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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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RunSCVELO resulted in AttributeError #152

Closed MinjieHu closed 12 months ago

MinjieHu commented 12 months ago

Hi,

Thanks again for the awesome pipeline.

I tried to analysis velocity with the example data and resulted in 

Error: AttributeError: can't set attribute

Here is the code I am using 

Error: AttributeError: can't set attribute

And here is the traceback

stop(structure(list(message = "AttributeError: can't set attribute\n",
call = NULL, cppstack = structure(list(file = "", line = -1L,
stack = c("/usr/local/lib/R/site-library/reticulate/libs/reticulate.so(Rcpp::stop(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x85) [0x7f0de34fd5d2]",
"/usr/local/lib/R/site-library/reticulate/libs/reticulate.so(+0x1f55b) [0x7f0de350055b]", ...
10._delegate_property_set at categorical.py#2460
9._setter at accessor.py#99
8.__setattr__ at base.py#178
7.set_legend at utils.py#555
6.scatter at scatter.py#668
5.velocity_embedding_stream at velocity_embedding_stream.py#252
4.SCVELO at SCP_analysis.py#188
3.(structure(function (...)
{
dots <- py_resolve_dots(list(...))
result <- py_call_impl(callable, dots$args, dots$keywords) ...
2.do.call(SCP_analysis$SCVELO, args)
1.RunSCVELO(srt = pancreas_sub, group_by = "SubCellType", linear_reduction = "PCA",
nonlinear_reduction = "UMAP")

The package versions loaded are 

R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] SeuratObject_4.1.3 Seurat_4.3.0       velocyto.R_0.6     Matrix_1.5-4       SCP_0.5.1          devtools_2.4.5    
[7] usethis_2.1.6     

loaded via a namespace (and not attached):
  [1] fs_1.6.2                    matrixStats_1.0.0           spatstat.sparse_3.0-1       bitops_1.0-7               
  [5] enrichplot_1.20.0           HDO.db_0.99.1               httr_1.4.6                  RColorBrewer_1.1-3         
  [9] doParallel_1.0.17           profvis_0.3.8               tools_4.3.0                 sctransform_0.3.5          
 [13] utf8_1.2.3                  R6_2.5.1                    mgcv_1.8-42                 lazyeval_0.2.2             
 [17] uwot_0.1.14                 GetoptLong_1.0.5            urlchecker_1.0.1            withr_2.5.0                
 [21] sp_1.6-0                    prettyunits_1.1.1           gridExtra_2.3               parallelDist_0.2.6         
 [25] progressr_0.13.0            cli_3.6.1                   Biobase_2.60.0              spatstat.explore_3.1-0     
 [29] scatterpie_0.2.0            spatstat.data_3.0-1         ggridges_0.5.4              pbapply_1.7-0              
 [33] slingshot_2.8.0             yulab.utils_0.0.6           Rsamtools_2.16.0            gson_0.1.0                 
 [37] DOSE_3.26.1                 R.utils_2.12.2              parallelly_1.35.0           sessioninfo_1.2.2          
 [41] rstudioapi_0.14             RSQLite_2.3.1               generics_0.1.3              gridGraphics_0.5-1         
 [45] shape_1.4.6                 ica_1.0-3                   spatstat.random_3.1-4       dplyr_1.1.2                
 [49] GO.db_3.17.0                fansi_1.0.4                 S4Vectors_0.38.1            abind_1.4-5                
 [53] R.methodsS3_1.8.2           lifecycle_1.0.3             yaml_2.3.7                  SummarizedExperiment_1.30.1
 [57] qvalue_2.32.0               BiocFileCache_2.8.0         Rtsne_0.16                  grid_4.3.0                 
 [61] blob_1.2.4                  promises_1.2.0.1            crayon_1.5.2                miniUI_0.1.1.1             
 [65] lattice_0.21-8              cowplot_1.1.1               KEGGREST_1.40.0             pillar_1.9.0               
 [69] knitr_1.42                  ComplexHeatmap_2.15.4       fgsea_1.26.0                GenomicRanges_1.52.0       
 [73] rjson_0.2.21                future.apply_1.10.0         codetools_0.2-19            fastmatch_1.1-3            
 [77] leiden_0.4.3                glue_1.6.2                  downloader_0.4              ggfun_0.0.9                
 [81] pcaMethods_1.92.0           data.table_1.14.8           remotes_2.4.2               treeio_1.24.0              
 [85] vctrs_0.6.2                 png_0.1-8                   gtable_0.3.3                cachem_1.0.8               
 [89] xfun_0.39                   princurve_2.1.6             S4Arrays_1.0.4              Signac_1.9.0               
 [93] mime_0.12                   tidygraph_1.2.3             survival_3.5-5              SingleCellExperiment_1.22.0
 [97] RcppRoll_0.3.0              iterators_1.0.14            ellipsis_0.3.2              fitdistrplus_1.1-11        
[101] ROCR_1.0-11                 nlme_3.1-162                ggtree_3.9.0                bit64_4.0.5                
[105] progress_1.2.2              filelock_1.0.2              RcppAnnoy_0.0.20            GenomeInfoDb_1.36.0        
[109] rprojroot_2.0.3             R.cache_0.16.0              irlba_2.3.5.1               KernSmooth_2.23-21         
[113] colorspace_2.1-0            BiocGenerics_0.46.0         DBI_1.1.3                   tidyselect_1.2.0           
[117] processx_3.8.1              proxyC_0.3.3                bit_4.0.5                   compiler_4.3.0             
[121] curl_5.0.0                  xml2_1.3.4                  DelayedArray_0.26.3         desc_1.4.2                 
[125] plotly_4.10.1               shadowtext_0.1.2            scales_1.2.1                lmtest_0.9-40              
[129] callr_3.7.3                 rappdirs_0.3.3              stringr_1.5.0               digest_0.6.31              
[133] goftest_1.2-3               spatstat.utils_3.0-2        rmarkdown_2.21              XVector_0.40.0             
[137] htmltools_0.5.5             pkgconfig_2.0.3             MatrixGenerics_1.12.3       intrinsicDimension_1.2.0   
[141] dbplyr_2.3.2                fastmap_1.1.1               rlang_1.1.1                 GlobalOptions_0.1.2        
[145] htmlwidgets_1.6.2           shiny_1.7.4                 farver_2.1.1                zoo_1.8-12                 
[149] jsonlite_1.8.4              BiocParallel_1.34.2         GOSemSim_2.26.0             R.oo_1.25.0                
[153] RCurl_1.98-1.12             magrittr_2.0.3              GenomeInfoDbData_1.2.10     ggplotify_0.1.0            
[157] patchwork_1.1.2             munsell_0.5.0               Rcpp_1.0.10                 TrajectoryUtils_1.8.0      
[161] ggnewscale_0.4.9            ape_5.7-1                   viridis_0.6.3               reticulate_1.28            
[165] stringi_1.7.12              ggraph_2.1.0                zlibbioc_1.46.0             MASS_7.3-60                
[169] plyr_1.8.8                  pkgbuild_1.4.0              parallel_4.3.0              listenv_0.9.0              
[173] ggrepel_0.9.3               deldir_1.0-6                Biostrings_2.68.1           graphlayouts_1.0.0         
[177] splines_4.3.0               tensor_1.5                  hms_1.1.3                   circlize_0.4.15            
[181] ps_1.7.5                    igraph_1.4.2                spatstat.geom_3.1-0         reshape2_1.4.4             
[185] biomaRt_2.56.0              stats4_4.3.0                pkgload_1.3.2               XML_3.99-0.14              
[189] evaluate_0.21               RcppParallel_5.1.7          foreach_1.5.2               tweenr_2.0.2               
[193] httpuv_1.6.10               RANN_2.6.1                  tidyr_1.3.0                 purrr_1.0.1                
[197] polyclip_1.10-4             future_1.32.0               clue_0.3-64                 scattermore_1.0            
[201] ggplot2_3.4.2               ggforce_0.4.1               xtable_1.8-4                tidytree_0.4.2             
[205] later_1.3.1                 viridisLite_0.4.2           tibble_3.2.1                clusterProfiler_4.8.1      
[209] aplot_0.1.10                yaImpute_1.0-33             memoise_2.0.1               AnnotationDbi_1.62.1       
[213] IRanges_2.34.0              cluster_2.1.4               globals_0.16.2              here_1.0.1

I have also tried to set up a totally new environment, but still resulted in the same error.

Thanks ahead for the help!

Minjie

zhanghao-njmu commented 12 months ago

Could you provide your Python environment information by running the installed_Python_pkgs() function?

MinjieHu commented 12 months ago

Sure. Here are they:

                          package      version                         requirement     channel
1                   _libgcc_mutex          0.1                   _libgcc_mutex=0.1 conda-forge
2                   _openmp_mutex          4.5                   _openmp_mutex=4.5 conda-forge
3                         anndata        0.9.2                       anndata=0.9.2        pypi
4                          attmap       0.13.2                       attmap=0.13.2 conda-forge
5                           attrs       23.1.0                        attrs=23.1.0 conda-forge
6                       backports          1.0                       backports=1.0 conda-forge
7              backports-zoneinfo        0.2.1            backports-zoneinfo=0.2.1        pypi
8   backports.functools_lru_cache        1.6.5 backports.functools_lru_cache=1.6.5 conda-forge
9          binutils_impl_linux-64       2.36.1       binutils_impl_linux-64=2.36.1 conda-forge
10              binutils_linux-64         2.36              binutils_linux-64=2.36 conda-forge
11                      biopython         1.81                      biopython=1.81 conda-forge
12                         bleach        6.0.0                        bleach=6.0.0 conda-forge
13                         blosc2        2.0.0                        blosc2=2.0.0        pypi
14                        boltons       23.0.0                      boltons=23.0.0 conda-forge
15                  brotli-python        1.0.9                 brotli-python=1.0.9 conda-forge
16                          bzip2        1.0.8                         bzip2=1.0.8 conda-forge
17                         c-ares       1.19.1                       c-ares=1.19.1 conda-forge
18                ca-certificates    2023.7.22           ca-certificates=2023.7.22 conda-forge
19                         cattrs       23.1.2                       cattrs=23.1.2 conda-forge
20                        certifi    2023.7.22                   certifi=2023.7.22 conda-forge
21                           cffi       1.15.1                         cffi=1.15.1 conda-forge
22                           cfgv        3.3.1                          cfgv=3.3.1 conda-forge
23             charset-normalizer        3.2.0            charset-normalizer=3.2.0 conda-forge
24                       cheetah3  3.2.6.post2                cheetah3=3.2.6.post2 conda-forge
25                          click        8.1.7                         click=8.1.7 conda-forge
26                          cmake       3.27.2                        cmake=3.27.2        pypi
27                       colorama        0.4.6                      colorama=0.4.6 conda-forge
28                          conda       23.1.0                        conda=23.1.0 conda-forge
29         conda-package-handling        2.2.0        conda-package-handling=2.2.0 conda-forge
30        conda-package-streaming        0.9.0       conda-package-streaming=0.9.0 conda-forge
31                      contourpy        1.1.0                     contourpy=1.1.0        pypi
32                   cryptography       41.0.3                 cryptography=41.0.3 conda-forge
33                           curl        8.2.1                          curl=8.2.1 conda-forge
34                         cycler       0.11.0                       cycler=0.11.0        pypi
35                         cython        3.0.0                        cython=3.0.0        pypi
36                        distlib        0.3.7                       distlib=0.3.7 conda-forge
37                       docutils       0.20.1                     docutils=0.20.1 conda-forge
38                           eido        0.2.1                          eido=0.2.1 conda-forge
39                 exceptiongroup        1.1.3                exceptiongroup=1.1.3 conda-forge
40                      fcsparser        0.2.4                     fcsparser=0.2.4        pypi
41                       filelock       3.12.2                     filelock=3.12.2 conda-forge
42                       filetype        1.2.0                      filetype=1.2.0 conda-forge
43                      fonttools       4.42.0                    fonttools=4.42.0        pypi
44                         future       0.18.3                       future=0.18.3 conda-forge
45              galaxy-containers       22.1.1            galaxy-containers=22.1.1 conda-forge
46               galaxy-tool-util       22.1.5             galaxy-tool-util=22.1.5 conda-forge
47                    galaxy-util       22.1.2                  galaxy-util=22.1.2 conda-forge
48              gcc_impl_linux-64       11.1.0            gcc_impl_linux-64=11.1.0 conda-forge
49                   gcc_linux-64       11.1.0                 gcc_linux-64=11.1.0 conda-forge
50                        gettext       0.21.1                      gettext=0.21.1 conda-forge
51                            git       2.41.0                          git=2.41.0 conda-forge
52                          gitdb       4.0.10                        gitdb=4.0.10 conda-forge
53                      gitpython       3.1.32                    gitpython=3.1.32 conda-forge
54                       greenlet        2.0.2                      greenlet=2.0.2 conda-forge
55              gxx_impl_linux-64       11.1.0            gxx_impl_linux-64=11.1.0 conda-forge
56                   gxx_linux-64       11.1.0                 gxx_linux-64=11.1.0 conda-forge
57                           h5py        3.9.0                          h5py=3.9.0        pypi
58                            icu         72.1                            icu=72.1 conda-forge
59                       identify       2.5.26                     identify=2.5.26 conda-forge
60                           idna          3.4                            idna=3.4 conda-forge
61                         igraph       0.10.2                       igraph=0.10.2        pypi
62             importlib-metadata        6.8.0            importlib-metadata=6.8.0 conda-forge
63            importlib_resources        6.0.1           importlib_resources=6.0.1 conda-forge
64                      iniconfig        2.0.0                     iniconfig=2.0.0 conda-forge
65                   itsdangerous        2.1.2                  itsdangerous=2.1.2 conda-forge
66                            jax       0.4.13                          jax=0.4.13        pypi
67                         jaxlib       0.4.13                       jaxlib=0.4.13        pypi
68                         jaxopt          0.8                          jaxopt=0.8        pypi
69                         jinja2        3.1.2                        jinja2=3.1.2 conda-forge
70                         joblib        1.3.2                        joblib=1.3.2        pypi
71                      jsonpatch         1.32                      jsonpatch=1.32 conda-forge
72                    jsonpointer          2.0                     jsonpointer=2.0 conda-forge
73                     jsonschema       4.19.0                   jsonschema=4.19.0 conda-forge
74      jsonschema-specifications     2023.7.1  jsonschema-specifications=2023.7.1 conda-forge
75        kernel-headers_linux-64       2.6.32      kernel-headers_linux-64=2.6.32 conda-forge
76                       keyutils        1.6.1                      keyutils=1.6.1 conda-forge
77                     kiwisolver        1.4.4                    kiwisolver=1.4.4        pypi
78                           krb5       1.21.2                         krb5=1.21.2 conda-forge
79               ld_impl_linux-64       2.36.1             ld_impl_linux-64=2.36.1 conda-forge
80                      leidenalg       0.10.1                    leidenalg=0.10.1        pypi
81                        libblas        3.9.0                       libblas=3.9.0 conda-forge
82                       libcblas        3.9.0                      libcblas=3.9.0 conda-forge
83                        libcurl        8.2.1                       libcurl=8.2.1 conda-forge
84                        libedit 3.1.20191231                libedit=3.1.20191231 conda-forge
85                          libev         4.33                          libev=4.33 conda-forge
86                       libexpat        2.5.0                      libexpat=2.5.0 conda-forge
87                         libffi        3.4.2                        libffi=3.4.2 conda-forge
88          libgcc-devel_linux-64       11.1.0        libgcc-devel_linux-64=11.1.0 conda-forge
89                      libgcc-ng       13.1.0                    libgcc-ng=13.1.0 conda-forge
90                 libgfortran-ng       13.1.0               libgfortran-ng=13.1.0 conda-forge
91                   libgfortran5       13.1.0                 libgfortran5=13.1.0 conda-forge
92                        libgomp       13.1.0                      libgomp=13.1.0 conda-forge
93                       libiconv         1.17                       libiconv=1.17 conda-forge
94                      liblapack        3.9.0                     liblapack=3.9.0 conda-forge
95                     libnghttp2       1.52.0                   libnghttp2=1.52.0 conda-forge
96                         libnsl        2.0.0                        libnsl=2.0.0 conda-forge
97                    libopenblas       0.3.23                  libopenblas=0.3.23 conda-forge
98                          libpq         15.4                          libpq=15.4 conda-forge
99                   libsanitizer       11.1.0                 libsanitizer=11.1.0 conda-forge
100                     libsqlite       3.42.0                    libsqlite=3.42.0 conda-forge
101                       libssh2       1.11.0                      libssh2=1.11.0 conda-forge
102      libstdcxx-devel_linux-64       11.1.0     libstdcxx-devel_linux-64=11.1.0 conda-forge
103                  libstdcxx-ng       13.1.0                 libstdcxx-ng=13.1.0 conda-forge
104                       libuuid       2.38.1                      libuuid=2.38.1 conda-forge
105                       libxml2       2.11.5                      libxml2=2.11.5 conda-forge
106                       libxslt       1.1.37                      libxslt=1.1.37 conda-forge
107                       libzlib       1.2.13                      libzlib=1.2.13 conda-forge
108                      llvmlite       0.38.1                     llvmlite=0.38.1        pypi
109                       logmuse        0.2.6                       logmuse=0.2.6 conda-forge
110                        loompy        3.0.7                        loompy=3.0.7        pypi
111                          lxml        4.9.3                          lxml=4.9.3 conda-forge
112                      markdown        3.4.4                      markdown=3.4.4 conda-forge
113                markdown-it-py        3.0.0                markdown-it-py=3.0.0 conda-forge
114                    markupsafe        2.1.3                    markupsafe=2.1.3 conda-forge
115                    matplotlib        3.6.3                    matplotlib=3.6.3        pypi
116                         mdurl        0.1.0                         mdurl=0.1.0 conda-forge
117                        mellon        1.3.1                        mellon=1.3.1        pypi
118                     ml-dtypes        0.2.0                     ml-dtypes=0.2.0        pypi
119                       msgpack        1.0.5                       msgpack=1.0.5        pypi
120                       natsort        8.4.0                       natsort=8.4.0        pypi
121                       ncurses          6.4                         ncurses=6.4 conda-forge
122                       ndindex          1.7                         ndindex=1.7        pypi
123                      networkx          3.1                        networkx=3.1        pypi
124                       nf-core          2.9                         nf-core=2.9    bioconda
125                       nodeenv        1.8.0                       nodeenv=1.8.0 conda-forge
126                         numba       0.55.2                        numba=0.55.2        pypi
127                       numexpr        2.8.5                       numexpr=2.8.5        pypi
128                         numpy       1.21.6                        numpy=1.21.6        pypi
129                numpy-groupies       0.9.22               numpy-groupies=0.9.22        pypi
130                       openssl        3.1.2                       openssl=3.1.2 conda-forge
131                    opt-einsum        3.3.0                    opt-einsum=3.3.0        pypi
132                         oyaml          1.0                           oyaml=1.0 conda-forge
133                     packaging         21.3                      packaging=21.3 conda-forge
134                      palantir        1.3.0                      palantir=1.3.0        pypi
135                        pandas        1.3.5                        pandas=1.3.5        pypi
136                         patsy        0.5.3                         patsy=0.5.3        pypi
137                         pcre2        10.40                         pcre2=10.40 conda-forge
138                         peppy       0.35.7                        peppy=0.35.7 conda-forge
139                          perl       5.32.1                         perl=5.32.1 conda-forge
140                        pillow       10.0.0                       pillow=10.0.0        pypi
141                           pip       23.2.1                          pip=23.2.1        pypi
142                         piper       0.12.3                        piper=0.12.3    bioconda
143                      pipestat        0.5.1                      pipestat=0.5.1 conda-forge
144          pkgutil-resolve-name       1.3.10         pkgutil-resolve-name=1.3.10 conda-forge
145                  platformdirs       3.10.0                 platformdirs=3.10.0 conda-forge
146                        pluggy        1.2.0                        pluggy=1.2.0 conda-forge
147                    pre-commit        3.1.1                    pre-commit=3.1.1 conda-forge
148                  progressbar2        4.2.0                  progressbar2=4.2.0        pypi
149                prompt-toolkit       3.0.39               prompt-toolkit=3.0.39 conda-forge
150                prompt_toolkit       3.0.39               prompt_toolkit=3.0.39 conda-forge
151                        psutil        5.9.5                        psutil=5.9.5 conda-forge
152                      psycopg2        2.9.6                      psycopg2=2.9.6 conda-forge
153               psycopg2-binary        2.9.7               psycopg2-binary=2.9.7        pypi
154                    py-cpuinfo        9.0.0                    py-cpuinfo=9.0.0        pypi
155                       pycosat        0.6.4                       pycosat=0.6.4 conda-forge
156                     pycparser         2.21                      pycparser=2.21 conda-forge
157                      pydantic      1.10.12                    pydantic=1.10.12 conda-forge
158                       pyfaidx      0.7.2.1                     pyfaidx=0.7.2.1    bioconda
159                         pygam        0.8.0                         pygam=0.8.0        pypi
160                      pygments       2.16.1                     pygments=2.16.1 conda-forge
161                   pynndescent       0.5.10                  pynndescent=0.5.10        pypi
162                     pyopenssl       23.2.0                    pyopenssl=23.2.0 conda-forge
163                     pyparsing        3.1.1                     pyparsing=3.1.1 conda-forge
164                       pysocks        1.7.1                       pysocks=1.7.1 conda-forge
165                        pytest        7.4.0                        pytest=7.4.0 conda-forge
166               pytest-workflow        2.0.1               pytest-workflow=2.0.1 conda-forge
167                        python       3.8.17                       python=3.8.17 conda-forge
168               python-dateutil        2.8.2               python-dateutil=2.8.2 conda-forge
169                 python-igraph       0.10.2                python-igraph=0.10.2        pypi
170                 python-tzdata       2023.3                python-tzdata=2023.3 conda-forge
171                  python-utils        3.7.0                  python-utils=3.7.0        pypi
172                    python_abi          3.8                      python_abi=3.8 conda-forge
173                          pytz       2023.3                         pytz=2023.3 conda-forge
174                        pyvcf3        1.0.3                        pyvcf3=1.0.3    bioconda
175                        pyyaml          6.0                          pyyaml=6.0 conda-forge
176                   questionary        2.0.0                   questionary=2.0.0 conda-forge
177                      readline          8.2                        readline=8.2 conda-forge
178                   referencing       0.30.2                  referencing=0.30.2 conda-forge
179                    refgenconf       0.12.2                   refgenconf=0.12.2    bioconda
180                      refgenie       0.12.1                     refgenie=0.12.1    bioconda
181                    repoze.lru          0.7                      repoze.lru=0.7 conda-forge
182                      requests       2.31.0                     requests=2.31.0 conda-forge
183                requests-cache        1.1.0                requests-cache=1.1.0 conda-forge
184                          rich       13.5.1                         rich=13.5.1 conda-forge
185                    rich-click        1.6.1                    rich-click=1.6.1 conda-forge
186                        routes        2.5.1                        routes=2.5.1 conda-forge
187                       rpds-py        0.9.2                       rpds-py=0.9.2 conda-forge
188                   ruamel.yaml      0.17.32                 ruamel.yaml=0.17.32 conda-forge
189              ruamel.yaml.clib        0.2.7              ruamel.yaml.clib=0.2.7 conda-forge
190                        scanpy        1.9.3                        scanpy=1.9.3        pypi
191                  scikit-learn        1.1.2                  scikit-learn=1.1.2        pypi
192                         scipy       1.10.1                        scipy=1.10.1        pypi
193                        scvelo        0.2.5                        scvelo=0.2.5        pypi
194                       seaborn       0.12.2                      seaborn=0.12.2        pypi
195                  session-info        1.0.0                  session-info=1.0.0        pypi
196                    setuptools       68.1.0                   setuptools=68.1.0        pypi
197                           six       1.16.0                          six=1.16.0 conda-forge
198                         smmap        3.0.5                         smmap=3.0.5 conda-forge
199              sortedcontainers        2.4.0              sortedcontainers=2.4.0 conda-forge
200                    sqlalchemy       1.4.39                   sqlalchemy=1.4.39   pkgs/main
201             sqlalchemy2-stubs     0.0.2a35          sqlalchemy2-stubs=0.0.2a35 conda-forge
202                      sqlmodel        0.0.8                      sqlmodel=0.0.8 conda-forge
203                   statsmodels       0.14.0                  statsmodels=0.14.0        pypi
204                   stdlib-list        0.9.0                   stdlib-list=0.9.0        pypi
205              sysroot_linux-64         2.12               sysroot_linux-64=2.12 conda-forge
206                        tables        3.8.0                        tables=3.8.0        pypi
207                      tabulate        0.9.0                      tabulate=0.9.0 conda-forge
208                     texttable        1.6.7                     texttable=1.6.7        pypi
209                 threadpoolctl        3.2.0                 threadpoolctl=3.2.0        pypi
210                            tk       8.6.12                           tk=8.6.12 conda-forge
211                         tomli        2.0.1                         tomli=2.0.1 conda-forge
212                         toolz       0.12.0                        toolz=0.12.0 conda-forge
213                          tqdm       4.66.1                         tqdm=4.66.1 conda-forge
214             typing-extensions        4.7.1             typing-extensions=4.7.1 conda-forge
215             typing_extensions        4.7.1             typing_extensions=4.7.1 conda-forge
216                       tzlocal        5.0.1                       tzlocal=5.0.1        pypi
217                      ubiquerg        0.6.3                      ubiquerg=0.6.3 conda-forge
218                         ujson        5.7.0                         ujson=5.7.0 conda-forge
219                       ukkonen        1.0.1                       ukkonen=1.0.1 conda-forge
220                    umap-learn        0.5.3                    umap-learn=0.5.3        pypi
221                 url-normalize        1.4.3                 url-normalize=1.4.3 conda-forge
222                       urllib3        2.0.4                       urllib3=2.0.4 conda-forge
223                   veracitools        0.1.3                   veracitools=0.1.3 conda-forge
224                versioned-hdf5       1.3.14               versioned-hdf5=1.3.14        pypi
225                    virtualenv      20.24.3                  virtualenv=20.24.3 conda-forge
226                       wcwidth        0.2.6                       wcwidth=0.2.6 conda-forge
227                  webencodings        0.5.1                  webencodings=0.5.1 conda-forge
228                         wheel       0.41.1                        wheel=0.41.1 conda-forge
229                        whoosh        2.7.4                        whoosh=2.7.4 conda-forge
230                            xz        5.2.6                            xz=5.2.6 conda-forge
231                        yacman        0.9.1                        yacman=0.9.1 conda-forge
232                          yaml        0.2.5                          yaml=0.2.5 conda-forge
233                          zipp       3.16.2                         zipp=3.16.2 conda-forge
234                 zipstream-new        1.1.8                 zipstream-new=1.1.8 conda-forge
235                     zstandard       0.19.0                    zstandard=0.19.0 conda-forge
236                          zstd        1.5.2                          zstd=1.5.2 conda-forge
zhanghao-njmu commented 12 months ago

This could be a bug in scvelo: https://github.com/theislab/scvelo/pull/1065 https://github.com/theislab/scvelo/issues/1091 https://github.com/theislab/scvelo/issues/1110

There seems to be a conflict between scvelo and pandas > 2.0, but the pandas version in the SCP environment is 1.3.5. You can try resetting the SCP Python environment by usingPrepareEnv(force = TRUE) first.

Additionally, reinstalling scvelo from GitHub may also be a potential solution to the issue you're facing:

# Start a new R session 
library(SCP)
library(reticulate)
py_install(packages = "git+https://github.com/theislab/scvelo.git@master",pip = TRUE)

If the installation fails, you can also install scvelo manually. Please make sure to use the SCP env's Python to install the package.

MinjieHu commented 12 months ago

Thanks for the instant response.

As you can see in my environment information, the pandas version I had is 1.3.5. I will try to re-install scvelo and see how it goes.

MinjieHu commented 12 months ago

After updating the scvelo, it works now!

Thank you again for the help!