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install issues about s-jsdm HOT 5 CLOSED

theoreticalecology avatar theoreticalecology commented on September 25, 2024
install issues

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Comments (5)

MaximilianPi avatar MaximilianPi commented on September 25, 2024

Hi Florian,
thats the macOS related issue which I mentioned earlier (see #18):
"conda version : 4.8.3" is not able to download the torch packages on macOS. Remove conda, install the previous version, and config conda to not update automatically to 4.8.3 via:

$ rm -r miniconda #remove old version
$wget https://repo.continuum.io/miniconda/Miniconda3-py37_4.8.2-MacOSX-x86_64.sh -O miniconda.sh
$bash miniconda.sh -b -p $HOME/miniconda
$export PATH="$HOME/miniconda/bin:$PATH"
$hash -r
$rm miniconda.sh
$conda config --set auto_update_conda false


$ conda info

     active environment : base
    active env location : /Users/Negorashi2011/opt/miniconda3
            shell level : 1
       user config file : /Users/Negorashi2011/.condarc
 populated config files :
          conda version : 4.8.3
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __osx=10.14.6
       base environment : /Users/Negorashi2011/opt/miniconda3  (writable)

           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/Negorashi2011/opt/miniconda3/pkgs
                          /Users/Negorashi2011/.conda/pkgs
       envs directories : /Users/Negorashi2011/opt/miniconda3/envs
                          /Users/Negorashi2011/.conda/envs
               platform : osx-64
             user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.6 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 502:20
             netrc file : None
           offline mode : False

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florianhartig avatar florianhartig commented on September 25, 2024

Hi Max, for me this still doesn't install automatically. I have now removed all my conda installations (pretty sure), and try to install, this is what I get

> install_sjSDM()
* Downloading 'https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh' ...
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh'
Content type 'application/x-sh' length 52755183 bytes (50.3 MB)
==================================================
downloaded 50.3 MB

* Installing Miniconda -- please wait a moment ...
PREFIX=/Users/florian/Library/r-miniconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): ...working... done                                       
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/florian/Library/r-miniconda

  added / updated specs:
    - asn1crypto==1.3.0=py37_0
    - ca-certificates==2020.1.1=0
    - certifi==2019.11.28=py37_0
    - cffi==1.14.0=py37hb5b8e2f_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h1de35cc_0
    - conda==4.8.2=py37_0
    - cryptography==2.8=py37ha12b0ac_0
    - idna==2.8=py37_0
    - libcxx==4.0.1=hcfea43d_1
    - libcxxabi==4.0.1=hcfea43d_1
    - libedit==3.1.20181209=hb402a30_0
    - libffi==3.2.1=h475c297_4
    - ncurses==6.2=h0a44026_0
    - openssl==1.1.1d=h1de35cc_4
    - pip==20.0.2=py37_1
    - pycosat==0.6.3=py37h1de35cc_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.1.0=py37_0
    - pysocks==1.7.1=py37_0
    - python.app==2=py37_10
    - python==3.7.6=h359304d_2
    - readline==7.0=h1de35cc_5
    - requests==2.22.0=py37_1
    - ruamel_yaml==0.15.87=py37h1de35cc_0
    - setuptools==45.2.0=py37_0
    - six==1.14.0=py37_0
    - sqlite==3.31.1=ha441bb4_0
    - tk==8.6.8=ha441bb4_0
    - tqdm==4.42.1=py_0
    - urllib3==1.25.8=py37_0
    - wheel==0.34.2=py37_0
    - xz==5.2.4=h1de35cc_4
    - yaml==0.1.7=hc338f04_2
    - zlib==1.2.11=h1de35cc_3


The following NEW packages will be INSTALLED:

  asn1crypto         pkgs/main/osx-64::asn1crypto-1.3.0-py37_0
  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2019.11.28-py37_0
  cffi               pkgs/main/osx-64::cffi-1.14.0-py37hb5b8e2f_0
  chardet            pkgs/main/osx-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/osx-64::conda-4.8.2-py37_0
  conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.6.0-py37h1de35cc_0
  cryptography       pkgs/main/osx-64::cryptography-2.8-py37ha12b0ac_0
  idna               pkgs/main/osx-64::idna-2.8-py37_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h475c297_4
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_0
  openssl            pkgs/main/osx-64::openssl-1.1.1d-h1de35cc_4
  pip                pkgs/main/osx-64::pip-20.0.2-py37_1
  pycosat            pkgs/main/osx-64::pycosat-0.6.3-py37h1de35cc_0
  pycparser          pkgs/main/osx-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/osx-64::pyopenssl-19.1.0-py37_0
  pysocks            pkgs/main/osx-64::pysocks-1.7.1-py37_0
  python             pkgs/main/osx-64::python-3.7.6-h359304d_2
  python.app         pkgs/main/osx-64::python.app-2-py37_10
  readline           pkgs/main/osx-64::readline-7.0-h1de35cc_5
  requests           pkgs/main/osx-64::requests-2.22.0-py37_1
  ruamel_yaml        pkgs/main/osx-64::ruamel_yaml-0.15.87-py37h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-45.2.0-py37_0
  six                pkgs/main/osx-64::six-1.14.0-py37_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-ha441bb4_0
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  tqdm               pkgs/main/noarch::tqdm-4.42.1-py_0
  urllib3            pkgs/main/osx-64::urllib3-1.25.8-py37_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py37_0
  xz                 pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
  yaml               pkgs/main/osx-64::yaml-0.1.7-hc338f04_2
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/florian/Library/r-miniconda

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.4.5.1         |           py37_0         155 KB
    conda-4.8.3                |           py37_0         2.8 MB
    idna-2.9                   |             py_1          49 KB
    libffi-3.2.1               |       h0a44026_6          43 KB
    openssl-1.1.1g             |       h1de35cc_0         2.2 MB
    pycparser-2.20             |             py_0          92 KB
    requests-2.23.0            |           py37_0          92 KB
    setuptools-46.1.3          |           py37_0         520 KB
    sqlite-3.31.1              |       h5c1f38d_1         2.4 MB
    tqdm-4.45.0                |             py_0          58 KB
    xz-5.2.5                   |       h1de35cc_0         282 KB
    ------------------------------------------------------------
                                           Total:         8.8 MB

The following packages will be UPDATED:

  certifi                                 2019.11.28-py37_0 --> 2020.4.5.1-py37_0
  conda                                        4.8.2-py37_0 --> 4.8.3-py37_0
  idna                    pkgs/main/osx-64::idna-2.8-py37_0 --> pkgs/main/noarch::idna-2.9-py_1
  libffi                                   3.2.1-h475c297_4 --> 3.2.1-h0a44026_6
  openssl                                 1.1.1d-h1de35cc_4 --> 1.1.1g-h1de35cc_0
  pycparser          pkgs/main/osx-64::pycparser-2.19-py37~ --> pkgs/main/noarch::pycparser-2.20-py_0
  requests                                    2.22.0-py37_1 --> 2.23.0-py37_0
  setuptools                                  45.2.0-py37_0 --> 46.1.3-py37_0
  sqlite                                  3.31.1-ha441bb4_0 --> 3.31.1-h5c1f38d_1
  tqdm                                          4.42.1-py_0 --> 4.45.0-py_0
  xz                                       5.2.4-h1de35cc_4 --> 5.2.5-h1de35cc_0



Downloading and Extracting Packages
setuptools-46.1.3    | 520 KB    | ########## | 100% 
requests-2.23.0      | 92 KB     | ########## | 100% 
xz-5.2.5             | 282 KB    | ########## | 100% 
tqdm-4.45.0          | 58 KB     | ########## | 100% 
idna-2.9             | 49 KB     | ########## | 100% 
openssl-1.1.1g       | 2.2 MB    | ########## | 100% 
libffi-3.2.1         | 43 KB     | ########## | 100% 
pycparser-2.20       | 92 KB     | ########## | 100% 
certifi-2020.4.5.1   | 155 KB    | ########## | 100% 
sqlite-3.31.1        | 2.4 MB    | ########## | 100% 
conda-4.8.3          | 2.8 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/florian/Library/r-miniconda/envs/r-reticulate

  added / updated specs:
    - numpy
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |              mkl           6 KB
    certifi-2020.4.5.1         |           py36_0         155 KB
    intel-openmp-2019.4        |              233         887 KB
    libgfortran-3.0.1          |       h93005f0_2         426 KB
    mkl-2019.4                 |              233       101.9 MB
    mkl-service-2.3.0          |   py36hfbe908c_0         202 KB
    mkl_fft-1.0.15             |   py36h5e564d8_0         139 KB
    mkl_random-1.1.0           |   py36ha771720_0         287 KB
    numpy-1.18.1               |   py36h7241aed_0           5 KB
    numpy-base-1.18.1          |   py36h6575580_1         3.9 MB
    pip-20.0.2                 |           py36_1         1.7 MB
    python-3.6.10              |       hc70fcce_1        17.1 MB
    readline-8.0               |       h1de35cc_0         326 KB
    setuptools-46.1.3          |           py36_0         511 KB
    six-1.14.0                 |           py36_0          26 KB
    wheel-0.34.2               |           py36_0          50 KB
    ------------------------------------------------------------
                                           Total:       127.7 MB

The following NEW packages will be INSTALLED:

  blas               pkgs/main/osx-64::blas-1.0-mkl
  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2020.4.5.1-py36_0
  intel-openmp       pkgs/main/osx-64::intel-openmp-2019.4-233
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h0a44026_6
  libgfortran        pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
  mkl                pkgs/main/osx-64::mkl-2019.4-233
  mkl-service        pkgs/main/osx-64::mkl-service-2.3.0-py36hfbe908c_0
  mkl_fft            pkgs/main/osx-64::mkl_fft-1.0.15-py36h5e564d8_0
  mkl_random         pkgs/main/osx-64::mkl_random-1.1.0-py36ha771720_0
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_0
  numpy              pkgs/main/osx-64::numpy-1.18.1-py36h7241aed_0
  numpy-base         pkgs/main/osx-64::numpy-base-1.18.1-py36h6575580_1
  openssl            pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
  pip                pkgs/main/osx-64::pip-20.0.2-py36_1
  python             pkgs/main/osx-64::python-3.6.10-hc70fcce_1
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-46.1.3-py36_0
  six                pkgs/main/osx-64::six-1.14.0-py36_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py36_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3



Downloading and Extracting Packages
numpy-1.18.1         | 5 KB      | ########## | 100% 
intel-openmp-2019.4  | 887 KB    | ########## | 100% 
mkl_random-1.1.0     | 287 KB    | ########## | 100% 
readline-8.0         | 326 KB    | ########## | 100% 
mkl-service-2.3.0    | 202 KB    | ########## | 100% 
blas-1.0             | 6 KB      | ########## | 100% 
certifi-2020.4.5.1   | 155 KB    | ########## | 100% 
wheel-0.34.2         | 50 KB     | ########## | 100% 
setuptools-46.1.3    | 511 KB    | ########## | 100% 
numpy-base-1.18.1    | 3.9 MB    | ########## | 100% 
six-1.14.0           | 26 KB     | ########## | 100% 
mkl_fft-1.0.15       | 139 KB    | ########## | 100% 
libgfortran-3.0.1    | 426 KB    | ########## | 100% 
pip-20.0.2           | 1.7 MB    | ########## | 100% 
mkl-2019.4           | 101.9 MB  | ########## | 100% 
python-3.6.10        | 17.1 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate r-reticulate
#
# To deactivate an active environment, use
#
#     $ conda deactivate

* Miniconda has been successfully installed at '/Users/florian/Library/r-miniconda'.

Installation failed... Try to install manually PyTorch (install instructions: https://github.com/TheoreticalEcology/s-jSDM
If the installation still fails, please report the following error on https://github.com/TheoreticalEcology/s-jSDM/issues
invalid 'path' argument

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MaximilianPi avatar MaximilianPi commented on September 25, 2024

Hi Florian,

  1. run the install_sjSDM() again (w/o removing miniconda or the env)
  2. can you please post the output of install_diagnostic() (the name is not yet updated)

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MaximilianPi avatar MaximilianPi commented on September 25, 2024

I found bug in the install_sjSDM function, can you please try it again with the latest version.

Btw, the automatic miniconda install, sjSDM install, and all the tests are now running in the automatic build test for ubuntu and windows... now only macos is left

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florianhartig avatar florianhartig commented on September 25, 2024

Now it works, great!

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