Errors in Set-up data files

[JuanLuGMid]

Hello,

First of all, thanks for this amazing tool. I'm getting errors when I run python calculate_organisms.py . Previously, I've downloaded the retrorules from https://retrorules.org/dl and did not get any problem. The errors looks like this:

Then, when I run pytest -v I get 44 failed, 67 passed tests. I suppose it is motivated by the errors in the image above. Something strage is that I do not have the folder 'organisms' in 'data'.

Thanks in advance.

[tduigou]

Hi @JuanLuGMid, did you double check you followed the instructions to create and activate the conda environement? What does conda list returns?

[JuanLuGMid]

Thanks for your answer. I reintalled RetroPathRL an I'm getting the same problem. I think I carefully followed the commands to create the environment (MCTS) and install the needed packages. If I run conda list I get:

# Name Version Build Channel atomicwrites 1.4.0 py_0 attrs 21.4.0 pyhd3eb1b0_0 blas 1.0 mkl cairo 1.14.12 hf171d8a_3 certifi 2021.5.30 py36haa95532_0 colorama 0.4.4 pyhd3eb1b0_0 freetype 2.10.4 hd328e21_0 icc_rt 2019.0.0 h0cc432a_1 icu 58.2 ha925a31_3 importlib-metadata 4.8.1 py36haa95532_0 importlib_metadata 4.8.1 hd3eb1b0_0 iniconfig 1.1.1 pyhd3eb1b0_0 intel-openmp 2022.0.0 haa95532_3663 jpeg 9e h2bbff1b_0 libboost 1.67.0 hd9e427e_4 libpng 1.6.37 h2a8f88b_0 libtiff 4.2.0 he0120a3_1 lz4-c 1.9.3 h2bbff1b_1 mkl 2018.0.3 1 mkl_fft 1.0.6 py36hdbbee80_0 mkl_random 1.0.1 py36h77b88f5_1 more-itertools 8.12.0 pyhd3eb1b0_0 numpy 1.15.4 py36ha559c80_0 numpy-base 1.15.4 py36h8128ebf_0 olefile 0.46 py36_0 packaging 21.3 pyhd3eb1b0_0 pandas 1.1.5 py36hd77b12b_0 pillow 8.3.1 py36h4fa10fc_0 pip 21.2.2 py36haa95532_0 pixman 0.40.0 h2bbff1b_1 pluggy 0.13.1 py36haa95532_0 py 1.11.0 pyhd3eb1b0_0 py-boost 1.67.0 py36h8300f20_4 pymongo 3.12.0 py36hd77b12b_0 pyparsing 3.0.4 pyhd3eb1b0_0 pytest 6.2.4 py36haa95532_2 python 3.6.13 h3758d61_0 python-dateutil 2.8.2 pyhd3eb1b0_0 pytz 2021.3 pyhd3eb1b0_0 pyyaml 5.4.1 py36h2bbff1b_1 rdkit 2019.03.1.0 py36h3d1ada6_1 rdkit rp3 0.0 dev_0 rp3-dcache 0.3 dev_0 scikit-learn 0.19.1 py36hae9bb9f_0 scipy 1.1.0 py36h4f6bf74_1 setuptools 58.0.4 py36haa95532_0 six 1.16.0 pyhd3eb1b0_1 sqlite 3.38.3 h2bbff1b_0 tbb 2021.5.0 h59b6b97_0 tbb4py 2021.3.0 py36h59b6b97_0 tk 8.6.11 h2bbff1b_1 toml 0.10.2 pyhd3eb1b0_0 typing_extensions 4.1.1 pyh06a4308_0 vc 14.2 h21ff451_1 vs2015_runtime 14.27.29016 h5e58377_2 wheel 0.37.1 pyhd3eb1b0_0 wincertstore 0.2 py36h7fe50ca_0 xz 5.2.5 h8cc25b3_1 yaml 0.2.5 he774522_0 zipp 3.6.0 pyhd3eb1b0_0 zlib 1.2.12 h8cc25b3_2 zstd 1.5.2 h19a0ad4_0

I checked after running calculate_organisms.py that organisms folder was created with some files inside. Nonetheless, the error persists.

[tduigou]

Hi @JuanLuGMid. Sorry for the delay. Did you finally solve the issue? If not, which operating system are you using?

[JuanLuGMid]

Hi, the problem was not solved. I am using Windows 10 Home

[tduigou]

Re-reading the thread, here what I think.

It is "normal" that some errors appear in the logs during the calculate_organisms.py execution. This is because some compounds defined in chassis appear to be not valid compounds. However, a folder should have been created at the end of the execution with some pickle files inside it.

RetroPathRL has been developped and tested using Linux and Mac operating systems. Some functionnalities embedded into the code -- the first one that come to my mind is the methods to time out / kill rule applications taking too much time -- will not work with a Windows OS. Hence, RetroPathRL is not fully usable with Windows.

I'll mention the OS compatibilities in the README so that this is clearly stated.

If you can use a Linux or Mac that should fix the issues you met. Sorry again for the delay.