PPanGGOLiN version 2.1.1 - Failed building new version

[seajane]

I tried installing manually from the GitHub repo as I am unable to use conda from my work computers. I used a virtual environment (venv) instead. I get the following error:
note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for PPanGGOLiN Failed to build PPanGGOLiN ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (PPanGGOLiN)

It looks like the python was copied in fine: ... copying ppanggolin/workflow/workflow.py -> build/lib.macosx-14.0-arm64-cpython-312/ppanggolin/workflow running build_ext building 'nem_stats' extension ...

This is where I start to see clang warnings in clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/lib_io.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/lib_io.o -fcommon -Wno-int-conversion ppanggolin/nem/NEM/lib_io.c:107:9: warning: 'gets' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead. [-Wdeprecated-declarations] gets( NameF ) ; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:162:1: note: 'gets' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ppanggolin/nem/NEM/lib_io.c:158:9: warning: 'gets' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead. [-Wdeprecated-declarations] gets( NameF ) ; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:162:1: note: 'gets' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ppanggolin/nem/NEM/lib_io.c:235:9: warning: 'gets' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead. [-Wdeprecated-declarations] gets( stringread ) ; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:162:1: note: 'gets' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ ppanggolin/nem/NEM/lib_io.c:283:9: warning: 'gets' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead. [-Wdeprecated-declarations] gets( stringread ) ; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:162:1: note: 'gets' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of gets(3), it is highly recommended that you use fgets(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 4 warnings generated. clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_alg.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_alg.o -fcommon -Wno-int-conversion ppanggolin/nem/NEM/nem_alg.c:1511:20: warning: incompatible pointer types passing 'FILE **' (aka 'struct __sFILE **') to parameter of type 'FILE *' (aka 'struct __sFILE *'); dereference with * [-Wincompatible-pointer-types] setbuf(FlogP, NULL); ^~~~~ * /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:175:31: note: passing argument to parameter here void setbuf(FILE * __restrict, char * __restrict); ^ 1 warning generated. clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_exe.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_exe.o -fcommon -Wno-int-conversion ppanggolin/nem/NEM/nem_exe.c:516:38: warning: incompatible pointer types passing 'float *' to parameter of type 'float **'; take the address with & [-Wincompatible-pointer-types] ClassifM ) ) != STS_OK ) ^~~~~~~~ & ppanggolin/nem/NEM/nem_exe.c:138:28: note: passing argument to parameter 'MatP' here float **MatP /* O and allocated (size : Nl * Nc) */ ^ ppanggolin/nem/NEM/nem_exe.c:542:35: warning: incompatible pointer types passing 'float *' to parameter of type 'float **'; take the address with & [-Wincompatible-pointer-types] ClassifM ) ) != STS_OK ) ^~~~~~~~ & ppanggolin/nem/NEM/nem_exe.c:147:28: note: passing argument to parameter 'ClassifMP' here float **ClassifMP /* O and allocated (Npt*Nk) */ ^ ppanggolin/nem/NEM/nem_exe.c:373:23: warning: comparison of integers of different signs: 'AlgoET' and 'int' [-Wsign-compare] if ( NemPara.Algo == -1 ) ~~~~~~~~~~~~ ^ ~~ ppanggolin/nem/NEM/nem_exe.c:389:25: warning: comparison of integers of different signs: 'CvemET' and 'int' [-Wsign-compare] if ( NemPara.CvTest == -1 ) { ~~~~~~~~~~~~~~ ^ ~~ ppanggolin/nem/NEM/nem_exe.c:402:25: warning: comparison of integers of different signs: 'FormET' and 'int' [-Wsign-compare] if ( NemPara.Format == -1 ) ~~~~~~~~~~~~~~ ^ ~~ ppanggolin/nem/NEM/nem_exe.c:421:37: warning: comparison of integers of different signs: 'FamilyET' and 'int' [-Wsign-compare] if ( StatModel.Spec.ClassFamily == -1 ) ~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ ppanggolin/nem/NEM/nem_exe.c:428:37: warning: comparison of integers of different signs: 'ProporET' and 'int' [-Wsign-compare] if ( StatModel.Spec.ClassPropor == -1 ) ~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ ppanggolin/nem/NEM/nem_exe.c:435:37: warning: comparison of integers of different signs: 'DisperET' and 'int' [-Wsign-compare] if ( StatModel.Spec.ClassDisper == -1 ) ~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ 8 warnings generated. clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_hlp.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_hlp.o -fcommon -Wno-int-conversion clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_mod.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_mod.o -fcommon -Wno-int-conversion clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_nei.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_nei.o -fcommon -Wno-int-conversion clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_rnd.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_rnd.o -fcommon -Wno-int-conversion clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -Ippanggolin/nem/NEM/ -I/Users/hkbouzek/Documents/GitHub/PPanGGOLiN/ppgg/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c ppanggolin/nem/NEM/nem_stats.c -o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_stats.o -fcommon -Wno-int-conversion clang -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -lomp build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/genmemo.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/lib_io.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_alg.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_exe.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_hlp.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_mod.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_nei.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_rnd.o build/temp.macosx-14.0-arm64-cpython-312/ppanggolin/nem/NEM/nem_stats.o -o build/lib.macosx-14.0-arm64-cpython-312/nem_stats.cpython-312-darwin.so ld: library 'omp' not found clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command '/usr/bin/clang' failed with exit code 1 [end of output]

[JeanMainguy]

Hi,

It looks like this issue might be related to macOS. Since we don’t have access to a Mac, I tried installing PPanGGOLIN on a macOS 14 runner using GitHub Actions. I had to remove argorn and infernal from the dependencies, but the installation seems to have worked fine.

Could you share how you installed PPanGGOLIN manually? That might help us figure out what's going on.

Thanks!

[seajane]

Sure!

1. I created a virtual environment python3 -m venv ppgg
2. Activated the environment source ppgg/bin/activate
3. Brew installed dependencies:
   brew update
brew upgrade
brew install mmseqs2
brew install mafft
brew install infernal
brew install aragorn
4. Clone repo git clone https://github.com/labgem/PPanGGOLiN.git
5. Change directory cd PPanGGOLiN
6. Install with pip3 pip3 install .

[JeanMainguy]

Thanks for you installation instruction.

From the logs you shared, it looks like the problem might be related to the compilation of the C code in ppanggolin. The message library 'omp' not found clang: error: seems to indicate that the OpenMP library is missing.

It might be helpful to install OpenMP, as suggested there: OpenMP Simple C Example with CMake:

brew install libomp

and then export the OpenMP_ROOT variable :

export OpenMP_ROOT=$(brew --prefix)/opt/libomp

[seajane]

Thank you for your comments. Unfortunately it didn't work. I did get different messages in the error that may be of use however:
check.warn(importable) /private/var/folders/cv/q414p25d6yv_4sfgsdft3b400000gq/T/pip-build-env-p4oyqhwq/overlay/lib/python3.12/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'ppanggolin.formats' is absent from the packages` configuration.

---

          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'ppanggolin.formats' as an importable package[^1],
          but it is absent from setuptools' `packages` configuration.

          This leads to an ambiguous overall configuration. If you want to distribute this
          package, please make sure that 'ppanggolin.formats' is explicitly added
          to the `packages` configuration field.

          Alternatively, you can also rely on setuptools' discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).

          You can read more about "package discovery" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

          If you don't want 'ppanggolin.formats' to be distributed and are
          already explicitly excluding 'ppanggolin.formats' via
          `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
          you can try to use `exclude_package_data`, or `include-package-data=False` in
          combination with a more fine grained `package-data` configuration.

          You can read more about "package data files" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


          [^1]: For Python, any directory (with suitable naming) can be imported,
                even if it does not contain any `.py` files.
                On the other hand, currently there is no concept of package data
                directory, all directories are treated like packages.
          ********************************************************************************`

I get the same sort of error for 'ppanggolin.formats', 'ppanggolin.graph', 'ppanggolin.info', 'ppanggolin.meta', 'ppanggolin.mod', 'ppanggolin.nem', 'ppanggolin.nem.NEM', 'ppanggolin.projection', 'ppanggolin.utility', 'ppanggolin.workflow'

[seajane]

I am no expert in this at all, but feel the problem may be related to OpenMP changes on macOS https://mac.r-project.org/openmp/

[JeanMainguy]

Hi,
It looks like the issue might be related to Python 3.12. You could try installing ppanggolin in a Python 3.10 environment instead of 3.12 with :

python3.10 -m venv ppgg

I gave it a shot on a macOS 14 GitHub runner using your method and managed to install it with Python 3.10 (here are the log), but not with Python 3.12 (though I ran into a different error than you did).

Hope that helps!