installation on macOS v10.14.6

[Abieskawa]

I have been trying to install axe on my computer. Here is my code:
brew install cmake
git clone --recursive https://github.com/kdmurray91/axe.git axe
cd axe
cmake .
make install axe

I have installed bioconda, so there is (base) in front of my username. Firstly, I doubt that there is something wrong with my enviornment, so I have tried to leave the base environment, but I got same error message.

Here is the error message:

WARNING: unknown config value 'latex_paper_size' in override, ignoring
WARNING: html_static_path entry '.static' does not exist

Exception occurred:
File "/opt/anaconda3/lib/python3.9/site-packages/sphinx/application.py", line 376, in build
os.unlink(envfile)
PermissionError: [Errno 13] Permission denied: '/Users/kenhsu/axe/doc/man/.doctrees/environment.pickle'
The full traceback has been saved in /var/folders/tt/22nmrjys36s6lql2bl2czw9w0000gq/T/sphinx-err-si44dp0u.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at https://github.com/sphinx-doc/sphinx/issues. Thanks!
make[2]: *** [docs/CMakeFiles/doc_man] Error 2
make[1]: *** [docs/CMakeFiles/doc_man.dir/all] Error 2
make: *** [all] Error 2

[kdm9]

Hello @Abieskawa,

It looks like Sphinx, which I use to build the documentation, is broken on your system. I have no Mac system on which I can test why, so for now, please comment out the section about building the documentation. Specifcally:

• edit CMakeLists.txt in the root of the repository, and comment out or delete the line ADD_SUBDIRECTORY(docs) which should be line 64.
• Re-run cmake . and subsequent steps (make, then make install)

If that doesn't work, let me know by reopening this issue.

[Abieskawa]

This is what I got from cmake .
CMake Deprecation Warning at src/libqes/CMakeLists.txt:1 (CMAKE_MINIMUM_REQUIRED):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- Release build of libqes version: 0.3.3-4-gc1039c7
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND)
-- Configuring done
CMake Warning (dev):
Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake
--help-policy CMP0042" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

qes

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /Users/kenhsu/axe

this is what I received from make
[ 3%] Building C object src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o
clang: error: no such file or directory: 'NOTFOUND'
make[2]: *** [src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o] Error 1
make[1]: *** [src/libqes/src/CMakeFiles/qes_static.dir/all] Error 2
make: *** [all] Error 2

[lcamVz]

I am facing the same error

[ 3%] Building C object src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o clang: error: no such file or directory: 'NOTFOUND' make[2]: *** [src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o] Error 1 make[1]: *** [src/libqes/src/CMakeFiles/qes_static.dir/all] Error 2 make: *** [all] Error 2

how have you resolved this?

[Abieskawa]

Hi, I used other computer with Ubuntu installed in windows 10 platform XD, I gave up my laptop.

…

On Sat, Jul 16, 2022 at 5:16 AM lcamVz ***@***.***> wrote: I am facing the same error [ 3%] Building C object src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o clang: error: no such file or directory: 'NOTFOUND' make[2]: *** [src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o] Error 1 make[1]: *** [src/libqes/src/CMakeFiles/qes_static.dir/all] Error 2 make: *** [all] Error 2 how have you resolved this? — Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALHTY5ONMPEJ23NBUEAPV6LVUHIMJANCNFSM5SAQS7BQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[kdm9]

I am facing the same error

[ 3%] Building C object src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o clang: error: no such file or directory: 'NOTFOUND' make[2]: *** [src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o] Error 1 make[1]: *** [src/libqes/src/CMakeFiles/qes_static.dir/all] Error 2 make: *** [all] Error 2

how have you resolved this?

Please give the full error log. the notfound bit means that Cmake couldn't find one of the dependencies, but it's not clear which unless you post the full log.

[kdm9]

If your log is the same as @Abieskawa, then it's an issue with openmp on OSX. You need to install (with homebrew or similar) a more recent and complete version of clang/llvm. See this issue on stackoverflow: https://stackoverflow.com/questions/43555410/enable-openmp-support-in-clang-in-mac-os-x-sierra-mojave

Please note: this is in no way specific to axe, any OpenMP-based program will have the same trouble so this is worth doing if you're going to be using this mac for any bioinformatics work.

[lcamVz]

I ended up installing it in the labs workstation on the WSL Ubuntu 20.04. No luck with the Mac OS.

[kdm9]

That's a shame @lcamVz, but I'm glad you got it working somewhere. OSX is hard, as I don't have access to a Mac on which to test. Out of interest, did you try and install an openmp-compatible C compiler as per that stack overflow post? If so, I assume that also failed?

[prototaxites]

In case it helps anyone, I got axe to compile on MacOS (Ventura, M1 Pro, arm64) with the following:

brew install libomp

And then

cmake . -DOpenMP_CXX_FLAGS="-Xclang -fopenmp -I/opt/homebrew/Cellar/libomp/15.0.7/include" -DOpenMP_C_FLAGS="-Xclang -fopenmp -I/opt/homebrew/Cellar/libomp/15.0.7/include" -DOpenMP_CXX_LIB_NAMES=libomp  -DOpenMP_C_LIB_NAMES=libomp -DOpenMP_libomp_LIBRARY=/opt/homebrew/Cellar/libomp/15.0.7/lib/libomp.dylib -DCMAKE_SHARED_LINKER_FLAGS="-L/opt/homebrew/Cellar/libomp/15.0.7/lib -lomp -Wl,-rpath,/opt/homebrew/Cellar/libomp/15.0.7/lib" -DCMAKE_BUILD_TYPE=Debug

make

I have no idea what changes need to be specified in the CMakeLists.txt file to make this work permanently, but hopefully this will be of use to someone else. If you have a different Homebrew install path/different libomp version you may have to specify the paths above differently.