoch avatar Mar 05 '21 16:03 dmurdoch

OK great. For reference, I'm using the CRAN Homebrew R cask (which allows for binary package installs), unlike the case in #44 .

mjsteinbaugh avatar Mar 05 '21 16:03 mjsteinbaugh

Actually I hit the same issue on Big Sur as well, so this isn't Catalina-specific.

mjsteinbaugh avatar Mar 05 '21 16:03 mjsteinbaugh

I'm sure it's a Homebrew issue, but it's possible rgl's install code could be modified to work with it. The things to look for:

  • Does x11() work in R? If not, then it's likely hopeless to get rgl fully working. Both use X11 to display. On macOS, that's provided by XQuartz; its recent updates have caused a lot of breakage.

  • If x11() works but rgl won't start, then there's hope, but it needs someone with a good knowledge of xquartz in Homebrew to see what rgl is doing wrong. It might be as simple as disabling the Darwin special-casing, or it might need more extensive changes.

  • I'm not going to be able to debug this: I use the CRAN build of R, and the xquartz.org build of XQuartz, and things are fine.

dmurdoch avatar Mar 05 '21 17:03 dmurdoch

I have the same problem here and I'm also using the cask from homebrew, but...

  • I don't see why should it be different than the one downloaded from CRAN since cask version just install cran version.
  • The same with XQuartz
  • I guess the issue is with the toolchain to build where some dependencies are installed with homebrew. Like libpng 
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c ABCLineSet.cpp -o ABCLineSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c BBoxDeco.cpp -o BBoxDeco.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Background.cpp -o Background.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c ClipPlane.cpp -o ClipPlane.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Color.cpp -o Color.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Disposable.cpp -o Disposable.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Light.cpp -o Light.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c LineSet.cpp -o LineSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c LineStripSet.cpp -o LineStripSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Material.cpp -o Material.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c NULLgui.cpp -o NULLgui.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c PlaneSet.cpp -o PlaneSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c PointSet.cpp -o PointSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c PrimitiveSet.cpp -o PrimitiveSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c RenderContext.cpp -o RenderContext.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Shape.cpp -o Shape.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c SphereMesh.cpp -o SphereMesh.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c SphereSet.cpp -o SphereSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c SpriteSet.cpp -o SpriteSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c String.cpp -o String.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Surface.cpp -o Surface.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c TextSet.cpp -o TextSet.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Texture.cpp -o Texture.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c Viewpoint.cpp -o Viewpoint.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c api.cpp -o api.o
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/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c device.cpp -o device.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c devicemanager.cpp -o devicemanager.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c fps.cpp -o fps.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c ftgl.cpp -o ftgl.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c geom.cpp -o geom.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c gl2ps.c -o gl2ps.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c glErrors.cpp -o glErrors.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c glgui.cpp -o glgui.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c gui.cpp -o gui.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c init.cpp -o init.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c par3d.cpp -o par3d.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c pixmap.cpp -o pixmap.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c platform.cpp -o platform.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c pretty.c -o pretty.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c render.cpp -o render.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c rglmath.cpp -o rglmath.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c rglview.cpp -o rglview.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c scene.cpp -o scene.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c select.cpp -o select.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c subscene.cpp -o subscene.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c win32gui.cpp -o win32gui.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c win32lib.cpp -o win32lib.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c x11gui.cpp -o x11gui.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL  -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -pipe -c x11lib.cpp -o x11lib.o

I don't know if that -DRGL_NO_OPENGL flag should be there.

In my case x11() works in R

luispuerto avatar Mar 06 '21 12:03 luispuerto

On 06/03/2021 7:20 a.m., Luis Puerto wrote:

I have the same problem here and I'm also using the cask from homebrew, but...

  • I don't see why should it be different than the one downloaded from CRAN since cask version just install cran version.
  • The same with XQuartz
  • I guess the issue is with the toolchain to build where some dependencies are installed with homebrew. Like|libpng|

You're using a different compiler for rgl than CRAN uses for R. The CRAN binaries are built with commands like

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -I/usr/X11/include -DDarwin -DNO_GL_PREFIX -I/opt/X11/include -DHAVE_FREETYPE -Iext/ftgl -I/usr/local/opt/freetype/include/freetype2 -Iext -I/usr/local/include -fPIC -Wall -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o

or

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_PNG_H -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -DRGL_NO_OPENGL -I/usr/local/include -fPIC -Wall -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o

depending on which version of the shared library is being built.

You are only getting the second type of build, because the configure script didn't find something it needs, and has defaulted to --disable-opengl (or you specified that explicitly).

dmurdoch avatar Mar 06 '21 13:03 dmurdoch

I haven't specified anything…

I have a rmakevars, thought:

# --------
# RMakevars
# --------

# General note
# - need to repeat options across C++ flavors (e.g., 11, 14)

# Homebrew bin / opt / lib locations
HB=/usr/local/bin
HO=/usr/local/opt
HL=/usr/local/lib
HI=/usr/local/include

# MacOS 10.14.6 Xcode header location (August 2019)
# (do "xcrun -show-sdk-path" in terminal to get path; change if yours is different)
XH=$(shell xcrun -show-sdk-path)

# ccache
CCACHE=$(HB)/ccache

# Make using all cores (set # to # of cores on your machine)
# Check https://stackoverflow.com/q/2499070 for more info. 
# Run `nproc` to check the number of threads https://stackoverflow.com/a/56607839
# As a rule of thumb the number should be between cores and threads. 
MAKE=make -j4

# GNU version (July 2020)
GNU_VER=10

# LLVM (Clang) compiler options
CC=$(CCACHE) $(HO)/llvm/bin/clang
CXX=$(CC)++
CXX98=$(CC)++
CXX11=$(CC)++
CXX14=$(CC)++
CXX17=$(CC)++

# FORTRAN
FC=$(CCACHE) $(HB)/gfortran-$(GNU_VER)
F77=$(FC)
FLIBS=-L$(HL)/gcc/$(GNU_VER) -lgfortran -lquadmath -lm

# STD libraries
CXX1XSTD=-std=c++0x
CXX11STD=-std=c++11
CXX14STD=-std=c++14
CXX17STD=-std=c++17

# FLAGS
STD_FLAGS=-g -O3 -Wall -pedantic -mtune=native -pipe
CFLAGS=$(STD_FLAGS)
CXXFLAGS=$(STD_FLAGS)
CXX98FLAGS=$(STD_FLAGS)
CXX11FLAGS=$(STD_FLAGS)
CXX14FLAGS=$(STD_FLAGS)
CXX17FLAGS=$(STD_FLAGS)

# Preprocessor FLAGS
# NB: -isysroot refigures the include path to the Xcode SDK we set above
CPPFLAGS=-isysroot $(XH) -I$(HI) \
  -I$(HO)/llvm/include -I$(HO)/openssl/include \
  -I$(HO)/gettext/include -I$(HO)/tcl-tk/include

# Linker flags (suggested by homebrew)
LDFLAGS+=-L$(HO)/llvm/lib -Wl,-rpath,$(HO)/llvm/lib

# Flags for OpenMP support that should allow packages that want to use
# OpenMP to do so (data.table), and other packages that bork with
# -fopenmp flag (stringi) to be left alone
SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_CXX98FLAGS=-fopenmp
SHLIB_OPENMP_CXX11FLAGS=-fopenmp
SHLIB_OPENMP_CXX14FLAGS=-fopenmp
SHLIB_OPENMP_CXX17FLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp
SHLIB_OPENMP_FFLAGS=-fopenmp

luispuerto avatar Mar 06 '21 13:03 luispuerto

/System/Library/Frameworks/OpenGL.framework/Headers is not present. The only folders under OpenGL.framework are Library, Resources and Versions.

I also tried this: https://methi1999.github.io/2020/08/19/opengl.html and I got an error.

luispuerto avatar Mar 06 '21 15:03 luispuerto

In fact, that include is also missing on my system. I should probably clean up the configure script.

I believe the OpenGL headers are being found in /usr/X11/include, though they are also present in /opt/X11/include. Those both have the same recent timestamp on my system, so were probably installed with XQuartz.

And just to be clear: I can't really help with debugging Homebrew. If you can work out what changes are needed in the configure script I'll try them out, but otherwise, I'd suggest changing to a more standard setup.

dmurdoch avatar Mar 06 '21 20:03 dmurdoch

@dmurdoch I totally understand about the no support for homebrew and appreciate the time you are taking to this.

I really want to know why this isn't working when I have these R and XQuartz installed from the binaries. Yeah, through a homebrew script, but from the binaries.

I can see that on those includes on X11 there a libpng16. I think that perhaps the problem is that the build is taking the homebrew one instead of the XQuartz one.

Perhaps you can force on the building script to use the one from XQuartz?

luispuerto avatar Mar 06 '21 21:03 luispuerto

By the way… I removed hombrew's libpng and my rmakevars, to see if there was something related to it.

Now it's not able to find libpng

Error in dyn.load(dynlib <- getDynlib(dir)) : 
  unable to load shared object '/Users/lpuerto/Library/R/4.x/library/00LOCK-rgl/00new/rgl/libs/rgl.so':
  dlopen(/Users/lpuerto/Library/R/4.x/library/00LOCK-rgl/00new/rgl/libs/rgl.so, 6): Library not loaded: /usr/local/opt/libpng/lib/libpng16.16.dylib
  Referenced from: /usr/local/opt/freetype/lib/libfreetype.6.dylib

Full building output: https://gist.github.com/f66dcdb558e1ce44d01732f5d821cdda

luispuerto avatar Mar 06 '21 21:03 luispuerto

Include a PR, and I'll test it.

dmurdoch avatar Mar 07 '21 00:03 dmurdoch