phyx installed

[ChaoShenzjs]

Hi, phyx must be made installed under python3?

[josephwb]

Python is only used (as a wrapper) to run the tests. They were updated to python3 syntax, but I thought they were backwards-compatible.

What error are you getting?

[ChaoShenzjs]

g++ -g -O2 -O3 -std=c++14 -fopenmp -Wall -DOMP -ffast-math -ftree-vectorize -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++: error：unrecognized command line option ‘-std=c++14’

[josephwb]

Sorry you are having problems.

This seems to be an issue with your C++ compiler. What does g++ --version return?

[ChaoShenzjs]

Thanks, I realized that my gcc version is too lower and needed to update.

2023年5月18日 22:50，Joseph W. Brown @.***> 写道：

Sorry you are having problems.

This seems to be an issue with your C++ compiler. What does g++ --version return?

— Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/176#issuecomment-1553180453, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF2MFW7WSZ3E2JTMBKOD2QDXGYZK5ANCNFSM6AAAAAAYGOY7DI. You are receiving this because you authored the thread.

[ChaoShenzjs]

Hi, I have updated the gcc and g++ version in my environment and also installed armadillo dependency using source in phyx/deps directory. But terminated at the make step in phyx/src, showwing: In file included from rate_model.cpp:5: rate_model.h:4:10: fatal error: armadillo: No such file or directory 4 | #include

2023年5月18日 22:50，Joseph W. Brown @.***> 写道：

Sorry you are having problems.

This seems to be an issue with your C++ compiler. What does g++ --version return?

— Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/176#issuecomment-1553180453, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF2MFW7WSZ3E2JTMBKOD2QDXGYZK5ANCNFSM6AAAAAAYGOY7DI. You are receiving this because you authored the thread.

[josephwb]

Did you do the armadillo installation step? Which OS are you using?

[ChaoShenzjs]

My OS is Centos7 and didthe armadillo installation step.

2023年5月19日 21:38，Joseph W. Brown @.***> 写道：

Did you do the armadillo installation step? Which OS are you using?

— Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/176#issuecomment-1554590054, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF2MFW7UWAGO3RMETZRGFOTXG5ZUFANCNFSM6AAAAAAYGOY7DI. You are receiving this because you authored the thread.

[josephwb]

Hrm. Which version of armadillo are you using? You need version >= 5.2. Did it install with no warnings? Do you have all of the dependencies installed?

[ChaoShenzjs]

Hmm, I have checked the dependencies and some were lost, unfortunately, it always causes some troubles to install these dependencies by apt-get or source code. I find that phyx could be install through conda but with a OS environment for Python3. You know that I wanna phyx as a dependencies for the phylogenetic pipeline of Yang & Smith, 2014, MBE. However, their scripts were written in Python27, which is incompatible when running the pipeline. A easier way is that I could install phyx by conda in python27. I think it’s a heartfelt wish for new learner who wants to use this pipeline. Best regards! Thank you so much!

2023年5月19日 23:19，Joseph W. Brown @.***> 写道：

Hrm. Which version of armadillo are you using? You need version >= 5.2. Did it install with no warnings? Do you have all of the dependencies https://github.com/FePhyFoFum/phyx/blob/master/README.md?plain=1#L179 installed?

— Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/176#issuecomment-1554744809, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF2MFW45TLK4BWULBNK2TGLXG6FQTANCNFSM6AAAAAAYGOY7DI. You are receiving this because you authored the thread.

[josephwb]

Phyx doesn't use python code, though; it is C++. The only time python is involved is as a wrapper for testing (and generating manpages), and really that it is for the developers to make sure things are not broken after code pushes.

The Y&S paper is almost 10 years old, so it is not surprising that some things do not work. Python2 was officially deprecated 3 years ago, which was about when we changed the syntax of our phyx tests. If you know python well it would not be too difficult to update Y&S to python3. It may even be as simple as changing the print calls; in fact, that was about the only thing done to our tests to 'upgrade' them to python3.

But the python version issue is really unrelated to building/running phyx. It seems that the compiler cannot find where armadillo is installed. Do you know where it was installed? If so you can 1) add an alias to your .bashrc file or 2) export your library path.

Let me know if that works.

[josephwb]

Can I close this @ChaoShenzjs?