Pcl 1.11.1 #59146

dtrodrigues · 2020-08-04T18:21:28Z

Have you followed the guidelines for contributing?
Have you checked that there aren't other open pull requests for the same formula update/change?
Have you built your formula locally with brew install --build-from-source <formula>, where <formula> is the name of the formula you're submitting?
Is your test running fine brew test <formula>, where <formula> is the name of the formula you're submitting?
Does your build pass brew audit --strict <formula> (after doing brew install <formula>)?

cc @SergioRAgostinho, previous attempt at #54706
Shim issue should be resolved by #56273
Should resolve Boost 1.73 issue in #59064

SMillerDev · 2020-08-05T06:42:44Z

Please also update the test to catch the boost issues.

dtrodrigues · 2020-08-05T18:07:57Z

Errors building test program on 10.14 and 10.15:

[ 50%] Building CXX object CMakeFiles/pcd_write.dir/pcd_write.cpp.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++ -DDISABLE_LIBUSB_1_0 -DDISABLE_PCAP -DDISABLE_PNG -Dqh_QHpointer -DvtkRenderingContext2D_AUTOINIT="1(vtkRenderingContextOpenGL2)" -DvtkRenderingCore_AUTOINIT="3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL2)" -isystem /usr/local/Cellar/vtk/8.2.0_10/include/vtk-8.2 -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -isystem /usr/local/include -isystem /usr/local/include/pcl-1.11 -isystem /usr/local/include/eigen3 -Os -w -pipe -march=nehalem -mmacosx-version-min=10.15 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk  -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -std=gnu++14 -o CMakeFiles/pcd_write.dir/pcd_write.cpp.o -c /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:42:
In file included from /usr/local/include/pcl-1.11/pcl/memory.h:48:
In file included from /usr/local/include/eigen3/Eigen/Core:96:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:245:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:317:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:318:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:319:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
      ~~^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/math.h:749:12: note: 'finite' declared here
extern int finite(double)
           ^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:42:
In file included from /usr/local/include/pcl-1.11/pcl/memory.h:48:
In file included from /usr/local/include/eigen3/Eigen/Core:96:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:245:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:320:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:321:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:322:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:323:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functional:731:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:42:
In file included from /usr/local/include/pcl-1.11/pcl/memory.h:48:
In file included from /usr/local/include/eigen3/Eigen/Core:96:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:245:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:324:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functional:760:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:42:
In file included from /usr/local/include/pcl-1.11/pcl/memory.h:48:
In file included from /usr/local/include/eigen3/Eigen/Core:96:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:245:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:325:9: error: no member named 'isless' in the global namespace
using ::isless;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:326:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:327:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:328:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:329:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:42:
In file included from /usr/local/include/pcl-1.11/pcl/memory.h:48:
In file included from /usr/local/include/eigen3/Eigen/Core:371:
/usr/local/include/eigen3/Eigen/src/Core/MathFunctions.h:719:16: error: no member named 'isfinite' in namespace 'std'; did you mean 'finite'?
    using std::isfinite;
          ~~~~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:319:9: note: 'finite' declared here
using ::isfinite;
        ^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:42:
In file included from /usr/local/include/pcl-1.11/pcl/memory.h:48:
In file included from /usr/local/include/eigen3/Eigen/Core:371:
/usr/local/include/eigen3/Eigen/src/Core/MathFunctions.h:734:16: error: no member named 'isinf' in namespace 'std'
    using std::isinf;
          ~~~~~^
/usr/local/include/eigen3/Eigen/src/Core/MathFunctions.h:749:16: error: no member named 'isnan' in namespace 'std'
    using std::isnan;
          ~~~~~^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:43:
/usr/local/include/pcl-1.11/pcl/pcl_macros.h:219:38: error: expected unqualified-id
bool pcl_isnan (T&& x) { return std::isnan (std::forward<T> (x)); }
                                     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/math.h:165:5: note: expanded from macro 'isnan'
    ( sizeof(x) == sizeof(float)  ? __inline_isnanf((float)(x))          \
    ^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:43:
/usr/local/include/pcl-1.11/pcl/pcl_macros.h:223:41: error: expected unqualified-id
bool pcl_isfinite (T&& x) { return std::isfinite (std::forward<T> (x)); }
                                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/math.h:155:5: note: expanded from macro 'isfinite'
    ( sizeof(x) == sizeof(float)  ? __inline_isfinitef((float)(x))       \
    ^
In file included from /tmp/pcl-test-20200805-22232-1lnfre8/pcd_write.cpp:2:
In file included from /usr/local/include/pcl-1.11/pcl/io/pcd_io.h:43:
/usr/local/include/pcl-1.11/pcl/pcl_macros.h:227:38: error: expected unqualified-id
bool pcl_isinf (T&& x) { return std::isinf (std::forward<T> (x)); }

SergioRAgostinho · 2020-08-06T13:21:03Z

PCL's CI has been bitten by this issue a couple of times. In the current CI setup we were forced to settle for command-line tools.
https://github.com/PointCloudLibrary/pcl/blob/84f694372b507e970f8447a84e6f2d787bea9d14/.ci/azure-pipelines/build/macos.yaml#L17

I'm unsure of homebrew's CI infrastructure but keep it in mind.

A juicy list of user reports of the same problem can be found at PointCloudLibrary/pcl#2601

dtrodrigues · 2020-08-07T05:39:06Z

Including std_cmake_args in the test block does add -DCMAKE_OSX_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk as a CMake argument , which matches what the Azure pipeline is doing: https://github.com/Homebrew/homebrew-core/pull/59146/checks?check_run_id=949839522#step:6:52 so I'm not completely sure what the difference is.

SergioRAgostinho · 2020-08-07T07:45:19Z

@dtrodrigues CMake is not picking up on the command line tools. It's using XCode's Toolchain.
https://github.com/Homebrew/homebrew-core/pull/59146/checks?check_run_id=949839522#step:6:132

My suspicion is that the command line tools are not present in the path you're specifying to CMake.

dtrodrigues · 2020-08-07T16:31:06Z

This is possibly related to Homebrew/brew#7426 . Looking at a smaller example like the osqp formula, when building, the C compiler is /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang but when testing, it is /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang. The build environment seems to clear out and explicitly set the path where as test does not.

Compared to #52532, this is a case where we want to use the CLT vs the sdk.

@Bo98 do you have any ideas?

Bo98 · 2020-08-07T18:26:12Z

The problematic flag is likely -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include. This should almost never be done - the compiler is perfectly capable of finding /usr/include itself with the correct -isysroot. The positioning of that flag is elevating it to be near the start of the include search path rather than near the end, which messes up C++ code.

This is likely a problem in a pkg-config file or CMake module of PCL or one of its dependencies.

dtrodrigues · 2020-08-12T12:48:42Z

I'm not really sure where to go from here. One part that puzzles me is that the library and some executables appear to build successfully during the install stage but the library isn't usable during the test stage.

The currently available Homebrew pcl version doesn't work with the current boost version (1.73) so the software right now is unusable, which isn't great.

Based on the comment from @Bo98, this may be an upstream issue with PCL or one of its dependencies, so we're kind of stuck until that is resolved.

Bo98 · 2020-08-12T13:22:32Z

One part that puzzles me is that the library and some executables appear to build successfully during the install stage but the library isn't usable during the test stage.

It's possibly because of the superenv's heroic work to make a fundamentally broken build somehow work.

Based on the comment from @Bo98, this may be an upstream issue with PCL or one of its dependencies, so we're kind of stuck until that is resolved.

I think it's a VTK bug. I can have a look but it might be a day or two before I manage to.

kunaltyagi · 2020-08-14T15:03:20Z

Change target to PCL 1.11.1?

SergioRAgostinho · 2020-08-15T10:12:48Z

Formula/pcl.rb

-      -DBUILD_simulation:BOOL=AUTO_OFF
+      -DBUILD_simulation:BOOL=OFF
      -DWITH_CUDA:BOOL=OFF
      -DWITH_DOCS:BOOL=OFF
+      -DWITH_OPENGL:BOOL=OFF


You might be able to enable these again now. We merged some last minute fixes after realizing that OpenGL is still being shipped in Catalina.

SergioRAgostinho · 2020-08-15T10:13:08Z

Formula/pcl.rb

@@ -13,39 +12,34 @@ class Pcl < Formula
    sha256 "d14889b636e81d1427a7d0300c028b571ac038e54b3760eba8900a7175d210c1" => :high_sierra
  end

-  depends_on "cmake" => :build
+  depends_on "cmake" => [:build, :test]
  depends_on "pkg-config" => :build
  depends_on "boost"
  depends_on "cminpack"


This is no longer needed

SergioRAgostinho · 2020-08-15T10:13:20Z

Formula/pcl.rb

  depends_on "pkg-config" => :build
  depends_on "boost"
  depends_on "cminpack"
  depends_on "eigen"
  depends_on "flann"
-  depends_on "glew"


This is needed again.

SergioRAgostinho · 2020-08-15T10:16:56Z

This is our current CI build pipeline in macos using homebrew.
https://github.com/PointCloudLibrary/pcl/blob/master/.ci/azure-pipelines/build/macos.yaml
You can enable pretty much everything besides examples, global tests and cuda code.

I can submit a PR later against your branch with the changes.

dtrodrigues · 2020-08-15T17:29:47Z

@SergioRAgostinho do you want to submit a new PR directly against homebrew-core with your desired changes and I can close this one?

SergioRAgostinho · 2020-08-16T09:43:15Z

Sure.

Formula/pcl.rb

dtrodrigues · 2020-08-31T01:07:16Z

@Bo98 you were right -- vtk installed by HomeBrew added those include paths:

 $ rg "usr/include"
vtk/8.2.0_10/lib/cmake/vtk-8.2/Modules/vtkpng.cmake
4:set(vtkpng_INCLUDE_DIRS "${VTK_INSTALL_PREFIX}/include/vtk-8.2;@@HOMEBREW_PREFIX@@/include;/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include")

vtk/8.2.0_10/lib/cmake/vtk-8.2/Modules/vtkexpat.cmake
4:set(vtkexpat_INCLUDE_DIRS "${VTK_INSTALL_PREFIX}/include/vtk-8.2;/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include")

vtk/8.2.0_10/lib/cmake/vtk-8.2/Modules/vtkzlib.cmake
4:set(vtkzlib_INCLUDE_DIRS "${VTK_INSTALL_PREFIX}/include/vtk-8.2;/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include")

vtk/8.2.0_10/lib/cmake/vtk-8.2/Modules/vtklibxml2.cmake
4:set(vtklibxml2_INCLUDE_DIRS "${VTK_INSTALL_PREFIX}/include/vtk-8.2;/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/libxml2")

After merging #60380 and rebasing on top of that, this PR should pass CI.

dtrodrigues · 2020-09-02T04:16:03Z

With the fix for vtk now in place, this should be good to go.

BrewTestBot · 2020-09-02T06:15:19Z

🤖 A scheduled task has triggered a merge.

dtrodrigues mentioned this pull request Aug 4, 2020

The pcl library installed by "brew install pcl" can not be used. #59064

Closed

dtrodrigues force-pushed the pcl-1.11.0 branch 2 times, most recently from 63ee8cc to 73b22b4 Compare August 5, 2020 15:00

dtrodrigues added help wanted Task(s) needing PRs from the community or maintainers test failure CI fails while running the test-do block labels Aug 5, 2020

SergioRAgostinho mentioned this pull request Aug 7, 2020

boost 1.73.0 breaks PCLPointCloud2 due to change in location of endian header PointCloudLibrary/pcl#4302

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dtrodrigues added the maintainer feedback Additional maintainers' opinions may be needed label Aug 7, 2020

dtrodrigues force-pushed the pcl-1.11.0 branch from 73b22b4 to c98f224 Compare August 8, 2020 02:27

SergioRAgostinho mentioned this pull request Aug 13, 2020

Enable pcl_simulation in osx PointCloudLibrary/pcl#4325

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dtrodrigues force-pushed the pcl-1.11.0 branch from c98f224 to 5f4e91c Compare August 15, 2020 01:33

dtrodrigues changed the title ~~Pcl 1.11.0~~ Pcl 1.11.1 Aug 15, 2020

SergioRAgostinho reviewed Aug 15, 2020

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KrisThielemans mentioned this pull request Aug 20, 2020

Clang 9.0.1 on OSX and CMake failure UCL/STIR#531

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dtrodrigues mentioned this pull request Aug 26, 2020

pcl formula depends on boost without version, but newest boost is incompatible #60192

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MikeMcQuaid reviewed Aug 26, 2020

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This was referenced Aug 30, 2020

vtk: clean up problematic include paths #60380

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rust 1.46.0 #60290

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dtrodrigues force-pushed the pcl-1.11.0 branch from 5f4e91c to 8996041 Compare August 31, 2020 00:48

bayandin mentioned this pull request Sep 1, 2020

rust build-from-source failures #57305

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dtrodrigues added 2 commits September 1, 2020 21:06

pcl 1.11.1

0e91d76

visp: revision bump for pcl

7e08ace

dtrodrigues force-pushed the pcl-1.11.0 branch from 8996041 to 7e08ace Compare September 2, 2020 01:07

dtrodrigues removed help wanted Task(s) needing PRs from the community or maintainers maintainer feedback Additional maintainers' opinions may be needed test failure CI fails while running the test-do block labels Sep 2, 2020

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Pcl 1.11.1 #59146

Pcl 1.11.1 #59146

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Pcl 1.11.1 #59146

Pcl 1.11.1 #59146

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