CMakeLists file missing?

[michaelcaterino]

Hi,

I'm trying to install Asteroid on macos 10.13.6. Got Cmake installed. Installed developer tools (needed xcrun). Getting closer, but am still having installation issues. It seems to expect a CMakeLists.txt file in the coraxlib directory. There are CMakeLists files in the root (Asteroid-1.0/), src/, src/asteroid/, core/, and test/ directories, but the installed coraxlib directory is empty. Am I missing a file? I'm not sure yet if that's leading to the subsequent MPI errors. For now I am assuming so.

Thanks,
Mike C.

Installation log and error text below:

iMac-2:Asteroid-1.0 mcaterino$ ./install.sh
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 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.

-- The C compiler identification is AppleClang 10.0.0.10001044
-- The CXX compiler identification is AppleClang 10.0.0.10001044
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CXX_STANDARD_14_SUPPORT
-- Performing Test CXX_STANDARD_14_SUPPORT - Success
CMake Error at CMakeLists.txt:24 (add_subdirectory):
The source directory

/Applications/SystematicsSoftware/Asteroid-1.0/coraxlib

does not contain a CMakeLists.txt file.

-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- Configuring incomplete, errors occurred!
make: *** No targets specified and no makefile found. Stop.
Now running unit tests...
PLEASE RUN THIS SCRIPT FROM THE ASTEROID ROOT DIRECTORY
./run_tests.sh: line 3: build/bin/test_stepwise_induced: No such file or directory
./run_tests.sh: line 4: build/bin/test_bitvector: No such file or directory
./run_tests.sh: line 5: build/bin/test_mappings: No such file or directory
./run_tests.sh: line 6: build/bin/test_unrooted_trees: No such file or directory
./run_tests.sh: line 7: build/bin/test_internode_distance: No such file or directory

[BenoitMorel]

Hi Mike, Thanks for your report. Habe you run git clone with --recursive when cloning the repository? Benoit Le mer. 19 juil. 2023, 20:16, michaelcaterino ***@***.***> a écrit :

…

Hi, I'm trying to install Asteroid on macos 10.13.6. Got Cmake installed. Installed developer tools (needed xcrun). Getting closer, but am still having installation issues. It seems to expect a CMakeLists.txt file in the coraxlib directory. There are CMakeLists files in the root (Asteroid-1.0/), src/, src/asteroid/, core/, and test/ directories, but the installed coraxlib directory is empty. Am I missing a file? I'm not sure yet if that's leading to the subsequent MPI errors. For now I am assuming so. Thanks, Mike C. *Installation log and error text below:* iMac-2:Asteroid-1.0 mcaterino$ ./install.sh CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 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. -- The C compiler identification is AppleClang 10.0.0.10001044 -- The CXX compiler identification is AppleClang 10.0.0.10001044 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CXX_STANDARD_14_SUPPORT -- Performing Test CXX_STANDARD_14_SUPPORT - Success CMake Error at CMakeLists.txt:24 (add_subdirectory): The source directory /Applications/SystematicsSoftware/Asteroid-1.0/coraxlib does not contain a CMakeLists.txt file. -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- Configuring incomplete, errors occurred! make: *** No targets specified and no makefile found. Stop. Now running unit tests... PLEASE RUN THIS SCRIPT FROM THE ASTEROID ROOT DIRECTORY ./run_tests.sh: line 3: build/bin/test_stepwise_induced: No such file or directory ./run_tests.sh: line 4: build/bin/test_bitvector: No such file or directory ./run_tests.sh: line 5: build/bin/test_mappings: No such file or directory ./run_tests.sh: line 6: build/bin/test_unrooted_trees: No such file or directory ./run_tests.sh: line 7: build/bin/test_internode_distance: No such file or directory — Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UL63I47BJDBYVO2DMDXRAP7TANCNFSM6AAAAAA2QJVBA4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[michaelcaterino]

Not the first time. But trying that now I have the following issues (also seeming to be related to coraxlib):

iMac-2:SystematicsSoftware mcaterino$ git clone --recursive https://github.com/BenoitMorel/Asteroid
Cloning into 'Asteroid'...
remote: Enumerating objects: 986, done.
remote: Counting objects: 100% (24/24), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 986 (delta 6), reused 9 (delta 4), pack-reused 962
Receiving objects: 100% (986/986), 211.08 KiB | 3.77 MiB/s, done.
Resolving deltas: 100% (675/675), done.
Submodule 'coraxlib' (https://codeberg.org/Exelixis-Lab/coraxlib.git) registered for path 'coraxlib'
Cloning into '/Applications/SystematicsSoftware/Asteroid/coraxlib'...
fatal: unable to access 'https://codeberg.org/Exelixis-Lab/coraxlib.git/': SSL certificate problem: certificate has expired
fatal: clone of 'https://codeberg.org/Exelixis-Lab/coraxlib.git' into submodule path '/Applications/SystematicsSoftware/Asteroid/coraxlib' failed
Failed to clone 'coraxlib'. Retry scheduled
Cloning into '/Applications/SystematicsSoftware/Asteroid/coraxlib'...
fatal: unable to access 'https://codeberg.org/Exelixis-Lab/coraxlib.git/': SSL certificate problem: certificate has expired
fatal: clone of 'https://codeberg.org/Exelixis-Lab/coraxlib.git' into submodule path '/Applications/SystematicsSoftware/Asteroid/coraxlib' failed
Failed to clone 'coraxlib' a second time, aborting

[BenoitMorel]

Oh I recently got a similar issue, this is coming from one of our dependencies :( Can you try to export the following variable before cloning? export GIT_SSL_NO_VERIFY=1 Please let me know if that works, such that I update the README. Do you know what xcrun is, or at least for why it was required? And how did you install it? Unfortunately I don't have a mac, but if I can add information to guide the next users, that would be awesome! Le mer. 19 juil. 2023 à 20:50, michaelcaterino ***@***.***> a écrit :

…

Not the first time. But trying that now I have the following issues (also seeming to be related to coraxlib): iMac-2:SystematicsSoftware mcaterino$ git clone --recursive https://github.com/BenoitMorel/Asteroid Cloning into 'Asteroid'... remote: Enumerating objects: 986, done. remote: Counting objects: 100% (24/24), done. remote: Compressing objects: 100% (20/20), done. remote: Total 986 (delta 6), reused 9 (delta 4), pack-reused 962 Receiving objects: 100% (986/986), 211.08 KiB | 3.77 MiB/s, done. Resolving deltas: 100% (675/675), done. Submodule 'coraxlib' (https://codeberg.org/Exelixis-Lab/coraxlib.git) registered for path 'coraxlib' Cloning into '/Applications/SystematicsSoftware/Asteroid/coraxlib'... fatal: unable to access 'https://codeberg.org/Exelixis-Lab/coraxlib.git/': SSL certificate problem: certificate has expired fatal: clone of 'https://codeberg.org/Exelixis-Lab/coraxlib.git' into submodule path '/Applications/SystematicsSoftware/Asteroid/coraxlib' failed Failed to clone 'coraxlib'. Retry scheduled Cloning into '/Applications/SystematicsSoftware/Asteroid/coraxlib'... fatal: unable to access 'https://codeberg.org/Exelixis-Lab/coraxlib.git/': SSL certificate problem: certificate has expired fatal: clone of 'https://codeberg.org/Exelixis-Lab/coraxlib.git' into submodule path '/Applications/SystematicsSoftware/Asteroid/coraxlib' failed Failed to clone 'coraxlib' a second time, aborting — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UPPKCGY5TY5CRGWQITXRAUADANCNFSM6AAAAAA2QJVBA4> . You are receiving this because you commented.Message ID: ***@***.***>

[michaelcaterino]

That does appear to have worked. I haven't had time to run the program yet, but the installation thinks it was successful. I will report back.

Oh, and xcrun is part of the Apple compiler, necessary for CMake to run. Some may have it installed by default, but I did not.

Installation was as follows:
In Terminal, type the following command string: 'xcode-select --install' and hit Enter. I was prompted for my password, and then had to accept a licensing agreement. There's a download involved, but the os knew where to get it from - no URL needed.

Thank you!
Mike

[michaelcaterino]

Success! Thank you for your help.

[BenoitMorel]

Great :) Thanks for the feedback Le jeu. 20 juil. 2023 à 14:39, michaelcaterino ***@***.***> a écrit :

…

Success! Thank you for your help. — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UNAP6VYNDU2SXX7TGTXRERI3ANCNFSM6AAAAAA2QJVBA4> . You are receiving this because you commented.Message ID: ***@***.***>