Error when doing Leiden clustering #184

s849 · 2022-03-04T01:00:48Z

Hi,

Thank you for developing such a wonderful tool. I am trying to run Giotto on my data sets but I ran into an issue when running doLeidenCluster. This is the error I get - any thoughts?

Thanks,

visium_kidney <- doLeidenCluster(gobject = visium_kidney, resolution = 0.4, n_iterations = 1000)
Error in bmerge(i, x, leftcols, rightcols, roll, rollends, nomatch, mult, :
x.cell_ID is type environment which is not supported by data.table join

plotUMAP(gobject = visium_kidney,

     cell_color = 'leiden_clus', show_NN_network = T, point_size = 2.5,

     save_param = list(save_name = '4_a_UMAP_leiden'))

Error in plot_point_layer_ggplot(ggobject = pl, annotated_DT_selected = annotated_DT_selected, :
leiden_clus is not a color or a column name

The text was updated successfully, but these errors were encountered:

RubD · 2022-03-04T01:16:36Z

Can you give us a bit more information? Which example are you running or are you using your own dataset?

See also https://rubd.github.io/Giotto_site/articles/github_issues.html for more information.

tdyoshida · 2022-03-29T19:56:46Z

Hi @RubD, I posted the same comment below on #165, which has been closed.
Sorry for duplicating comments, but I still haven't figured out what might be the problem.
I appreciate your help!

Comment copied from #165
When I tried to run the steps in Visium Brain vignette, I got an error when running the code in part 4.

visium_brain <- doLeidenCluster(gobject = visium_brain, resolution = 0.4, n_iterations = 1000)

Error in bmerge(i, x, leftcols, rightcols, roll, rollends, nomatch, mult,  : 
  x.cell_ID is type environment which is not supported by data.table join

I followed everything before this step as in the vignette, and successfully reproduced the results.
You mentioned above that version 1.1.0 contains some bugs, but it looks like v1.1.0 is the latest release on GitHub, and the following command installs 1.1.0

remotes::install_github("RubD/Giotto")

packageVersion("Giotto")
'1.1.0'

After reading comments by @Jluo21 and @lijiacd985, I checked 'leidenalg' and 'python-louvain' in my giotto_env.

# Name                    Version                   Build  Channel
leidenalg                 0.8.7            py36hefe7e0e_0    conda-forge
python-louvain            0.15               pyhd8ed1ab_1    conda-forge

I'm including some more information below. I truly appreciate your help!

Giotto:::checkGiottoEnvironment()
giotto environment found at 
/Users/tdyoshida/Library/r-miniconda/envs/giotto_env/bin/pythonw 
[1] TRUE

Giotto:::showProcessingSteps(visium_brain)
 0_subset 

 1_subset 

 2_filter 

 3_normalize 

 4_gene_stats 

 5_cell_stats 

 6_hvg 
	 name info:  hvg 

 7_pca 
	 name info:  pca 

 8_umap 
	 name info:  pca umap 

 9_tsne 
	 name info:  pca tsne 

 10_nn_network 
	 name info:  pca sNN.pca

str(visium_brain, max.level = 3)
Formal class 'giotto' [package "Giotto"] with 19 slots
  ..@ raw_exprs          :Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
  ..@ norm_expr          : num [1:14814, 1:2698] 0 0 0 0.364 0.364 ...
  .. ..- attr(*, "dimnames")=List of 2
  ..@ norm_scaled_expr   : num [1:14814, 1:2698] -0.263 -0.28 -0.284 0.2 0.732 ...
  .. ..- attr(*, "dimnames")=List of 2
  ..@ custom_expr        : NULL
  ..@ spatial_locs       :Classes ‘data.table’ and 'data.frame':	2698 obs. of  3 variables:
  .. ..$ sdimx  : int [1:2698] 8229 4169 2518 7678 3137 4100 2518 5614 6646 5270 ...
  .. ..$ sdimy  : int [1:2698] -7237 -1611 -8315 -2927 -6280 -7477 -5681 -1970 -5441 -9272 ...
  .. ..$ cell_ID: chr [1:2698] "AAACAAGTATCTCCCA-1" "AAACAATCTACTAGCA-1" "AAACACCAATAACTGC-1" "AAACAGAGCGACTCCT-1" ...
  .. ..- attr(*, ".internal.selfref")=<externalptr> 
  ..@ cell_metadata      :Classes ‘data.table’ and 'data.frame':	2698 obs. of  7 variables:
  .. ..$ cell_ID   : chr [1:2698] "AAACAAGTATCTCCCA-1" "AAACAATCTACTAGCA-1" "AAACACCAATAACTGC-1" "AAACAGAGCGACTCCT-1" ...
  .. ..$ in_tissue : int [1:2698] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ array_row : int [1:2698] 50 3 59 14 42 52 37 6 35 67 ...
  .. ..$ array_col : int [1:2698] 102 43 19 94 28 42 19 64 79 59 ...
  .. ..$ nr_genes  : num [1:2698] 5215 3637 6236 4495 5952 ...
  .. ..$ perc_genes: num [1:2698] 35.2 24.6 42.1 30.3 40.2 ...
  .. ..$ total_expr: num [1:2698] 3795 3022 3571 3556 3594 ...
  .. ..- attr(*, ".internal.selfref")=<externalptr> 
  .. ..- attr(*, "sorted")= chr "cell_ID"
  ..@ gene_metadata      :Classes ‘data.table’ and 'data.frame':	14814 obs. of  7 variables:
  .. ..$ gene_ID      : chr [1:14814] "Xkr4" "Gm19938" "Sox17" "Mrpl15" ...
  .. ..$ nr_cells     : num [1:14814] 251 296 315 1817 1355 ...
  .. ..$ perc_cells   : num [1:14814] 9.3 11 11.7 67.3 50.2 ...
  .. ..$ total_expr   : num [1:14814] 71.7 89.7 96.5 814.5 488 ...
  .. ..$ mean_expr    : num [1:14814] 0.0266 0.0332 0.0358 0.3019 0.1809 ...
  .. ..$ mean_expr_det: num [1:14814] 0.286 0.303 0.306 0.448 0.36 ...
  .. ..$ hvg          : chr [1:14814] "no" "no" "no" "no" ...
  .. ..- attr(*, ".internal.selfref")=<externalptr> 
  ..@ cell_ID            : Named chr [1:2698] "AAACAAGTATCTCCCA-1" "AAACAATCTACTAGCA-1" "AAACACCAATAACTGC-1" "AAACAGAGCGACTCCT-1" ...
  .. ..- attr(*, "names")= chr [1:2698] "2" "3" "4" "5" ...
  ..@ gene_ID            : Named chr [1:14814] "Xkr4" "Gm19938" "Sox17" "Mrpl15" ...
  .. ..- attr(*, "names")= chr [1:14814] "1" "3" "6" "9" ...
  ..@ spatial_network    : NULL
  ..@ spatial_grid       : NULL
  ..@ spatial_enrichment : NULL
  ..@ dimension_reduction:List of 1
  .. ..$ cells:List of 3
  ..@ nn_network         :List of 1
  .. ..$ sNN:List of 1
  ..@ images             :List of 1
  .. ..$ image:List of 4
  .. .. ..- attr(*, "class")= chr [1:2] "list" "imageGiottoObj"
  ..@ parameters         :List of 11
  .. ..$ 0_subset     : Named int [1:2] 2290 0
  .. .. ..- attr(*, "names")= chr [1:2] "cells removed" "genes removed"
  .. ..$ 1_subset     : Named int [1:2] 4 7311
  .. .. ..- attr(*, "names")= chr [1:2] "cells removed" "genes removed"
  .. ..$ 2_filter     : Named chr [1:4] "raw" "1" "1000" "50"
  .. .. ..- attr(*, "names")= chr [1:4] "used expression values" "gene expression threshold" "minimum # of genes detected per cell" "minimum times a gene is detected over all cells"
  .. ..$ 3_normalize  : Named chr [1:9] "standard" "yes" "6000" "yes" ...
  .. .. ..- attr(*, "names")= chr [1:9] "normalization method" "normalized to library size" "scalefactor" "log-normalized" ...
  .. ..$ 4_gene_stats : Named chr [1:2] "normalized" "0"
  .. .. ..- attr(*, "names")= chr [1:2] "expression values used" "detection_threshold"
  .. ..$ 5_cell_stats : Named chr [1:2] "normalized" "0"
  .. .. ..- attr(*, "names")= chr [1:2] "expression values used" "detection_threshold"
  .. ..$ 6_hvg        : Named chr [1:11] "cov_groups" "normalized" "scaled" "custom" ...
  .. .. ..- attr(*, "names")= chr [1:11] "method used" "expression values1" "expression values2" "expression values3" ...
  .. ..$ 7_pca        : Named chr [1:10] "cells" "normalized" "scaled" "custom" ...
  .. .. ..- attr(*, "names")= chr [1:10] "reduction type:" "expression values1" "expression values2" "expression values3" ...
  .. ..$ 8_umap       : Named chr [1:14] "cells" "pca" "pca" "10" ...
  .. .. ..- attr(*, "names")= chr [1:14] "reduction type" "dimension reduction used" "name for dimension reduction" "dimensions used" ...
  .. ..$ 9_tsne       : Named chr [1:13] "cells" "pca" "pca" "10" ...
  .. .. ..- attr(*, "names")= chr [1:13] "reduction type" "dimension reduction used" "name for dimension reduction" "dimensions used" ...
  .. ..$ 10_nn_network: Named chr [1:12] "sNN" "pca" "pca" "10" ...
  .. .. ..- attr(*, "names")= chr [1:12] "nearest-neighbour type" "dimension reduction used" "name for dimension reduction" "dimensions used" ...
  ..@ instructions       :List of 11
  .. ..$ python_path: chr "/Users/tdyoshida/Library/r-miniconda/envs/giotto_env/bin/pythonw"
  .. ..$ show_plot  : logi FALSE
  .. ..$ return_plot: logi TRUE
  .. ..$ save_plot  : logi TRUE
  .. ..$ save_dir   : chr "R/Giotto/"
  .. ..$ plot_format: chr "png"
  .. ..$ dpi        : num 300
  .. ..$ units      : chr "in"
  .. ..$ height     : num 9
  .. ..$ width      : num 9
  .. ..$ is_docker  : logi FALSE
  ..@ offset_file        : NULL
  ..@ OS_platform        : chr "unix"

sessionInfo()

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] data.table_1.14.2 Giotto_1.1.0      forcats_0.5.1     stringr_1.4.0     dplyr_1.0.8       purrr_0.3.4      
 [7] readr_2.1.2       tidyr_1.2.0       tibble_3.1.6      ggplot2_3.3.5     tidyverse_1.3.1  

loaded via a namespace (and not attached):
 [1] matrixStats_0.61.0   fs_1.5.2             lubridate_1.8.0      RColorBrewer_1.1-2   httr_1.4.2          
 [6] rprojroot_2.0.2      tools_4.1.1          backports_1.4.1      DT_0.21              utf8_1.2.2          
[11] R6_2.5.1             uwot_0.1.11          DBI_1.1.2            colorspace_2.0-3     withr_2.5.0         
[16] prettyunits_1.1.1    processx_3.5.2       tidyselect_1.1.2     curl_4.3.2           compiler_4.1.1      
[21] textshaping_0.3.6    cli_3.2.0            rvest_1.0.2          flashClust_1.01-2    xml2_1.3.3          
[26] labeling_0.4.2       scales_1.1.1         callr_3.7.0          systemfonts_1.0.4    digest_0.6.29       
[31] dbscan_1.1-10        rmarkdown_2.13       R.utils_2.11.0       pkgconfig_2.0.3      htmltools_0.5.2     
[36] dbplyr_2.1.1         fastmap_1.1.0        FactoMineR_2.4       htmlwidgets_1.5.4    rlang_1.0.2         
[41] readxl_1.3.1         rstudioapi_0.13      FNN_1.1.3            generics_0.1.2       farver_2.1.0        
[46] jsonlite_1.8.0       R.oo_1.24.0          magrittr_2.0.2       leaps_3.1            Matrix_1.4-0        
[51] Rcpp_1.0.8.3         munsell_0.5.0        fansi_1.0.2          reticulate_1.24      lifecycle_1.0.1     
[56] RcppZiggurat_0.1.6   R.methodsS3_1.8.1    scatterplot3d_0.3-41 stringi_1.7.6        yaml_2.3.5          
[61] MASS_7.3-55          pkgbuild_1.3.1       Rtsne_0.15           grid_4.1.1           parallel_4.1.1      
[66] ggrepel_0.9.1        crayon_1.5.0         lattice_0.20-45      haven_2.4.3          cowplot_1.1.1       
[71] hms_1.1.1            magick_2.7.3         ps_1.6.0             knitr_1.37           pillar_1.7.0        
[76] igraph_1.2.11        reprex_2.0.1         glue_1.6.2           evaluate_0.15        remotes_2.4.2       
[81] modelr_0.1.8         png_0.1-7            vctrs_0.3.8          tzdb_0.2.0           cellranger_1.1.0    
[86] gtable_0.3.0         assertthat_0.2.1     xfun_0.30            Rfast_2.0.6          broom_0.7.12        
[91] RSpectra_0.16-0      ragg_1.2.2           cluster_2.1.2        ellipsis_0.3.2       here_1.0.1

drieslab · 2022-03-29T20:13:49Z

Can you look at #207 and see if that fixes the issue? Basically reinstalling the Giotto environment with specific versions for each python module seems to do the trick. It seems like some of the python module outputs has slightly changed which causes this error.

tdyoshida · 2022-03-30T15:30:24Z

Hi @drieslab, thank you for your comment.

I tried installGiottoEnvironment(force_environment = T), but unfortunately it did not fix the issue.

visium_brain <- doLeidenCluster(gobject = visium_brain, resolution = 0.4, n_iterations = 1000)
Error in bmerge(i, x, leftcols, rightcols, roll, rollends, nomatch, mult,  : 
  x.cell_ID is type environment which is not supported by data.table join

I'm including the output of installGiottoEnvironment(force_environment = T) at the end of my comment, in case it helps.
I noticed there was a warning regarding conda version, but my conda is v 4.12.0
I don't know why there is a warning (and don't know if it matters).

I appreciate any further suggestions!

==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base conda

conda -V
conda 4.12.0

 giotto environment found at 
 /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/bin/pythonw 

Remove all packages in environment /Users/tdyoshida/Library/r-miniconda/envs/giotto_env:


## Package Plan ##

  environment location: /Users/tdyoshida/Library/r-miniconda/envs/giotto_env


The following packages will be REMOVED:

  arpack-3.7.0-hefb7bc6_2
  bzip2-1.0.8-h0d85af4_4
  ca-certificates-2021.10.8-h033912b_0
  certifi-2021.5.30-py36h79c6626_0
  cycler-0.11.0-pyhd8ed1ab_0
  freetype-2.10.4-h4cff582_1
  glpk-4.65-h0f52abe_1004
  gmp-6.2.1-h2e338ed_0
  icu-69.1-he49afe7_0
  igraph-0.9.7-hacf96bb_0
  jbig-2.1-h0d85af4_2003
  joblib-1.1.0-pyhd8ed1ab_0
  jpeg-9e-h0d85af4_0
  kiwisolver-1.3.1-py36hc61eee1_1
  lcms2-2.12-h577c468_0
  leidenalg-0.8.7-py36hefe7e0e_0
  lerc-3.0-he49afe7_0
  libblas-3.9.0-13_osx64_openblas
  libcblas-3.9.0-13_osx64_openblas
  libcxx-13.0.1-hc203e6f_0
  libdeflate-1.10-h0d85af4_0
  libffi-3.4.2-h0d85af4_5
  libgfortran-5.0.0-9_3_0_h6c81a4c_23
  libgfortran5-9.3.0-h6c81a4c_23
  libiconv-1.16-haf1e3a3_0
  liblapack-3.9.0-13_osx64_openblas
  libopenblas-0.3.18-openmp_h3351f45_0
  libpng-1.6.37-h7cec526_2
  libtiff-4.3.0-h17f2ce3_3
  libwebp-base-1.2.2-h0d85af4_1
  libxml2-2.9.12-h7e28ab6_1
  libzlib-1.2.11-h6c3fc93_1014
  llvm-openmp-13.0.1-hcb1a161_1
  lz4-c-1.9.3-he49afe7_1
  matplotlib-base-3.3.4-py36h4ea959b_0
  metis-5.1.0-h2e338ed_1006
  mpfr-4.1.0-h0f52abe_1
  ncurses-6.3-he49afe7_0
  networkx-2.6.3-pyhd8ed1ab_1
  numpy-1.19.5-py36h08b5fde_2
  olefile-0.46-pyh9f0ad1d_1
  openjpeg-2.4.0-h6e7aa92_1
  openssl-1.1.1n-h6c3fc93_0
  pandas-1.1.5-py36h2be6da3_0
  pillow-8.3.2-py36h950f3bb_0
  pip-20.0.2-py36_1
  pyparsing-3.0.7-pyhd8ed1ab_0
  python-3.6.15-haf480d7_0_cpython
  python-dateutil-2.8.2-pyhd8ed1ab_0
  python-igraph-0.9.6-py36h576965e_0
  python-louvain-0.15-pyhd8ed1ab_1
  python.app-2-py36_10
  python_abi-3.6-2_cp36m
  pytz-2022.1-pyhd8ed1ab_0
  readline-8.1-h05e3726_0
  scikit-learn-0.24.2-py36h979b75d_1
  scipy-1.5.3-py36h4f136de_1
  setuptools-58.0.4-py36hecd8cb5_0
  six-1.16.0-pyh6c4a22f_0
  sqlite-3.37.1-hb516253_0
  suitesparse-5.10.1-h7aff33d_1
  tbb-2021.5.0-h940c156_0
  texttable-1.6.4-pyhd8ed1ab_0
  threadpoolctl-3.1.0-pyh8a188c0_0
  tk-8.6.12-h5dbffcc_0
  tornado-6.1-py36hfa26744_1
  wheel-0.37.1-pyhd8ed1ab_0
  xz-5.2.5-haf1e3a3_1
  zlib-1.2.11-h6c3fc93_1014
  zstd-1.5.2-h582d3a0_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

 |---- install giotto environment ----| 
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/tdyoshida/Library/r-miniconda/envs/giotto_env

  added / updated specs:
    - python=3.8


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
  ca-certificates    conda-forge/osx-64::ca-certificates-2021.10.8-h033912b_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libzlib            conda-forge/osx-64::libzlib-1.2.11-h6c3fc93_1014
  ncurses            conda-forge/osx-64::ncurses-6.3-he49afe7_0
  openssl            conda-forge/osx-64::openssl-3.0.2-h6c3fc93_1
  pip                conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython
  python_abi         conda-forge/osx-64::python_abi-3.8-2_cp38
  readline           conda-forge/osx-64::readline-8.1-h05e3726_0
  setuptools         conda-forge/osx-64::setuptools-61.2.0-py38h50d1736_3
  sqlite             conda-forge/osx-64::sqlite-3.37.1-hb516253_0
  tk                 conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h6c3fc93_1014


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /Users/tdyoshida/Library/r-miniconda/envs/giotto_env

  added / updated specs:
    - python=3.6


The following NEW packages will be INSTALLED:

  certifi            conda-forge/osx-64::certifi-2016.9.26-py36_0
  libcxx             conda-forge/osx-64::libcxx-13.0.1-hc203e6f_0

The following packages will be REMOVED:

  python_abi-3.8-2_cp38

The following packages will be SUPERSEDED by a higher-priority channel:

  pip                conda-forge/noarch::pip-22.0.4-pyhd8e~ --> conda-forge/osx-64::pip-20.0.2-py36_1
  setuptools         conda-forge::setuptools-61.2.0-py38h5~ --> pkgs/main::setuptools-58.0.4-py36hecd8cb5_0

The following packages will be DOWNGRADED:

  openssl                                  3.0.2-h6c3fc93_1 --> 1.1.1n-h6c3fc93_0
  python                          3.8.13-h66c20e1_0_cpython --> 3.6.15-haf480d7_0_cpython


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /Users/tdyoshida/Library/r-miniconda/envs/giotto_env

  added / updated specs:
    - leidenalg==0.8.7
    - networkx==2.6.3
    - pandas==1.1.5
    - python-igraph==0.9.6
    - python-louvain==0.15
    - python.app==2
    - python=3.6
    - scikit-learn==0.24.2


The following NEW packages will be INSTALLED:

  arpack             conda-forge/osx-64::arpack-3.7.0-hefb7bc6_2
  cycler             conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
  freetype           conda-forge/osx-64::freetype-2.10.4-h4cff582_1
  glpk               conda-forge/osx-64::glpk-4.65-h0f52abe_1004
  gmp                conda-forge/osx-64::gmp-6.2.1-h2e338ed_0
  icu                conda-forge/osx-64::icu-69.1-he49afe7_0
  igraph             conda-forge/osx-64::igraph-0.9.7-hacf96bb_0
  jbig               conda-forge/osx-64::jbig-2.1-h0d85af4_2003
  joblib             conda-forge/noarch::joblib-1.1.0-pyhd8ed1ab_0
  jpeg               conda-forge/osx-64::jpeg-9e-h0d85af4_0
  kiwisolver         conda-forge/osx-64::kiwisolver-1.3.1-py36hc61eee1_1
  lcms2              conda-forge/osx-64::lcms2-2.12-h577c468_0
  leidenalg          conda-forge/osx-64::leidenalg-0.8.7-py36hefe7e0e_0
  lerc               conda-forge/osx-64::lerc-3.0-he49afe7_0
  libblas            conda-forge/osx-64::libblas-3.9.0-13_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-13_osx64_openblas
  libdeflate         conda-forge/osx-64::libdeflate-1.10-h0d85af4_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_23
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_23
  libiconv           conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
  liblapack          conda-forge/osx-64::liblapack-3.9.0-13_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.18-openmp_h3351f45_0
  libpng             conda-forge/osx-64::libpng-1.6.37-h7cec526_2
  libtiff            conda-forge/osx-64::libtiff-4.3.0-h17f2ce3_3
  libwebp-base       conda-forge/osx-64::libwebp-base-1.2.2-h0d85af4_1
  libxml2            conda-forge/osx-64::libxml2-2.9.12-h7e28ab6_1
  llvm-openmp        conda-forge/osx-64::llvm-openmp-13.0.1-hcb1a161_1
  lz4-c              conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
  matplotlib-base    conda-forge/osx-64::matplotlib-base-3.3.4-py36h4ea959b_0
  metis              conda-forge/osx-64::metis-5.1.0-h2e338ed_1006
  mpfr               conda-forge/osx-64::mpfr-4.1.0-h0f52abe_1
  networkx           conda-forge/noarch::networkx-2.6.3-pyhd8ed1ab_1
  numpy              conda-forge/osx-64::numpy-1.19.5-py36h08b5fde_2
  olefile            conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  openjpeg           conda-forge/osx-64::openjpeg-2.4.0-h6e7aa92_1
  pandas             conda-forge/osx-64::pandas-1.1.5-py36h2be6da3_0
  pillow             conda-forge/osx-64::pillow-8.3.2-py36h950f3bb_0
  pyparsing          conda-forge/noarch::pyparsing-3.0.7-pyhd8ed1ab_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python-igraph      conda-forge/osx-64::python-igraph-0.9.6-py36h576965e_0
  python-louvain     conda-forge/noarch::python-louvain-0.15-pyhd8ed1ab_1
  python.app         pkgs/main/osx-64::python.app-2-py36_10
  python_abi         conda-forge/osx-64::python_abi-3.6-2_cp36m
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  scikit-learn       conda-forge/osx-64::scikit-learn-0.24.2-py36h979b75d_1
  scipy              conda-forge/osx-64::scipy-1.5.3-py36h4f136de_1
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  suitesparse        conda-forge/osx-64::suitesparse-5.10.1-h7aff33d_1
  tbb                conda-forge/osx-64::tbb-2021.5.0-h940c156_0
  texttable          conda-forge/noarch::texttable-1.6.4-pyhd8ed1ab_0
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.1.0-pyh8a188c0_0
  tornado            conda-forge/osx-64::tornado-6.1-py36hfa26744_1
  zstd               conda-forge/osx-64::zstd-1.5.2-h582d3a0_0

The following packages will be UPDATED:

  certifi                                  2016.9.26-py36_0 --> 2021.5.30-py36h79c6626_0


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


==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base conda



# All requested packages already installed.

Activated conda python: /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/bin/python
Collecting smfishhmrf
  Using cached smfishHmrf-1.3.3-py3-none-any.whl (51 kB)
Requirement already satisfied, skipping upgrade: matplotlib in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from smfishhmrf) (3.3.4)
Collecting seaborn
  Using cached seaborn-0.11.2-py3-none-any.whl (292 kB)
Requirement already satisfied, skipping upgrade: scipy in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from smfishhmrf) (1.5.3)
Requirement already satisfied, skipping upgrade: pandas in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from smfishhmrf) (1.1.5)
Requirement already satisfied, skipping upgrade: numpy in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from smfishhmrf) (1.19.5)
Requirement already satisfied, skipping upgrade: pillow>=6.2.0 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from matplotlib->smfishhmrf) (8.3.2)
Requirement already satisfied, skipping upgrade: cycler>=0.10 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from matplotlib->smfishhmrf) (0.11.0)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from matplotlib->smfishhmrf) (3.0.7)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from matplotlib->smfishhmrf) (1.3.1)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.1 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from matplotlib->smfishhmrf) (2.8.2)
Requirement already satisfied, skipping upgrade: pytz>=2017.2 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from pandas->smfishhmrf) (2022.1)
Requirement already satisfied, skipping upgrade: six>=1.5 in /Users/tdyoshida/Library/r-miniconda/envs/giotto_env/lib/python3.6/site-packages (from python-dateutil>=2.1->matplotlib->smfishhmrf) (1.16.0)
Installing collected packages: seaborn, smfishhmrf
Successfully installed seaborn-0.11.2 smfishhmrf-1.3.3

kendrix10 mentioned this issue Feb 27, 2024

Unable to run doLeidenCluster #920

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Error when doing Leiden clustering #184

Error when doing Leiden clustering #184

s849 commented Mar 4, 2022

RubD commented Mar 4, 2022

tdyoshida commented Mar 29, 2022

drieslab commented Mar 29, 2022 •

edited

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tdyoshida commented Mar 30, 2022

Error when doing Leiden clustering #184

Error when doing Leiden clustering #184

Comments

s849 commented Mar 4, 2022

RubD commented Mar 4, 2022

tdyoshida commented Mar 29, 2022

drieslab commented Mar 29, 2022 • edited Loading

tdyoshida commented Mar 30, 2022

drieslab commented Mar 29, 2022 •

edited

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