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KrishnaswamyLab / phateR

PHATE dimensionality reduction method implemented in R
GNU General Public License v2.0
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Error running Phate from R and/or re-installing python pahte from R #52

Closed semmrich closed 3 years ago

semmrich commented 3 years ago

Hello, I installed PhateR on 7/11/2020 on a win10 PC via RStudio using the github installation tutorial with

reticulate::py_install("phate", pip=TRUE)
devtools::install_github("KrishnaswamyLab/phateR")

which worked fine. I run phate to create the initial parameter for t, then optimize on knn and decay - great!

Today I wanted to rerun with other data and got this error:

> Phate.rerun <- phate(t(GetAssayData(object = S.NOmp, slot = "counts")), knn = 5, decay = 40, t = "auto", init = NULL)
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'phate'
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'phate'
Error: $ operator is invalid for atomic vectors

I then checked some similar issues reported on github for Phate, and tried this:

> reticulate::py_discover_config(required_module = "phate")
python:         C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
libpython:      C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/python38.dll
pythonhome:     C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate
version:        3.8.6 | packaged by conda-forge | (default, Oct  7 2020, 18:22:52) [MSC v.1916 64 bit (AMD64)]
Architecture:   64bit
numpy:          C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/Lib/site-packages/numpy
numpy_version:  1.19.4

seems to me there is no python phate module anymore... why? Because via RStudio r-miniconda are installed into C:/User/AppData, which files can be removed with time? No idea...

Ok, so I reinstalled phate as above, and got another error:

> reticulate::py_install("phate", pip=TRUE)
Collecting phate
  Using cached phate-1.0.4-py3-none-any.whl (23 kB)
Requirement already satisfied, skipping upgrade: numpy>=1.16.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (1.19.4)
Requirement already satisfied, skipping upgrade: tasklogger>=1.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (1.0.0)
Requirement already satisfied, skipping upgrade: future in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (0.18.2)
Requirement already satisfied, skipping upgrade: scipy>=1.1.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (1.5.3)
Requirement already satisfied, skipping upgrade: Deprecated in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (1.2.10)
Collecting s-gd2>=1.5
  Using cached s_gd2-1.8.tar.gz (53 kB)
Collecting scprep>=0.11.1
  Using cached scprep-1.0.10-py3-none-any.whl (99 kB)
Requirement already satisfied, skipping upgrade: graphtools>=1.3.1 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (1.5.2)
Requirement already satisfied, skipping upgrade: scikit-learn>=0.20.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (0.23.2)
Requirement already satisfied, skipping upgrade: matplotlib>=3.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from phate) (3.3.2)
Requirement already satisfied, skipping upgrade: wrapt<2,>=1.10 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from Deprecated->phate) (1.12.1)
Collecting decorator>=4.3.0
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting pandas>=0.25
  Using cached pandas-1.1.4-cp38-cp38-win_amd64.whl (8.9 MB)
Requirement already satisfied, skipping upgrade: pygsp>=0.5.1 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from graphtools>=1.3.1->phate) (0.5.1)
Requirement already satisfied, skipping upgrade: joblib>=0.11 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from scikit-learn>=0.20.0->phate) (0.17.0)
Requirement already satisfied, skipping upgrade: threadpoolctl>=2.0.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from scikit-learn>=0.20.0->phate) (2.1.0)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.1 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from matplotlib>=3.0->phate) (2.8.1)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from matplotlib>=3.0->phate) (2.4.7)
Requirement already satisfied, skipping upgrade: pillow>=6.2.0 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from matplotlib>=3.0->phate) (8.0.1)
Requirement already satisfied, skipping upgrade: certifi>=2020.06.20 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from matplotlib>=3.0->phate) (2020.6.20)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from matplotlib>=3.0->phate) (1.3.1)
Requirement already satisfied, skipping upgrade: cycler>=0.10 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from matplotlib>=3.0->phate) (0.10.0)
Collecting pytz>=2017.2
  Using cached pytz-2020.4-py2.py3-none-any.whl (509 kB)
Requirement already satisfied, skipping upgrade: six>=1.5 in c:\users\fuchsdeluxe\appdata\local\r-miniconda\envs\r-reticulate\lib\site-packages (from python-dateutil>=2.1->matplotlib>=3.0->phate) (1.15.0)
Building wheels for collected packages: s-gd2
  Building wheel for s-gd2 (setup.py): started
  Building wheel for s-gd2 (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: 'C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\fuchsdeluxe\\AppData\\Local\\Temp\\pip-install-hs7k5ddf\\s-gd2\\setup.py'"'"'; __file__='"'"'C:\\Users\\fuchsdeluxe\\AppData\\Local\\Temp\\pip-install-hs7k5ddf\\s-gd2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\fuchsdeluxe\AppData\Local\Temp\pip-wheel-o5tdvr1e'
       cwd: C:\Users\fuchsdeluxe\AppData\Local\Temp\pip-install-hs7k5ddf\s-gd2\
  Complete output (17 lines):
  C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\lib\distutils\extension.py:131: UserWarning: Unknown Extension options: 'headers'
    warnings.warn(msg)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.8
  creating build\lib.win-amd64-3.8\s_gd2
  copying s_gd2\s_gd2.py -> build\lib.win-amd64-3.8\s_gd2
  copying s_gd2\version.py -> build\lib.win-amd64-3.8\s_gd2
  copying s_gd2\__init__.py -> build\lib.win-amd64-3.8\s_gd2
  creating build\lib.win-amd64-3.8\s_gd2\swig
  copying s_gd2\swig\layout.py -> build\lib.win-amd64-3.8\s_gd2\swig
  copying s_gd2\swig\__init__.py -> build\lib.win-amd64-3.8\s_gd2\swig
  running build_ext
  building '_layout' extension
  error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
  ----------------------------------------
  ERROR: Failed building wheel for s-gd2
  Running setup.py clean for s-gd2
Failed to build s-gd2
Installing collected packages: s-gd2, decorator, pytz, pandas, scprep, phate
    Running setup.py install for s-gd2: started
    Running setup.py install for s-gd2: finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\fuchsdeluxe\\AppData\\Local\\Temp\\pip-install-hs7k5ddf\\s-gd2\\setup.py'"'"'; __file__='"'"'C:\\Users\\fuchsdeluxe\\AppData\\Local\\Temp\\pip-install-hs7k5ddf\\s-gd2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\fuchsdeluxe\AppData\Local\Temp\pip-record-5spr47f1\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\Include\s-gd2'
         cwd: C:\Users\fuchsdeluxe\AppData\Local\Temp\pip-install-hs7k5ddf\s-gd2\
    Complete output (17 lines):
    C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\lib\distutils\extension.py:131: UserWarning: Unknown Extension options: 'headers'
      warnings.warn(msg)
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.8
    creating build\lib.win-amd64-3.8\s_gd2
    copying s_gd2\s_gd2.py -> build\lib.win-amd64-3.8\s_gd2
    copying s_gd2\version.py -> build\lib.win-amd64-3.8\s_gd2
    copying s_gd2\__init__.py -> build\lib.win-amd64-3.8\s_gd2
    creating build\lib.win-amd64-3.8\s_gd2\swig
    copying s_gd2\swig\layout.py -> build\lib.win-amd64-3.8\s_gd2\swig
    copying s_gd2\swig\__init__.py -> build\lib.win-amd64-3.8\s_gd2\swig
    running build_ext
    building '_layout' extension
    error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
    ----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\fuchsdeluxe\\AppData\\Local\\Temp\\pip-install-hs7k5ddf\\s-gd2\\setup.py'"'"'; __file__='"'"'C:\\Users\\fuchsdeluxe\\AppData\\Local\\Temp\\pip-install-hs7k5ddf\\s-gd2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\fuchsdeluxe\AppData\Local\Temp\pip-record-5spr47f1\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\FUCHSD~1\AppData\Local\R-MINI~1\envs\R-RETI~1\Include\s-gd2' Check the logs for full command output.
Error: Error installing package(s): "phate"

Then I installed MS VC++ 2015-2019 Redist. 14.28.29325. And got exactly same error as above.

What can I do to resolve this?

Thanks in advance, Stephan

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] phateR_1.0.5                dyno_0.1.2                  dynwrap_1.2.1               dynplot_1.0.2.9000          dynmethods_1.0.5           
 [6] dynguidelines_1.0.0         dynfeature_1.0.0.9000       corrplot_0.84               scmap_1.12.0                MAST_1.16.0                
[11] Seurat_3.2.2                patchwork_1.0.1.9000        scran_1.18.1                scater_1.18.2               SingleCellExperiment_1.12.0
[16] SummarizedExperiment_1.20.0 Biobase_2.50.0              GenomicRanges_1.42.0        GenomeInfoDb_1.26.0         IRanges_2.24.0             
[21] S4Vectors_0.28.0            BiocGenerics_0.36.0         MatrixGenerics_1.2.0        tictoc_1.0                  futile.matrix_1.2.7        
[26] Matrix_1.3-0                gridExtra_2.3               gtable_0.3.0                rowr_1.1.3                  fgsea_1.16.0               
[31] VennDiagram_1.6.20          futile.logger_1.4.3         data.table_1.13.2           matrixStats_0.57.0          GSVA_1.38.0                
[36] BBmisc_1.11                 tibble_3.0.4                readxl_1.3.1                ggplot2_3.3.2               gplots_3.1.0               
[41] dplyr_1.0.2                 hash_2.2.6.1               

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1            GA_3.2                    tidyr_1.1.2               knitr_1.30                bit64_4.0.5              
  [6] irlba_2.3.3               DelayedArray_0.16.0       rpart_4.1-15              RCurl_1.98-1.2            generics_0.1.0           
 [11] cowplot_1.1.0             lambda.r_1.2.4            RSQLite_2.2.1             RANN_2.6.1                carrier_0.1.0            
 [16] proxy_0.4-24              future_1.20.1             bit_4.0.4                 spatstat.data_1.4-3       httpuv_1.5.4             
 [21] assertthat_0.2.1          viridis_0.5.1             xfun_0.19                 RMTstat_0.3               hms_0.5.3                
 [26] promises_1.1.1            fansi_0.4.1               caTools_1.18.0            igraph_1.2.6              DBI_1.1.0                
 [31] htmlwidgets_1.5.2         dyndimred_1.0.3           purrr_0.3.4               ellipsis_0.3.1            backports_1.2.0          
 [36] annotate_1.68.0           RcppParallel_5.0.2        deldir_0.2-3              sparseMatrixStats_1.2.0   vctrs_0.3.4              
 [41] remotes_2.2.0             ROCR_1.0-11               abind_1.4-7               withr_2.3.0               ggforce_0.3.2            
 [46] googleVis_0.6.9           checkmate_2.0.0           sctransform_0.3.1         goftest_1.2-2             cluster_2.1.0            
 [51] lazyeval_0.2.2            crayon_1.3.4              babelwhale_1.0.1          edgeR_3.32.0              pkgconfig_2.0.3          
 [56] tweenr_1.0.1              nlme_3.1-150              vipor_0.4.5               rlang_0.4.8               globals_0.13.1           
 [61] lifecycle_0.2.0           miniUI_0.1.1.1            rsvd_1.0.3                cellranger_1.1.0          randomForest_4.6-14      
 [66] polyclip_1.10-0           lmtest_0.9-38             graph_1.68.0              zoo_1.8-9                 beeswarm_0.2.3           
 [71] ggridges_0.5.2            processx_3.4.4            png_0.1-8                 viridisLite_0.3.0         bitops_1.0-6             
 [76] KernSmooth_2.23-18        blob_1.2.1                DelayedMatrixStats_1.12.0 lambda.tools_1.0.9        stringr_1.4.0            
 [81] parallelly_1.21.0         readr_1.4.0               beachmat_2.6.1            scales_1.1.1              memoise_1.1.0            
 [86] GSEABase_1.52.0           magrittr_1.5              plyr_1.8.6                ica_1.0-2                 zlibbioc_1.36.0          
 [91] compiler_4.0.3            dqrng_0.2.1               tinytex_0.27              RColorBrewer_1.1-2        fitdistrplus_1.1-1       
 [96] cli_2.1.0                 XVector_0.30.0            listenv_0.8.0             pbapply_1.4-3             ps_1.4.0                 
[101] formatR_1.7.1             MASS_7.3-53               mgcv_1.8-33               tidyselect_1.1.0          stringi_1.5.3            
[106] yaml_2.2.1                BiocSingular_1.6.0        locfit_1.5-9.4            ggrepel_0.8.2             fastmatch_1.1-1          
[111] tools_4.0.3               future.apply_1.6.0        rstudioapi_0.12           foreach_1.5.1             bluster_1.0.0            
[116] rje_1.10.16               farver_2.0.3              Rtsne_0.15                ggraph_2.0.3              proxyC_0.1.5             
[121] digest_0.6.27             shiny_1.5.0               dynparam_1.0.1            Rcpp_1.0.5                scuttle_1.0.0            
[126] later_1.1.0.1             RcppAnnoy_0.0.16          httr_1.4.2                AnnotationDbi_1.52.0      colorspace_2.0-0         
[131] XML_3.99-0.5              tensor_1.5                ranger_0.12.1             reticulate_1.18           splines_4.0.3            
[136] uwot_0.1.8                lmds_0.1.0                statmod_1.4.35            spatstat.utils_1.17-0     graphlayouts_0.7.1       
[141] sessioninfo_1.1.1         plotly_4.9.2.1            xtable_1.8-6              jsonlite_1.7.1            futile.options_1.0.1     
[146] spatstat_1.64-1           tidygraph_1.2.0           testthat_3.0.0            R6_2.5.0                  pillar_1.4.6             
[151] htmltools_0.5.0           mime_0.9.2                glue_1.4.2                fastmap_1.0.1             BiocParallel_1.24.1      
[156] BiocNeighbors_1.8.0       class_7.3-17              codetools_0.2-18          lattice_0.20-41           ggbeeswarm_0.6.0         
[161] leiden_0.3.5              gtools_3.8.2              survival_3.2-7            limma_3.46.0              dynutils_1.0.5           
[166] munsell_0.5.0             e1071_1.7-4               GenomeInfoDbData_1.2.4    iterators_1.0.13          reshape2_1.4.4
scottgigante commented 3 years ago

@semmrich I would remove the virtualenv unless you have a good reason to want to keep it. Just remove the folder C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/ and then run reticulate::py_discover_config("phate") and let me know what you get.

semmrich commented 3 years ago

I removed the folder and rerun:

> reticulate::py_discover_config("phate")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: C:\Users\fuchsdeluxe\AppData\Local\r-miniconda\envs\r-reticulate

  added / updated specs:
    - numpy
    - python=3.6

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.6.20          |   py36hd36e781_2         151 KB  conda-forge
    intel-openmp-2020.3        |     h57928b3_311         2.0 MB  conda-forge
    numpy-1.19.4               |   py36hd1b969e_1         4.8 MB  conda-forge
    python-3.6.11              |h6f26aa1_2_cpython        18.9 MB  conda-forge
    python_abi-3.6             |          1_cp36m           4 KB  conda-forge
    setuptools-49.6.0          |   py36hd36e781_2         919 KB  conda-forge
    wincertstore-0.2           |py36h9f0ad1d_1005          15 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        26.8 MB

The following NEW packages will be INSTALLED:

  certifi            conda-forge/win-64::certifi-2020.6.20-py36hd36e781_2
  intel-openmp       conda-forge/win-64::intel-openmp-2020.3-h57928b3_311
  libblas            conda-forge/win-64::libblas-3.8.0-20_mkl
  libcblas           conda-forge/win-64::libcblas-3.8.0-20_mkl
  liblapack          conda-forge/win-64::liblapack-3.8.0-20_mkl
  mkl                pkgs/main/win-64::mkl-2020.2-256
  numpy              conda-forge/win-64::numpy-1.19.4-py36hd1b969e_1
  pip                conda-forge/noarch::pip-20.2.4-py_0
  python             conda-forge/win-64::python-3.6.11-h6f26aa1_2_cpython
  python_abi         conda-forge/win-64::python_abi-3.6-1_cp36m
  setuptools         conda-forge/win-64::setuptools-49.6.0-py36hd36e781_2
  vc                 conda-forge/win-64::vc-14.1-h869be7e_1
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.16.27012-h30e32a0_2
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  wincertstore       conda-forge/win-64::wincertstore-0.2-py36h9f0ad1d_1005

Downloading and Extracting Packages
setuptools-49.6.0    | 919 KB    | ########## | 100% 
intel-openmp-2020.3  | 2.0 MB    | ########## | 100% 
numpy-1.19.4         | 4.8 MB    | ########## | 100% 
python_abi-3.6       | 4 KB      | ########## | 100% 
certifi-2020.6.20    | 151 KB    | ########## | 100% 
python-3.6.11        | 18.9 MB   | ########## | 100% 
wincertstore-0.2     | 15 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.9.1

Please update conda by running

    $ conda update -n base -c defaults conda

#
# To activate this environment, use
#
#     $ conda activate C:\Users\fuchsdeluxe\AppData\Local\r-miniconda\envs\r-reticulate
#
# To deactivate an active environment, use
#
#     $ conda deactivate

python:         C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
libpython:      C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/python36.dll
pythonhome:     C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate
version:        3.6.11 (default, Aug  5 2020, 19:41:03) [MSC v.1916 64 bit (AMD64)]
Architecture:   64bit
numpy:          C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/Lib/site-packages/numpy
numpy_version:  1.19.4

Still get the module not found error...

Just curious, why should I deinstall that virtualenv (which I do not need, just did it bc of the phate intallation error msg above) error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/

scottgigante commented 3 years ago

Interesting. Looks like by doing py_discover_config, it is automatically creating a new virtualenv. You're getting the compilation error because s_gd2 is trying to install from source rather than from a wheel. But in theory, if you've successfully installed phate on system Python, you shouldn't need to reinstall. Let's try the following:

  1. Remove the virtualenv (again)
  2. Run in bash pip freeze and post the output here
  3. Run in python import phate; print(phate.__version__) and post the output here
  4. Run in R reticulate::py_config() and post the output here
semmrich commented 3 years ago

Freshly installed the ubuntu bash for win10:

Welcome to Ubuntu 20.04.1 LTS (GNU/Linux 4.19.128-microsoft-standard x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/advantage

  System information as of Wed Nov 11 13:41:21 EST 2020

  System load:  0.23               Processes:             8
  Usage of /:   0.4% of 250.98GB   Users logged in:       0
  Memory usage: 1%                 IPv4 address for eth0: 172.17.246.94
  Swap usage:   0%

1 update can be installed immediately.
0 of these updates are security updates.
To see these additional updates run: apt list --upgradable

The list of available updates is more than a week old.
To check for new updates run: sudo apt update

This message is shown once once a day. To disable it please create the
/home/fuchsdeluxe/.hushlogin file.
fuchsdeluxe@DESKTOP-UB6CF8Q:~$ pip freeze

Command 'pip' not found, but there are 18 similar ones.

sry for being such a n00b... do I have to configure this somehow? I installed r-miniconda through reticulate, maybe thats why the linux cannot find a pip installer? I can start a python installation made outside of R though with this by python3

fuchsdeluxe@DESKTOP-UB6CF8Q:~$ python3
Python 3.8.2 (default, Jul 16 2020, 14:00:26)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 1+3
4
>>>
scottgigante commented 3 years ago

No problem at all. You can access pip with python3 -m pip but if reticulate is using miniconda then you should run reticulate::py_config() to work out which python you should install PHATE from.

semmrich commented 3 years ago

I got it to run again finally, this is what worked: 1) Remove the folder C:/Users/fuchsdeluxe/AppData/Local/r-miniconda/envs/r-reticulate/ 2) Run reticulate::py_config() 3) Run reticulate::py_install("phate", pip=TRUE) This time reinstallation of python phate run through without the error that I posted originally, and the R phateR package worked fine. (I just hope I do not have to this again and again after every reboot or whatever caused the initial post problem...) Thank you so much for your quick responses and your patience! This is a powerful tool for unbiased lineage hierarchy ordering, will cite your work Stephan

scottgigante commented 3 years ago

Great! Glad we could work it out.