[BUG] Metaclass conflict

[patron-michael]

Hello,

When I try to run EnDecon_individual_methods in GPU mode I obtain that error : Erreur : TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases.

I make multiple tests and that error is raise when I use MuSiC, SPOTlight, cell2location and Stereoscope.

Maybe some conflict in packages.

Here my R session info :

R version 4.2.1 (2022-06-23)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /shared/ifbstor1/software/miniconda/envs/r-4.2.1/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] scigenex_1.3.1        dynamicTreeCut_1.63-1 qlcMatrix_0.9.7      
 [4] sparsesvd_0.2-1       slam_0.1-50           iheatmapr_0.5.1      
 [7] igraph_1.4.1          testthat_3.1.6        magrittr_2.0.3       
[10] devtools_2.4.5        usethis_2.1.6         EnDecon_0.2.0        
[13] scatterpie_0.1.8      SeuratDisk_0.0.0.9020 Seurat_4.3.0         
[16] wrMisc_1.11.1         MuSiC_1.0.0           ggplot2_3.4.1        
[19] TOAST_1.12.0          quadprog_1.5-8        limma_3.54.1         
[22] EpiDISH_2.14.1        nnls_1.4              pcaMethods_1.90.0    
[25] Biobase_2.58.0        BiocGenerics_0.44.0   hdf5r_1.3.7          
[28] BiocManager_1.30.19   GOfuncR_1.18.0        vioplot_0.4.0        
[31] zoo_1.8-11            sm_2.2-5.7.1          RColorBrewer_1.1-3   
[34] reshape2_1.4.4        dplyr_1.1.0           tibble_3.1.8         
[37] cowplot_1.1.1         Matrix_1.5-3          tidyr_1.3.0          
[40] here_1.0.1            SeuratObject_4.1.3    sp_1.6-0             

loaded via a namespace (and not attached):
  [1] ica_1.0-3                   corpcor_1.6.10              class_7.3-21               
  [4] ps_1.7.2                    foreach_1.5.2               lmtest_0.9-40              
  [7] rprojroot_2.0.3             crayon_1.5.2                MASS_7.3-58.2              
 [10] MAST_1.24.1                 nlme_3.1-162                backports_1.4.1            
 [13] ggcorrplot_0.1.4            GOSemSim_2.22.0             rlang_1.0.6                
 [16] argparse_2.2.2              XVector_0.38.0              ROCR_1.0-11                
 [19] irlba_2.3.5.1               SparseM_1.81                callr_3.7.3                
 [22] L1pack_0.41-2               BiocParallel_1.32.5         bit64_4.0.5                
 [25] glue_1.6.2                  pheatmap_1.0.12             rngtools_1.5.2             
 [28] sctransform_0.3.5           parallel_4.2.1              processx_3.8.0             
 [31] spatstat.sparse_3.0-0       AnnotationDbi_1.60.0        classInt_0.4-8             
 [34] dotCall64_1.0-2             DOSE_3.22.1                 spatstat.geom_3.0-6        
 [37] mcmc_0.9-7                  tidyselect_1.2.0            SummarizedExperiment_1.28.0
 [40] fitdistrplus_1.1-8          sf_1.0-7                    org.Mm.eg.db_3.15.0        
 [43] xtable_1.8-4                MatrixModels_0.5-1          evaluate_0.20              
 [46] cli_3.4.1                   zlibbioc_1.44.0             rstudioapi_0.14            
 [49] miniUI_0.1.1.1              fastmatrix_0.4-1245         fastmatch_1.1-3            
 [52] pbmcapply_1.5.1             locfdr_1.1-8                treeio_1.20.2              
 [55] maps_3.4.1                  fields_14.1                 shiny_1.7.4                
 [58] xfun_0.37                   pkgbuild_1.4.0              cluster_2.1.4              
 [61] tidygraph_1.2.3             KEGGREST_1.38.0             lpSolve_5.6.18             
 [64] quantreg_5.94               ggrepel_0.9.3               ape_5.6-2                  
 [67] mapplots_1.5.1              listenv_0.9.0               Biostrings_2.66.0          
 [70] png_0.1-8                   reshape_0.8.9               future_1.31.0              
 [73] withr_2.5.0                 bitops_1.0-7                ggforce_0.4.1              
 [76] plyr_1.8.8                  e1071_1.7-13                DWLS_0.1.0                 
 [79] coda_0.19-4                 pillar_1.8.1                cachem_1.0.7               
 [82] fs_1.6.1                    clusterProfiler_4.4.4       RcppML_0.3.7               
 [85] SCDC_0.0.0.9000             vctrs_0.5.2                 ellipsis_0.3.2             
 [88] generics_0.1.3              NMF_0.25                    tools_4.2.1                
 [91] DeconRNASeq_1.40.0          munsell_0.5.0               tweenr_2.0.2               
 [94] fgsea_1.22.0                proxy_0.4-27                DelayedArray_0.24.0        
 [97] fastmap_1.1.0               compiler_4.2.1              pkgload_1.3.2              
[100] abind_1.4-5                 httpuv_1.6.9                sessioninfo_1.2.2          
[103] pkgmaker_0.32.8             plotly_4.10.1               GenomeInfoDbData_1.2.9     
[106] gridExtra_2.3               MCMCpack_1.6-3              lattice_0.20-45            
[109] deldir_1.0-6                utf8_1.2.2                  later_1.3.0                
[112] jsonlite_1.8.3              GGally_2.1.2                concaveman_1.1.0           
[115] scales_1.2.1                docopt_0.7.1                tidytree_0.4.1             
[118] pbapply_1.7-0               lazyeval_0.2.2              promises_1.2.0.1           
[121] doParallel_1.0.17           goftest_1.2-3               spatstat.utils_3.0-1       
[124] reticulate_1.28             checkmate_2.1.0             rmarkdown_2.20             
[127] SPOTlight_0.1.7             Rtsne_0.16                  downloader_0.4             
[130] uwot_0.1.14                 yaml_2.3.7                  survival_3.5-3             
[133] htmltools_0.5.4             memoise_2.0.1               profvis_0.3.7              
[136] graphlayouts_0.8.4          IRanges_2.32.0              STdeconvolve_1.3.1         
[139] viridisLite_0.4.1           digest_0.6.30               assertthat_0.2.1           
[142] mime_0.12                   registry_0.5-1              spacexr_2.2.0              
[145] spam_2.9-1                  units_0.8-1                 RSQLite_2.2.20             
[148] yulab.utils_0.0.5           future.apply_1.10.0         remotes_2.4.2              
[151] data.table_1.14.8           urlchecker_1.0.1            blob_1.2.3                 
[154] S4Vectors_0.36.1            splines_4.2.1               RCurl_1.98-1.10            
[157] colorspace_2.1-0            GenomicRanges_1.50.2        aplot_0.1.8                
[160] Rcpp_1.0.10                 RANN_2.6.1                  enrichplot_1.16.2          
[163] fansi_1.0.3                 brio_1.1.3                  parallelly_1.34.0          
[166] R6_2.5.1                    grid_4.2.1                  ggridges_0.5.4             
[169] lifecycle_1.0.3             xbioc_0.1.19                limSolve_1.5.6             
[172] leiden_0.4.3                fastcluster_1.2.3           DO.db_2.9                  
[175] qvalue_2.30.0               Giotto_1.1.2                CARD_1.0                   
[178] RcppAnnoy_0.0.20            org.Hs.eg.db_3.15.0         iterators_1.0.14           
[181] spatstat.explore_3.0-6      stringr_1.4.1               htmlwidgets_1.6.1          
[184] polyclip_1.10-4             purrr_1.0.1                 shadowtext_0.1.2           
[187] gridGraphics_0.5-1          mgcv_1.8-41                 globals_0.16.2             
[190] patchwork_1.1.2             spatstat.random_3.1-3       progressr_0.13.0           
[193] codetools_0.2-19            matrixStats_0.63.0          GO.db_3.15.0               
[196] gtools_3.9.4                prettyunits_1.1.1           SingleCellExperiment_1.20.0
[199] gridBase_0.4-7              GenomeInfoDb_1.34.9         gtable_0.3.1               
[202] DBI_1.1.3                   stats4_4.2.1                ggfun_0.0.9                
[205] tensor_1.5                  httr_1.4.5                  KernSmooth_2.23-20         
[208] stringi_1.7.8               farver_2.1.1                viridis_0.6.2              
[211] ggtree_3.6.2                ggplotify_0.1.0             scattermore_0.8            
[214] bit_4.0.5                   MatrixGenerics_1.10.0       spatstat.data_3.0-0        
[217] ggraph_2.1.0                pkgconfig_2.0.3             knitr_1.42

And my yml env file:

name: /shared/projects/spatialtranscriptomicthymus/conda/env/ST_analysis
channels:
  - conda-forge
  - bioconda
  - pytorch
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - binutils_impl_linux-64=2.40=hf600244_0
  - blosc=1.21.3=hafa529b_0
  - boost-cpp=1.78.0=h75c5d50_1
  - bwidget=1.9.14=ha770c72_1
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.18.1=h7f98852_0
  - ca-certificates=2022.12.7=ha878542_0
  - cairo=1.16.0=ha61ee94_1014
  - cfitsio=4.2.0=hd9d235c_0
  - curl=7.88.1=hdc1c0ab_0
  - expat=2.5.0=h27087fc_0
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=hab24e00_0
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - freetype=2.12.1=hca18f0e_1
  - freexl=1.0.6=h166bdaf_1
  - fribidi=1.0.10=h36c2ea0_0
  - gcc_impl_linux-64=12.2.0=hcc96c02_19
  - geos=3.11.1=h27087fc_0
  - geotiff=1.7.1=h7157cca_5
  - gettext=0.21.1=h27087fc_0
  - gfortran_impl_linux-64=12.2.0=h55be85b_19
  - giflib=5.2.1=h36c2ea0_2
  - glpk=5.0=h445213a_0
  - gmp=6.2.1=h58526e2_0
  - graphite2=1.3.13=h58526e2_1001
  - gsl=2.7=he838d99_0
  - gxx_impl_linux-64=12.2.0=hcc96c02_19
  - harfbuzz=6.0.0=h8e241bc_0
  - hdf4=4.2.15=h9772cbc_5
  - hdf5=1.12.2=nompi_h4df4325_101
  - icu=70.1=h27087fc_0
  - jpeg=9e=h0b41bf4_3
  - json-c=0.16=hc379101_0
  - kealib=1.5.0=ha7026e8_0
  - kernel-headers_linux-64=2.6.32=he073ed8_15
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.20.1=h81ceb04_0
  - lcms2=2.14=hfd0df8a_1
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libaec=1.0.6=hcb278e6_1
  - libblas=3.9.0=16_linux64_openblas
  - libcblas=3.9.0=16_linux64_openblas
  - libcurl=7.88.1=hdc1c0ab_0
  - libdeflate=1.17=h0b41bf4_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-devel_linux-64=12.2.0=h3b97bd3_19
  - libgcc-ng=12.2.0=h65d4601_19
  - libgdal=3.6.2=h10cbb15_3
  - libgfortran-ng=12.2.0=h69a702a_19
  - libgfortran5=12.2.0=h337968e_19
  - libglib=2.74.1=h606061b_1
  - libgomp=12.2.0=h65d4601_19
  - libiconv=1.17=h166bdaf_0
  - libkml=1.3.0=h37653c0_1015
  - liblapack=3.9.0=16_linux64_openblas
  - libnetcdf=4.8.1=nompi_h261ec11_106
  - libnghttp2=1.51.0=hff17c54_0
  - libnsl=2.0.0=h7f98852_0
  - libopenblas=0.3.21=pthreads_h78a6416_3
  - libpng=1.6.39=h753d276_0
  - libpq=15.2=hb675445_0
  - librttopo=1.1.0=ha49c73b_12
  - libsanitizer=12.2.0=h46fd767_19
  - libspatialite=5.0.1=h7c8129e_22
  - libsqlite=3.40.0=h753d276_0
  - libssh2=1.10.0=hf14f497_3
  - libstdcxx-devel_linux-64=12.2.0=h3b97bd3_19
  - libstdcxx-ng=12.2.0=h46fd767_19
  - libtiff=4.5.0=h6adf6a1_2
  - libuuid=2.32.1=h7f98852_1000
  - libwebp-base=1.2.4=h166bdaf_0
  - libxcb=1.13=h7f98852_1004
  - libxml2=2.10.3=h7463322_0
  - libzip=1.9.2=hc929e4a_1
  - libzlib=1.2.13=h166bdaf_4
  - lz4-c=1.9.4=hcb278e6_0
  - make=4.3=hd18ef5c_1
  - ncurses=6.3=h27087fc_1
  - nspr=4.35=h27087fc_0
  - nss=3.88=he45b914_0
  - openjpeg=2.5.0=hfec8fc6_2
  - openssl=3.0.8=h0b41bf4_0
  - pandoc=2.19.2=h32600fe_1
  - pango=1.50.13=hd33c08f_0
  - pcre2=10.40=hc3806b6_0
  - pip=23.0.1=pyhd8ed1ab_0
  - pixman=0.40.0=h36c2ea0_0
  - poppler=22.12.0=h091648b_1
  - poppler-data=0.4.12=hd8ed1ab_0
  - postgresql=15.2=h3248436_0
  - proj=9.1.0=h8ffa02c_1
  - pthread-stubs=0.4=h36c2ea0_1001
  - python=3.9.16=h2782a2a_0_cpython
  - r-backports=1.4.1=r42h06615bd_1
  - r-base=4.2.2=ha7d60f8_3
  - r-bit=4.0.5=r42h06615bd_0
  - r-bit64=4.0.5=r42h06615bd_1
  - r-checkmate=2.1.0=r42h06615bd_1
  - r-class=7.3_21=r42h133d619_0
  - r-classint=0.4_8=r42h8da6f51_0
  - r-cli=3.6.0=r42h38f115c_0
  - r-clustree=0.5.0=r42hc72bb7e_1
  - r-colorspace=2.1_0=r42h133d619_0
  - r-cpp11=0.4.3=r42hc72bb7e_0
  - r-crayon=1.5.2=r42hc72bb7e_1
  - r-dbi=1.1.3=r42hc72bb7e_1
  - r-digest=0.6.31=r42h38f115c_0
  - r-dplyr=1.1.0=r42h38f115c_0
  - r-e1071=1.7_13=r42h38f115c_0
  - r-ellipsis=0.3.2=r42h06615bd_1
  - r-fansi=1.0.4=r42h133d619_0
  - r-farver=2.1.1=r42h7525677_1
  - r-fastmap=1.1.1=r42h38f115c_0
  - r-generics=0.1.3=r42hc72bb7e_1
  - r-ggforce=0.4.1=r42h7525677_1
  - r-ggplot2=3.4.1=r42hc72bb7e_0
  - r-ggraph=2.1.0=r42h7525677_1
  - r-ggrepel=0.9.3=r42h38f115c_0
  - r-glue=1.6.2=r42h06615bd_1
  - r-graphlayouts=0.8.4=r42h7525677_0
  - r-gridextra=2.3=r42hc72bb7e_1004
  - r-gtable=0.3.1=r42hc72bb7e_1
  - r-hdf5r=1.3.8=r42haf92f5d_0
  - r-igraph=1.4.1=r42h65ed38e_0
  - r-isoband=0.2.7=r42h38f115c_1
  - r-jsonlite=1.8.4=r42h133d619_0
  - r-kernsmooth=2.23_20=r42hd009a43_1
  - r-labeling=0.4.2=r42hc72bb7e_2
  - r-lattice=0.20_45=r42h06615bd_1
  - r-lifecycle=1.0.3=r42hc72bb7e_1
  - r-magrittr=2.0.3=r42h06615bd_1
  - r-mass=7.3_58.2=r42h133d619_0
  - r-matrix=1.5_3=r42h5f7b363_0
  - r-mgcv=1.8_41=r42h5f7b363_0
  - r-munsell=0.5.0=r42hc72bb7e_1005
  - r-nlme=3.1_162=r42hac0b197_0
  - r-pillar=1.8.1=r42hc72bb7e_1
  - r-pkgconfig=2.0.3=r42hc72bb7e_2
  - r-polyclip=1.10_4=r42h7525677_0
  - r-proxy=0.4_27=r42h06615bd_1
  - r-purrr=1.0.1=r42h133d619_0
  - r-r.methodss3=1.8.2=r42hc72bb7e_1
  - r-r.oo=1.25.0=r42hc72bb7e_1
  - r-r.utils=2.12.2=r42hc72bb7e_0
  - r-r6=2.5.1=r42hc72bb7e_1
  - r-rcolorbrewer=1.1_3=r42h785f33e_1
  - r-rcpp=1.0.10=r42h38f115c_0
  - r-rcpparmadillo=0.11.4.4.0=r42h358215d_0
  - r-rcppeigen=0.3.3.9.3=r42h9f5de39_0
  - r-rcppparallel=5.1.6=r42h38f115c_0
  - r-rlang=1.0.6=r42h7525677_1
  - r-s2=1.1.1=r42h5be344c_0
  - r-scales=1.2.1=r42hc72bb7e_1
  - r-sf=1.0_7=r42h282678f_6
  - r-stanheaders=2.21.0_7=r42haa30946_1
  - r-stringi=1.7.12=r42h1ae9187_0
  - r-stringr=1.5.0=r42h785f33e_0
  - r-systemfonts=1.0.4=r42h0ff29ef_1
  - r-tibble=3.1.8=r42h06615bd_1
  - r-tidygraph=1.2.3=r42h38f115c_0
  - r-tidyr=1.3.0=r42h38f115c_0
  - r-tidyselect=1.2.0=r42hc72bb7e_0
  - r-tweenr=2.0.2=r42h7525677_1
  - r-units=0.8_1=r42h38f115c_0
  - r-utf8=1.2.3=r42h133d619_0
  - r-vctrs=0.5.2=r42h38f115c_0
  - r-viridis=0.6.2=r42hc72bb7e_1
  - r-viridislite=0.4.1=r42hc72bb7e_1
  - r-withr=2.5.0=r42hc72bb7e_1
  - r-wk=0.7.1=r42h38f115c_0
  - readline=8.1.2=h0f457ee_0
  - sed=4.8=he412f7d_0
  - setuptools=67.4.0=pyhd8ed1ab_0
  - snappy=1.1.9=hbd366e4_2
  - sqlite=3.40.0=h4ff8645_0
  - sysroot_linux-64=2.12=he073ed8_15
  - tiledb=2.13.2=hd532e3d_0
  - tk=8.6.12=h27826a3_0
  - tktable=2.10=hb7b940f_3
  - tzcode=2022g=h166bdaf_0
  - tzdata=2022g=h191b570_0
  - udunits2=2.2.28=hc3e0081_0
  - wheel=0.38.4=pyhd8ed1ab_0
  - xerces-c=3.2.4=h55805fa_1
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.7.2=h7f98852_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-libxt=1.2.1=h7f98852_2
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - zlib=1.2.13=h166bdaf_4
  - zstd=1.5.2=h3eb15da_6
  - pip:
    - absl-py==1.4.0
    - aiohttp==3.8.4
    - aiosignal==1.3.1
    - async-timeout==4.0.2
    - attrs==22.2.0
    - cached-property==1.5.2
    - cachetools==5.3.0
    - certifi==2022.9.24
    - charset-normalizer==3.1.0
    - click==8.1.3
    - frozenlist==1.3.3
    - google-auth==2.16.2
    - google-auth-oauthlib==0.4.6
    - grpcio==1.51.3
    - h5py==3.8.0
    - idna==3.4
    - importlib-metadata==6.0.0
    - joblib==1.2.0
    - jupyter-client==8.0.3
    - llvmlite==0.39.1
    - markdown==3.4.1
    - multidict==6.0.4
    - nest-asyncio==1.5.6
    - numba==0.56.4
    - numpy==1.21.6
    - numpyro==0.9.2
    - oauthlib==3.2.2
    - opt-einsum==3.3.0
    - pandas==1.3.5
    - protobuf==3.20.1
    - pyasn1==0.4.8
    - pyasn1-modules==0.2.8
    - pynndescent==0.5.8
    - python-dateutil==2.8.2
    - pytz==2022.7.1
    - pyzmq==25.0.1
    - requests==2.28.2
    - requests-oauthlib==1.3.1
    - rsa==4.9
    - scikit-learn==1.2.2
    - scipy==1.7.3
    - six==1.16.0
    - tensorboard==2.12.0
    - tensorboard-data-server==0.7.0
    - tensorboard-plugin-wit==1.8.1
    - texttable==1.6.7
    - threadpoolctl==3.1.0
    - torch==1.13.1+cu116
    - torchaudio==0.13.1+cu116
    - torchvision==0.14.1+cu116
    - tornado==6.2
    - tqdm==4.65.0
    - umap-learn==0.5.3
    - urllib3==1.26.15
    - yarl==1.8.2
    - zipp==3.15.0
prefix: /shared/projects/spatialtranscriptomicthymus/conda/env/ST_analysis