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I've encountered multiple installation issues trying to install from source, in part due to the sheer number of dependencies the project requires.
I'm on macOS, with my default compiler being clang 18.1.8 (homebrewed version), on x86_64.
Attempting to create a fresh python environment will all of the dependencies needed for multipers via mamba (or conda) currently doesn't work for my system
Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
...
error libmamba Could not solve for environment specs
...
gudhi 3.8.0 would require
│ └─ libcxx >=15.0.7 , which conflicts with any installable versions previously reported;
critical libmamba Could not solve for environment specs
The first big issue seems to be conda version of gudhi, which introduces many outdated dependencies which can't resolve. For example, if I use the latest packages from all of those dependencies except gudhi (installed via pip), and then I run:
mambainstallgudhi
Within said virtualenv, I recieve the following output:
If I just install gudhi from pip, the wheel installs fine.
The second big issue for me comes from trying to compile from source. I recieve hundreds of errors, though they all seem to be of the same type (and linked to TBB), they're all like:
/Users/mpiekenbrock/opt/miniconda3/envs/multipers/include/tbb/../oneapi/tbb/detail/_task.h:216:13: error: aligned deallocation functionoftype'void (void *, std::align_val_t) noexcept' is only available on macOS 10.14 or newer
virtual ~task() = default;
^
Attached below is the full log, though it's practically the same thing repeated many times.
Interesting, I can actually install gudhi-devel perfectly fine; I think that's likley due to the fact that they use cmake (which uses pkgconfig) to find these large system libraries I've already installed in my system long ago (like tbb), whereas it looks like multipers is relying on a pure python-dependency approach, which might not support linking as smoothly as pkgconfig
The text was updated successfully, but these errors were encountered:
For the dependencies, I need to investigate a bit, as, in the case of "from source compilation", I haven't updated that in a while;
My issue is that I want to use the less source as possible (i.e., only from conda) and have similar installation between OSes which may add unnecessary problems.
Also, I don't have access to a macOS machine, so if you have a working environment, I'd be happy to have it.
According to the current GitHub workflow (which builds + tests + sends to pypi) the following environment should work without any issue on any up-to-date Linux or macOS machine
Regarding your compilation error, this is due to an (old) Apple clang issue, which I used to point out, but I forgot to re-add to the documentation when I rewrote it. This should be solved by disabling a compilation optimization, by uncommenting a line in the setup file.
There is also this workaround in the workflow which is possible.
Part of 6773
I've encountered multiple installation issues trying to install from source, in part due to the sheer number of dependencies the project requires.
I'm on macOS, with my default compiler being clang 18.1.8 (homebrewed version), on x86_64.
Attempting to create a fresh python environment will all of the dependencies needed for multipers via mamba (or conda) currently doesn't work for my system
In particular,
Yields multiple error messages of the form:
Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
...
error libmamba Could not solve for environment specs
...
gudhi 3.8.0 would require
│ └─ libcxx >=15.0.7 , which conflicts with any installable versions previously reported;
critical libmamba Could not solve for environment specs
The first big issue seems to be conda version of gudhi, which introduces many outdated dependencies which can't resolve. For example, if I use the latest packages from all of those dependencies except gudhi (installed via pip), and then I run:
Within said virtualenv, I recieve the following output:
dependency hell
pkgs/main/noarch No change pkgs/r/osx-64 No change pkgs/r/noarch No change nodefaults/osx-64 No change nodefaults/noarch No change pkgs/main/osx-64 5.9MB @ 4.3MB/s 1.4s conda-forge/noarch 15.3MB @ 6.4MB/s 2.2s conda-forge/osx-64 31.6MB @ 6.0MB/s 5.3s Pinned packages: - python 3.11.* Transaction Prefix: /Users/mpiekenbrock/opt/miniconda3/envs/multipers Updating specs: - gudhi Package Version Build Channel Size ──────────────────────────────────────────────────────────────────────────────────────── Install: ──────────────────────────────────────────────────────────────────────────────────────── + pcre 8.45 h23ab428_0 pkgs/main Cached + pandoc 2.12 hecd8cb5_3 pkgs/main Cached + gmp 6.2.1 he9d5cce_3 pkgs/main Cached + expat 2.6.2 hcec6c5f_0 pkgs/main Cached + mpfr 4.0.2 h9066e36_1 pkgs/main Cached + ipython_genutils 0.2.0 pyhd3eb1b0_1 pkgs/main Cached + pyrsistent 0.17.3 py36haf1e3a3_0 pkgs/main Cached + entrypoints 0.3 py36_0 pkgs/main Cached + async_generator 1.10 pyhd3eb1b0_0 pkgs/main Cached + zipp 3.6.0 pyhd3eb1b0_0 pkgs/main Cached + dataclasses 0.8 pyh4f3eec9_6 pkgs/main Cached + testpath 0.5.0 pyhd3eb1b0_0 pkgs/main Cached + importlib-metadata 4.8.1 py36hecd8cb5_0 pkgs/main Cached + immutables 0.16 py36h9ed2024_0 pkgs/main Cached + importlib_metadata 4.8.1 hd3eb1b0_0 pkgs/main Cached + contextvars 2.4 py_0 pkgs/main Cached + cryptography 35.0.0 py36h2fd3fbb_0 pkgs/main Cached + brotlipy 0.7.0 py36h9ed2024_1003 pkgs/main Cached + dbus 1.13.18 h18a8e69_0 pkgs/main Cached + qt 5.9.7 h468cd18_1 pkgs/main Cached + boost-cpp 1.67.0 h1de35cc_4 pkgs/main Cached + backcall 0.2.0 pyhd3eb1b0_0 pkgs/main Cached + olefile 0.46 pyhd3eb1b0_0 pkgs/main Cached + pickleshare 0.7.5 pyhd3eb1b0_1003 pkgs/main Cached + munkres 1.1.4 py_0 pkgs/main 14kB + pyopenssl 22.0.0 pyhd3eb1b0_0 pkgs/main Cached + cgal 4.12 py36h8634a1c_1 conda-forge Cached + gudhi 2.3.0 py36h83d4a3d_0 conda-forge Cached + nbclassic 0.2.6 pyhd3eb1b0_0 pkgs/main Cached Remove: ──────────────────────────────────────────────────────────────────────────────────────── - 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Then, I actually run into issues even in the install, recieving an unknown error of the following:
If I just install gudhi from pip, the wheel installs fine.
The second big issue for me comes from trying to compile from source. I recieve hundreds of errors, though they all seem to be of the same type (and linked to TBB), they're all like:
Attached below is the full log, though it's practically the same thing repeated many times.
multipers_cpp.txt
Interesting, I can actually install
gudhi-devel
perfectly fine; I think that's likley due to the fact that they use cmake (which uses pkgconfig) to find these large system libraries I've already installed in my system long ago (like tbb), whereas it looks likemultipers
is relying on a pure python-dependency approach, which might not support linking as smoothly as pkgconfigThe text was updated successfully, but these errors were encountered: