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Published 20 hours ago • verified publisher icon Irrationone

Problem to install cellassign in Rstudio

Open key1356 opened this issue 6 years ago • 2 comments

Hi, I can not install cellassign in Rstudio. I even tried R console with the same errors happen. There are several errors that I do not know if they are separate or derive from the same problem.

devtools::install_github("Irrationone/cellassign") Downloading GitHub repo Irrationone/cellassign@master These packages have more recent versions available. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: Biobase (2.42.0 -> 2.44.0) [CRAN] 5: BiocGenerics (0.28.0 -> 0.30.0) [CRAN] 6: BiocParallel (1.16.6 -> 1.18.1) [CRAN] 7: edgeR (3.24.3 -> 3.26.8) [CRAN] 8: limma (3.38.3 -> 3.40.6) [CRAN] 9: matrixStats (0.54.0 -> 0.55.0) [CRAN] 10: lambda.r (1.2.3 -> 1.2.4 ) [CRAN] 11: RcppAnnoy (0.0.12 -> 0.0.13) [CRAN] 12: RcppHNSW (0.1.0 -> 0.2.0 ) [CRAN] 13: pkgconfig (2.0.2 -> 2.0.3 ) [CRAN] 14: digest (0.6.20 -> 0.6.21) [CRAN] 15: ellipsis (0.2.0.1 -> 0.3.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 √ checking for file 'C:\Users\key\AppData\Local\Temp\RtmpgtITQJ\remotes2b401eec5abe\Irrationone-cellassign-dc8ee37/DESCRIPTION' ...

  • preparing 'cellassign': √ checking DESCRIPTION meta-information ...
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
  • looking to see if a 'data/datalist' file should be added
  • building 'cellassign_0.99.11.tar.gz'

Installing package into ‘C:/Users/key/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)

  • installing source package 'cellassign' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'rowSums' Warning: multiple methods tables found for 'colSums' Warning: multiple methods tables found for 'rowMeans' Warning: multiple methods tables found for 'colMeans' ** inst ** byte-compile and prepare package for lazy loading Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'rowSums' Warning: multiple methods tables found for 'colSums' Warning: multiple methods tables found for 'rowMeans' Warning: multiple methods tables found for 'colMeans' ** help *** installing help indices converting help for package 'cellassign' finding HTML links ... done cellassign html
    cellprobs html
    celltypes html
    dot-onLoad html
    example_TME_markers html
    example_cellassign_fit html
    example_rho html
    example_sce html
    extract_expression_matrix html
    get_mle_cell_type html
    holik_data html
    inference_tensorflow html
    initialize_X html
    marker_list_to_mat html
    mleparams html
    print.cellassign html
    simulate_cellassign html
    ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location *** arch - i386 Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'rowSums' Warning: multiple methods tables found for 'colSums' Warning: multiple methods tables found for 'rowMeans' Warning: multiple methods tables found for 'colMeans' Error: package or namespace load failed for 'cellassign': .onLoad failed in loadNamespace() for 'cellassign', details: call: initialize_python(required_module, use_environment) error: Your current architecture is 32bit however this version of Python is compiled for 64bit. Error: loading failed Execution halted *** arch - x64 Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'lengths' Warning: multiple methods tables found for 'rowSums' Warning: multiple methods tables found for 'colSums' Warning: multiple methods tables found for 'rowMeans' Warning: multiple methods tables found for 'colMeans' ERROR: loading failed for 'i386'
  • removing 'C:/Users/key/Documents/R/win-library/3.6/cellassign' Error: Failed to install 'cellassign' from GitHub

When I install python 64bit, It complains alternatively about:

error: Your current architecture is 64bit however this version of Python is compiled for 32bit.

Also to confirm Tensorflow installation I tried:

library("tensorflow", lib.loc="~/R/win-library/3.6") Warning message: multiple methods tables found for ‘lengths’ sess = tf$Session() C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\framework\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\framework\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\framework\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\framework\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\framework\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\framework\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) WARNING:tensorflow:From C:\Users\KEY\AppData\Local\CONTIN~1\ANACON~1\envs\R-TENS~1\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

hello <- tf$constant('Hello, TensorFlow!') sess$run(hello) b'Hello, TensorFlow!'

I think it has something to do with Tensorflow detection.

key1356 avatar Sep 24 '19 18:09 key1356

Also I can not install it through conda:

(tf-cell) C:\Users\key>conda install -c conda-forge -c bioconda r-cellassign Collecting package metadata (current_repodata.json): done Solving environment: failed with current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed

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

  • r-cellassign

Current channels:

  • https://conda.anaconda.org/conda-forge/win-64
  • https://conda.anaconda.org/conda-forge/noarch
  • https://conda.anaconda.org/bioconda/win-64
  • https://conda.anaconda.org/bioconda/noarch
  • https://repo.anaconda.com/pkgs/main/win-64
  • https://repo.anaconda.com/pkgs/main/noarch
  • https://repo.anaconda.com/pkgs/r/win-64
  • https://repo.anaconda.com/pkgs/r/noarch
  • https://repo.anaconda.com/pkgs/msys2/win-64
  • https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

key1356 avatar Sep 25 '19 01:09 key1356

Okay this looks like the same issue we're having fun with over in #52 which I think is a windows-specific can't locate correct version of tensorflow as per here https://github.com/rstudio/tensorflow/issues/95

Can you post the output of tensorflow::tf_config() and reticulate::py_config() ?

Thanks

kieranrcampbell avatar Oct 08 '19 23:10 kieranrcampbell