ramintoosi/ROSS

PackagesNotFoundError:

Opened this issue · 3 comments

surjendumaity commented

C:\Users\surje\Documents\GitHub\ROSS>conda env create -f environment.yml
C:\Users\surje\anaconda3\Lib\argparse.py:2005: FutureWarning: remote_definition is deprecated and will be removed in 25.9. Use conda env create --file=URL instead.
action(self, namespace, argument_values, option_string)
Channels:

  • defaults
  • conda-forge
    Platform: win-64
    Collecting package metadata (repodata.json): done
    Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • zlib==1.2.11=h7f8727e_4
  • xz==5.2.5=h7b6447c_0
  • tk==8.6.11=h1ccaba5_0
  • sqlite==3.37.0=hc218d9a_0
  • shapely==1.7.1=py39h1728cc4_0
  • setuptools==58.0.4=py39h06a4308_0
  • readline==8.1.2=h7f8727e_1
  • python==3.9.7=h12debd9_1
  • pip==21.2.4=py39h06a4308_0
  • pandas==1.4.2=py39h295c915_0
  • openssl==1.1.1s=h7f8727e_0
  • numexpr==2.8.1=py39h6abb31d_0
  • ncurses==6.3=h7f8727e_2
  • mkl_random==1.2.2=py39h51133e4_0
  • mkl_fft==1.3.1=py39hd3c417c_0
  • mkl-service==2.4.0=py39h7f8727e_0
  • mkl==2021.4.0=h06a4308_640
  • markupsafe==2.0.1=py39h27cfd23_0
  • libstdcxx-ng==9.3.0=hd4cf53a_17
  • libgomp==9.3.0=h5101ec6_17
  • libgcc-ng==9.3.0=h5101ec6_17
  • libffi==3.3=he6710b0_2
  • ld_impl_linux-64==2.35.1=h7274673_9
  • intel-openmp==2021.4.0=h06a4308_3561
  • geos==3.8.0=he6710b0_0
  • certifi==2022.9.24=py39h06a4308_0
  • ca-certificates==2022.10.11=h06a4308_0
  • bottleneck==1.3.4=py39hce1f21e_0
  • _openmp_mutex==4.5=1_gnu

Current channels:

ramintoosi commented

Thank you for choosing ROSS for your research! I see you're using Windows to run ROSS, which I haven't personally tested yet. To help, I’ve prepared a requirements.txt file, which is attached to this comment. Please download it and follow these steps:

conda create -n ross python=3.9
conda activate ross
pip install -r requirements.txt

After setting it up, please verify if the code runs as expected. I currently don’t have access to a Windows OS to test these dependencies directly, but this setup should work. If you encounter any issues, please let me know, and we can work together to prepare an installation guide for Windows users.

Download requirements.txt

Giwon-DukeBME commented

Can you also provide me a requirement.txt for Apple Silicon?
the problem is I can't download pyyawt using macOS
Thanks!

ramintoosi commented

This seems to be an issue with the pyyawt package. For macOS, especially on Apple Silicon, you might need to build it from source. Here’s how you can do it (PyYAWT Doc):

git clone https://github.com/holgern/pyyawt
cd pyyawt
python setup.py install

Unfortunately, I don’t have access to macOS to test this process.

If building from source doesn’t work, another option is to modify the code to disable the use of wavelets. To do this:

  1. Open the file: ross_backend/resources/funcs/detection.py.
  2. Comment out the following line (line 4): 
    import pyyawt
  3. Comment out lines 43-45: 
        elif method == 'wavelet':
        c, l = pyyawt.wavedec(data, 2, 'db3')
        thr = thr_factor * pyyawt.denoising.wnoisest(c, l)[1]

These are the only parts of the code that rely on pyyawt for wavelet-based detection.

Please let us know which solution worked for you so that others encountering the same issue can benefit.