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shiboken2@5.15.2 install fails #337

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TristanDebrunner opened this issue Jul 13, 2022 · 15 comments
Closed

shiboken2@5.15.2 install fails #337

TristanDebrunner opened this issue Jul 13, 2022 · 15 comments

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@TristanDebrunner
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TristanDebrunner commented Jul 13, 2022 •
edited

I am trying to brew install --only-dependencies freecad as described in the README, but the install fails at shiboken2@5.15.2.

I am running MacOS Monterey on a MacBook Pro with M1 Max.

Output of brew install freecad/freecad/shiboken2@5.15.2:

==> Downloading https://download.qt.io/official_releases/QtForPython/pyside2/PySide2-5.15.2-src/pyside-setup-opensource-src-5.15.2.tar.xz
Already downloaded: /Users/tristan/Library/Caches/Homebrew/downloads/1250b0074c8d43c55c7efb1d9dcefaa1c469a48527b2cb08a59a6c9d2fb02e8a--pyside-setup-opensource-src-5.15.2.tar.xz
==> Installing shiboken2@5.15.2 from freecad/freecad
==> cmake -DBUILD_TYPE=Release -DBUILD_TESTS:BOOL=OFF -DPYTHON_EXECUTABLE=/opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/bin/python3.9 -DPYTHON_LIBRARY=/opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/lib/libpython3.9.dylib -DPYTHON_INCLUDE_DIR=
==> make -j10 install
Last 15 lines from /Users/tristan/Library/Logs/Homebrew/shiboken2@5.15.2/02.make:
make[1]: *** [libshiboken/CMakeFiles/libshiboken.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 77%] Building CXX object ApiExtractor/CMakeFiles/apiextractor.dir/docparser.cpp.o
cd /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DCMAKE_CXX_COMPILER=\"/opt/homebrew/Library/Homebrew/shims/mac/super/clang++\" -DHAVE_LIBXSLT -DHAVE_QTXMLPATTERNS -DQT_CORE_LIB -DQT_NETWORK_LIB -DQT_NO_DEBUG -DQT_XMLPATTERNS_LIB -DQT_XML_LIB -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor/apiextractor_autogen/include -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor/parser -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/libxml2 -iframework /opt/homebrew/opt/qt@5/lib -isystem /opt/homebrew/opt/qt@5/lib/QtCore.framework/Headers -isystem /opt/homebrew/opt/qt@5/./mkspecs/macx-clang-arm64 -isystem /opt/homebrew/opt/qt@5/lib/QtXml.framework/Headers -isystem /opt/homebrew/opt/qt@5/lib/QtXmlPatterns.framework/Headers -isystem /opt/homebrew/opt/qt@5/lib/QtNetwork.framework/Headers -Wall -fvisibility=hidden -Wno-strict-aliasing -D QT_NO_CAST_FROM_ASCII -D QT_NO_CAST_TO_ASCII -O3 -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk   -fPIC -fPIC -std=gnu++11 -MD -MT ApiExtractor/CMakeFiles/apiextractor.dir/docparser.cpp.o -MF CMakeFiles/apiextractor.dir/docparser.cpp.o.d -o CMakeFiles/apiextractor.dir/docparser.cpp.o -c /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor/docparser.cpp
[ 78%] Building CXX object ApiExtractor/CMakeFiles/apiextractor.dir/doxygenparser.cpp.o
cd /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DCMAKE_CXX_COMPILER=\"/opt/homebrew/Library/Homebrew/shims/mac/super/clang++\" -DHAVE_LIBXSLT -DHAVE_QTXMLPATTERNS -DQT_CORE_LIB -DQT_NETWORK_LIB -DQT_NO_DEBUG -DQT_XMLPATTERNS_LIB -DQT_XML_LIB -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor/apiextractor_autogen/include -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor/parser -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/libxml2 -iframework /opt/homebrew/opt/qt@5/lib -isystem /opt/homebrew/opt/qt@5/lib/QtCore.framework/Headers -isystem /opt/homebrew/opt/qt@5/./mkspecs/macx-clang-arm64 -isystem /opt/homebrew/opt/qt@5/lib/QtXml.framework/Headers -isystem /opt/homebrew/opt/qt@5/lib/QtXmlPatterns.framework/Headers -isystem /opt/homebrew/opt/qt@5/lib/QtNetwork.framework/Headers -Wall -fvisibility=hidden -Wno-strict-aliasing -D QT_NO_CAST_FROM_ASCII -D QT_NO_CAST_TO_ASCII -O3 -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk   -fPIC -fPIC -std=gnu++11 -MD -MT ApiExtractor/CMakeFiles/apiextractor.dir/doxygenparser.cpp.o -MF CMakeFiles/apiextractor.dir/doxygenparser.cpp.o.d -o CMakeFiles/apiextractor.dir/doxygenparser.cpp.o -c /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor/doxygenparser.cpp
[ 80%] Building CXX object ApiExtractor/CMakeFiles/apiextractor.dir/qtdocparser.cpp.o
cd /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DCMAKE_CXX_COMPILER=\"/opt/homebrew/Library/Homebrew/shims/mac/super/clang++\" -DHAVE_LIBXSLT -DHAVE_QTXMLPATTERNS -DQT_CORE_LIB -DQT_NETWORK_LIB -DQT_NO_DEBUG -DQT_XMLPATTERNS_LIB -DQT_XML_LIB -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor/apiextractor_autogen/include -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor -I/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor/parser -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/libxml2 -iframework /opt/homebrew/opt/qt@5/lib -isystem /opt/homebrew/opt/qt@5/lib/QtCore.framework/Headers -isystem /opt/homebrew/opt/qt@5/./mkspecs/macx-clang-arm64 -isystem /opt/homebrew/opt/qt@5/lib/QtXml.framework/Headers -isystem /opt/homebrew/opt/qt@5/lib/QtXmlPatterns.framework/Headers -isystem /opt/homebrew/opt/qt@5/lib/QtNetwork.framework/Headers -Wall -fvisibility=hidden -Wno-strict-aliasing -D QT_NO_CAST_FROM_ASCII -D QT_NO_CAST_TO_ASCII -O3 -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk   -fPIC -fPIC -std=gnu++11 -MD -MT ApiExtractor/CMakeFiles/apiextractor.dir/qtdocparser.cpp.o -MF CMakeFiles/apiextractor.dir/qtdocparser.cpp.o.d -o CMakeFiles/apiextractor.dir/qtdocparser.cpp.o -c /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/ApiExtractor/qtdocparser.cpp
[ 81%] Linking CXX static library libapiextractor.a
cd /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor && /opt/homebrew/Cellar/cmake/3.23.2/bin/cmake -P CMakeFiles/apiextractor.dir/cmake_clean_target.cmake
cd /tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/macbuild5.15.2/ApiExtractor && /opt/homebrew/Cellar/cmake/3.23.2/bin/cmake -E cmake_link_script CMakeFiles/apiextractor.dir/link.txt --verbose=1
/usr/bin/ar qc libapiextractor.a CMakeFiles/apiextractor.dir/apiextractor_autogen/mocs_compilation.cpp.o CMakeFiles/apiextractor.dir/apiextractor.cpp.o CMakeFiles/apiextractor.dir/abstractmetabuilder.cpp.o CMakeFiles/apiextractor.dir/abstractmetalang.cpp.o CMakeFiles/apiextractor.dir/fileout.cpp.o CMakeFiles/apiextractor.dir/graph.cpp.o CMakeFiles/apiextractor.dir/messages.cpp.o CMakeFiles/apiextractor.dir/propertyspec.cpp.o CMakeFiles/apiextractor.dir/reporthandler.cpp.o CMakeFiles/apiextractor.dir/sourcelocation.cpp.o CMakeFiles/apiextractor.dir/typeparser.cpp.o CMakeFiles/apiextractor.dir/typesystem.cpp.o CMakeFiles/apiextractor.dir/typesystemparser.cpp.o CMakeFiles/apiextractor.dir/include.cpp.o CMakeFiles/apiextractor.dir/typedatabase.cpp.o CMakeFiles/apiextractor.dir/clangparser/compilersupport.cpp.o CMakeFiles/apiextractor.dir/clangparser/clangparser.cpp.o CMakeFiles/apiextractor.dir/clangparser/clangbuilder.cpp.o CMakeFiles/apiextractor.dir/clangparser/clangdebugutils.cpp.o CMakeFiles/apiextractor.dir/clangparser/clangutils.cpp.o CMakeFiles/apiextractor.dir/parser/codemodel.cpp.o CMakeFiles/apiextractor.dir/parser/enumvalue.cpp.o CMakeFiles/apiextractor.dir/xmlutils.cpp.o CMakeFiles/apiextractor.dir/xmlutils_libxslt.cpp.o CMakeFiles/apiextractor.dir/xmlutils_qt.cpp.o CMakeFiles/apiextractor.dir/docparser.cpp.o CMakeFiles/apiextractor.dir/doxygenparser.cpp.o CMakeFiles/apiextractor.dir/qtdocparser.cpp.o
/usr/bin/ranlib libapiextractor.a
[ 81%] Built target apiextractor
make: *** [all] Error 2

Do not report this issue to Homebrew/brew or Homebrew/core!
@ipatch
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ipatch commented Jul 13, 2022

try installing shiboken2@5.15.5 instead of shiboken2@5.15.2

brew install shiboken2@5.15.5

unfortunately i haven't generated a shiboken bottle for that release/arch of macos so you'll have to build it from source for time being.

@TristanDebrunner
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I tried all the versions except freecad/freecad/shiboken2-python3_10@5.15.2, and they have all failed. Here's the 5.15.5 output:

==> Downloading https://ghcr.io/v2/homebrew/core/llvm/manifests/14.0.6_1
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/llvm/blobs/sha256:bb22d243ad001cd69c26ebe670684701ef03d9d3895773d30b907d90c645a744
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:bb22d243ad001cd69c26ebe670684701ef03d9d3895773d30b907d90c645a744?se=2022-07-14T19%3A15%3A00Z&sig=FHhiQXe%2B%2Fe8ex1EyKv2hmeJJ193GBsR5w3YVGGFjdz4%3D&sp=r&spr=https&sr=b&sv=2019-12-12
######################################################################## 100.0%
==> Downloading https://download.qt.io/official_releases/QtForPython/pyside2/PySide2-5.15.5-src/pyside-setup-opensource-src-5.15.5.zip
Already downloaded: /Users/tristan/Library/Caches/Homebrew/downloads/7e478bd63671464e429850a09bc66eeda44c95ddd8ab0b66cfc8224ffd477cc9--pyside-setup-opensource-src-5.15.5.zip
==> Installing shiboken2@5.15.5 from freecad/freecad
==> Installing dependencies for freecad/freecad/shiboken2@5.15.5: llvm
==> Installing freecad/freecad/shiboken2@5.15.5 dependency: llvm
==> Pouring llvm--14.0.6_1.arm64_monterey.bottle.tar.gz
🍺  /opt/homebrew/Cellar/llvm/14.0.6_1: 5,851 files, 983.5MB
==> Installing freecad/freecad/shiboken2@5.15.5
==> Patching
Error: Failure while executing; `patch -g 0 -f -p1` exited with 1. Here's the output:
patching file sources/shiboken2/libshiboken/pep384impl.cpp
Hunk #1 FAILED at 707.
1 out of 1 hunk FAILED -- saving rejects to file sources/shiboken2/libshiboken/pep384impl.cpp.rej
patching file sources/shiboken2/libshiboken/sbknumpyarrayconverter.cpp
patch unexpectedly ends in middle of line
Hunk #1 FAILED at 116.
1 out of 1 hunk FAILED -- saving rejects to file sources/shiboken2/libshiboken/sbknumpyarrayconverter.cpp.rej

I tried to look at the files mentioned in the error message, but haven't been able to find them.

@ipatch
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ipatch commented Jul 14, 2022

yes correct. there's an issue with the patch for shiboken2@5.15.5 presently. #336

i'm working on getting that resolved at the moment.

@TristanDebrunner
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Ah, missed that issue. I'll wait for the fix and try again

@ipatch
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ipatch commented Jul 15, 2022

try with pr #344

@TristanDebrunner
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That PR makes progress, I'm no longer erroring out on the patch step. The error is now in the make step, just like the original issue. I found this in the make log:

/tmp/shiboken2A5.15.5-20220715-48643-uc6jqc/pyside-setup-opensource-src-5.15.5/sources/shiboken2/libshiboken/sbknumpyarrayconverter.cpp:119:22: error: use of undeclared identifier 'NPY_ARRAY_UPDATEIFCOPY'
        if ((flags & NPY_ARRAY_UPDATEIFCOPY) != 0)
                     ^
1 error generated.
make[2]: *** [libshiboken/CMakeFiles/libshiboken.dir/sbknumpyarrayconverter.cpp.o] Error 1

I went back and looked at the log from the 5.15.2 install, and it has the same error:

/tmp/shiboken2A5.15.2-20220713-10029-10z34xd/pyside-setup-opensource-src-5.15.2/sources/shiboken2/libshiboken/sbknumpyarrayconverter.cpp:119:22: error: use of undeclared identifier 'NPY_ARRAY_UPDATEIFCOPY'
        if ((flags & NPY_ARRAY_UPDATEIFCOPY) != 0)
                     ^
1 error generated.
make[2]: *** [libshiboken/CMakeFiles/libshiboken.dir/sbknumpyarrayconverter.cpp.o] Error 1

Is there a numpy requirement that I may not be fulfilling? Not sure if this gives you useful info about my system:

$ brew list numpy
/opt/homebrew/Cellar/numpy/1.23.1/bin/f2py
/opt/homebrew/Cellar/numpy/1.23.1/bin/f2py3
/opt/homebrew/Cellar/numpy/1.23.1/bin/f2py3.10
/opt/homebrew/Cellar/numpy/1.23.1/bin/f2py3.9
/opt/homebrew/Cellar/numpy/1.23.1/lib/python3.10/ (862 files)
/opt/homebrew/Cellar/numpy/1.23.1/lib/python3.9/ (862 files)

@plaes
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plaes commented Jul 16, 2022 •
edited

Apparently this symbol has been dropped from Numpy since 1.23:

The UPDATEIFCOPY array flag has been removed together with the enum NPY_ARRAY_UPDATEIFCOPY. The associated (and deprecated) PyArray_XDECREF_ERR was also removed. These were all deprecated in 1.14. They are replaced by WRITEBACKIFCOPY, that requires calling PyArray_ResoveWritebackIfCopy before the array is deallocated.

https://numpy.org/doc/stable/release/1.23.0-notes.html?highlight=npy_array_updateifcopy#expired-deprecations

@ipatch
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ipatch commented Jul 16, 2022

Apparently this symbol has been dropped from Numpy since 1.23:

The UPDATEIFCOPY array flag has been removed together with the enum NPY_ARRAY_UPDATEIFCOPY. The associated (and deprecated) PyArray_XDECREF_ERR was also removed. These were all deprecated in 1.14. They are replaced by WRITEBACKIFCOPY, that requires calling PyArray_ResoveWritebackIfCopy before the array is deallocated.

https://numpy.org/doc/stable/release/1.23.0-notes.html?highlight=npy_array_updateifcopy#expired-deprecations

yeah thats what the patch file aims to resolve

  • patch shiboken2 source tarball to be compatible with the numpy v1.23 api
  • theres additional patch to allow the same tarball to build against python 3.10

both patches were inlined into the shiboken2@5.15.5

make sure youre attempting to install that version and not an older version of shiboken2

to complicate matters apparently some formatting is lost after ci modifies the shiboken2 formula to add the bottle blocks (that was fun edge case to figure out 😭)

so attempted to move the 2 patches out into separate files with separate commits to allow the shiboken2 formula file (tarball) ref the required patches and hopefully not run into ci issue above. also i used the github provided .patch for these two required patches.

IMHO, i have never run into such an issue patching software using the patch cmd and editing the formula files. not sure if there some edge case with the shiboken2 tarball but hopefully ill figure it out later this week. presently afk 📱

@ipatch
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ipatch commented Jul 17, 2022 •
edited

okay #345 should fix this, will require manually building of the formula, as the inline patch with CRLF has issues with the current CI unfortunately.

@TristanDebrunner
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With the latest fixes, brew install shiboken2@5.15.5 succeeds!

Unfortunately, brew install --only-dependencies freecad still tries to use 5.15.2, which fails. Is there a way to force the use of 5.15.5 instead?

@ipatch
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ipatch commented Jul 18, 2022 •
edited

Unfortunately, brew install --only-dependencies freecad still tries to use 5.15.2, which fails. Is there a way to force the use of 5.15.5 instead?

yeah, unfortunately until i or somebody else fixes the main freecad.rb formula file you'll have to manually build freecad using cmake or install from a pre built binary package.

@Vittorio1993
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With the latest fixes, brew install shiboken2@5.15.5 succeeds!

Unfortunately, brew install --only-dependencies freecad still tries to use 5.15.2, which fails. Is there a way to force the use of 5.15.5 instead?

Did you manage to build it manually?

@TristanDebrunner
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TristanDebrunner commented Aug 3, 2022 •
edited

Sorry, I had some other stuff come up that slowed down this project.

I was able to take the list of packages that brew install --only-dependencies freecad would've installed, and brew install them individually, replacing 5.15.2 with 5.15.5. I got through most of the build, but ran into issues with MakeMacBundleRelocatable.py that I haven't fully resolved. That's not really a homebrew issue though.

UPDATE: Just saw #348. That seems to be the same problem I ran into

@ipatch
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ipatch commented Aug 3, 2022

Sorry, I had some other stuff come up that slowed down this project.

I was able to take the list of packages that brew install --only-dependencies freecad would've installed, and brew install them individually, replacing 5.15.2 with 5.15.5. I got through most of the build, but ran into issues with MakeMacBundleRelocatable.py that I haven't fully resolved. That's not really a homebrew issue though.

UPDATE: Just saw #348. That seems to be the same problem I ran into

good to know that i'm not the only person running into that issue. 👍

@ipatch
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ipatch commented Aug 17, 2022

brew install --only-dependencies freecad

i believe me merging in the following commit should resolve the above mentioned issues,

addab68

if you run into any more issues feel free to comment on this issue or even open a new & separate issue.

@ipatch ipatch closed this as completed Aug 17, 2022
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@plaes @ipatch @TristanDebrunner @Vittorio1993