-isystem /usr/include doesn't work with gcc6

[micahscopes]

I'm compiling on Arch Linux, and am getting dependencies from Arch's package manager. Headers are stored in /usr/include. I've configured all my header directories using the helpful instructions at the top of the Makefile.

However, I run into errors that stdlib.h cannot be found. I traced it to this issue: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129#c1

So I've gone and commented out most of the *_INCL_DIR variables, since they end up in -isystem arguments. That works, for the most part, except when those variables are needed for other reasons, in which case I go and delete the -isystem line.

I've been able to get openvdb to compile, but am not sure how I'd fix the Makefile to handle more general cases, like people using gcc < 6

Any advice?

[OpenVDB-DevTeam]

Since /usr/include/ is searched by default, you can set *_INCL_DIR to some nonexistent directory, or to an existing directory that contains no headers. Or just change -isystem to -I, if you don't mind seeing lots of compiler warnings.

[phcerdan]

I can reproduce this with gcc 9.1.
To fix it, just set option in CMake to not use isystem from imported targets, I found the reference in the CMake maillist here:

cmake ../src -DCMAKE_NO_SYSTEM_FROM_IMPORTED:BOOL=TRUE 

This is the first time I faced this in CMake, probably has to do with the way (non standard?) OpenVDB is importing targets.

[frispete]

Thanks for the trick @phcerdan, same happens here for llvm builds on openSUSE Tumbleweed (a rolling release). Here's the public build: https://build.opensuse.org/package/live_build_log/home:frispete:blender/openvdb/openSUSE_Tumbleweed/x86_64
BTW, the build triggers (a few too) many warnings due to some openexr/tbb deprecations.

A further note on packaging: it happens, that the library base is not /usr/lib for some 64bit distributions.
check the less than optimal %prep section of: https://build.opensuse.org/package/view_file/home:frispete:blender/openvdb/openvdb.spec?expand=1

[anil100391]

Shouldn't the usage of concerned cmake flag be mentioned in README building section?

[syoyo]

More proper fix may be removing ${IlmBase_INCLUDE_DIR}/../
in

https://github.com/AcademySoftwareFoundation/openvdb/blob/master/cmake/FindIlmBase.cmake#L325

(and do same thing for FindOpenEXR.cmake)

This path is expanded to /usr/include/OpenEXR/.. in apt installed OpenEXR(IlmBase) on Ubuntu 18.04.

I have confirmed OpenVDB compiles fine at least on Ubuntu 18.04 by deleting these include paths.

[Hideman85]

Same issue on master commit f077a14
The fix -DCMAKE_NO_SYSTEM_FROM_IMPORTED:BOOL=TRUE works but can't compile without