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jingshuw / SAVERX

R package for transfer learning of single-cell RNA-seq denoising
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Error in py_module_import(module, convert = convert) : ImportError: cannot import name 'getargspec_no_self' from 'scipy._lib._util' #20

Open bschilder opened 3 years ago

bschilder commented 3 years ago

Just installed SAVERX and ran into this error message in the example.

# install_github("jingshuw/SAVERX")
library(SAVERX)
library(reticulate)
reticulate::use_condaenv("/opt/anaconda3/envs/echoR")
reticulate::use_python("/opt/anaconda3/envs/echoR/bin/python3.7")
reticulate::py_install("sctransfer", pip = T)

 file <- saverx("~/Downloads/shekhar_downsampled.csv")
[1] "Input file is: ~/Downloads/shekhar_downsampled.csv"
[1] "Use a pretrained model: No"
[1] "Processed file saved as: 1613680966.07345/tmpdata.rds"
[1] "Data preprocessed ..."
Error in py_module_import(module, convert = convert) : 
  ImportError: cannot import name 'getargspec_no_self' from 'scipy._lib._util' (/opt/anaconda3/envs/echoR/lib/python3.7/site-packages/scipy/_lib/_util.py)
>

Thanks!, Brian

Conda env

``` ⋊> ~/D/model_celltype_conservation on main ⨯ conda list (echoR) 20:43:33 # packages in environment at /opt/anaconda3/envs/echoR: # # Name Version Build Channel _r-mutex 1.0.0 anacondar_1 absl-py 0.11.0 pypi_0 pypi anndata 0.7.5 py37hf985489_0 conda-forge arrow-cpp 0.15.1 py37hb41def8_6 astunparse 1.6.3 pypi_0 pypi attrs 20.3.0 pyhd3eb1b0_0 bcftools 1.10.2 h27336cd_0 bioconda bioconductor-annotationdbi 1.48.0 r36_0 bioconda bioconductor-annotationfilter 1.10.0 r36_0 bioconda bioconductor-biobase 2.46.0 r36h01d97ff_0 bioconda bioconductor-biocfilecache 1.10.0 r36_0 bioconda bioconductor-biocgenerics 0.32.0 r36_0 bioconda bioconductor-biocparallel 1.20.0 r36h6de7cb9_0 bioconda bioconductor-biomart 2.42.0 r36_0 bioconda bioconductor-biostrings 2.54.0 r36h01d97ff_0 bioconda bioconductor-biovizbase 1.34.0 r36h01d97ff_0 bioconda bioconductor-bsgenome 1.54.0 r36_0 bioconda bioconductor-delayedarray 0.12.0 r36h01d97ff_0 bioconda bioconductor-ensdb.hsapiens.v75 2.99.0 r36_6 bioconda bioconductor-ensembldb 2.10.0 r36_0 bioconda bioconductor-genomeinfodb 1.22.0 r36_0 bioconda bioconductor-genomeinfodbdata 1.2.2 r36_0 bioconda bioconductor-genomicalignments 1.22.0 r36h01d97ff_0 bioconda bioconductor-genomicfeatures 1.38.0 r36_0 bioconda bioconductor-genomicranges 1.38.0 r36h01d97ff_0 bioconda bioconductor-ggbio 1.34.0 r36_0 bioconda bioconductor-graph 1.64.0 r36h01d97ff_0 bioconda bioconductor-iranges 2.20.0 r36h01d97ff_0 bioconda bioconductor-organismdbi 1.28.0 r36_0 bioconda bioconductor-protgenerics 1.18.0 r36_0 bioconda bioconductor-rbgl 1.62.1 r36h6de7cb9_0 bioconda bioconductor-rgraphviz 2.30.0 r36h6de7cb9_0 bioconda bioconductor-rhtslib 1.18.0 r36h90b7f41_1 bioconda bioconductor-rsamtools 2.2.0 r36h6de7cb9_0 bioconda bioconductor-rtracklayer 1.46.0 r36h01d97ff_0 bioconda bioconductor-s4vectors 0.24.0 r36h01d97ff_0 bioconda bioconductor-snpstats 1.36.0 r36h01d97ff_0 bioconda bioconductor-summarizedexperiment 1.16.0 r36_0 bioconda bioconductor-suprahex 1.24.0 r36_0 bioconda bioconductor-variantannotation 1.32.0 r36h01d97ff_0 bioconda bioconductor-xvector 0.26.0 r36h01d97ff_0 bioconda bioconductor-zlibbioc 1.32.0 r36h01d97ff_0 bioconda bitarray 1.6.1 py37h9ed2024_0 blas 2.11 openblas conda-forge bokeh 2.2.3 py37_0 boost-cpp 1.67.0 h1de35cc_4 brotli 1.0.9 hb1e8313_2 brotlipy 0.7.0 py37h9ed2024_1003 bwidget 1.9.11 1 bzip2 1.0.8 h1de35cc_0 c-ares 1.16.1 haf1e3a3_0 ca-certificates 2020.12.5 h033912b_0 conda-forge cachetools 4.2.1 pypi_0 pypi cairo 1.16.0 h0ab9d94_1001 conda-forge certifi 2020.12.5 py37hf985489_1 conda-forge cffi 1.14.3 py37h2125817_2 chardet 3.0.4 py37hecd8cb5_1003 clang 10.0.0 default_hf57f61e_0 clang_osx-64 4.0.1 h1ce6c1d_16 anaconda clangxx 10.0.0 default_hf57f61e_0 clangxx_osx-64 4.0.1 h22b1bf0_16 click 7.1.2 py_0 cloudpickle 1.6.0 py_0 cryptography 3.2.1 py37hbcfaee0_1 curl 7.67.0 ha441bb4_0 cycler 0.10.0 pypi_0 pypi cytoolz 0.11.0 py37haf1e3a3_0 dask 2.30.0 py_0 dask-core 2.30.0 py_0 decorator 4.4.2 py_0 deprecated 1.2.10 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h1de35cc_3 zstandard 0.14.1 py37h23ab428_0 zstd 1.3.7 h5bba6e5_0 ```

R Session Info

``` > sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] reticulate_1.18 SAVERX_1.0.2 SeuratObject_4.0.0 [4] Seurat_4.0.0 SummarizedExperiment_1.20.0 Biobase_2.50.0 [7] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2 IRanges_2.24.1 [10] S4Vectors_0.28.1 BiocGenerics_0.36.0 MatrixGenerics_1.2.1 [13] matrixStats_0.58.0 dplyr_1.0.4 loaded via a namespace (and not attached): [1] rappdirs_0.3.3 rtracklayer_1.50.0 [3] scattermore_0.7 ggthemes_4.2.4 [5] R.methodsS3_1.8.1 tidyr_1.1.2 [7] knitr_1.31 ggplot2_3.3.3 [9] bit64_4.0.5 R.utils_2.10.1 [11] irlba_2.3.3 DelayedArray_0.16.1 [13] data.table_1.13.6 rpart_4.1-15 [15] RCurl_1.98-1.2 generics_0.1.0 [17] callr_3.5.1 cowplot_1.1.1 [19] usethis_2.0.1 RSQLite_2.2.3 [21] RANN_2.6.1 proxy_0.4-24 [23] future_1.21.0 bit_4.0.4 [25] spatstat.data_2.0-0 webshot_0.5.2 [27] xml2_1.3.2 httpuv_1.5.5 [29] assertthat_0.2.1 viridis_0.5.1 [31] xfun_0.21 One2One_0.1.0 [33] hms_1.0.0 evaluate_0.14 [35] promises_1.2.0.1 TSP_1.1-10 [37] DEoptimR_1.0-8 progress_1.2.2 [39] caTools_1.18.1 dendextend_1.14.0 [41] dbplyr_2.1.0 readxl_1.3.1 [43] igraph_1.2.6 DBI_1.1.1 [45] htmlwidgets_1.5.3 purrr_0.3.4 [47] ellipsis_0.3.1 RSpectra_0.16-0 [49] biomaRt_2.46.3 deldir_0.2-9 [51] vctrs_0.3.6 SingleCellExperiment_1.12.0 [53] remotes_2.2.0 here_1.0.1 [55] TTR_0.24.2 ROCR_1.0-11 [57] abind_1.4-5 cachem_1.0.3 [59] RcppEigen_0.3.3.9.1 withr_2.4.1 [61] BSgenome_1.58.0 robustbase_0.93-7 [63] vcd_1.4-8 sctransform_0.3.2 [65] GenomicAlignments_1.26.0 xts_0.12.1 [67] prettyunits_1.1.1 goftest_1.2-2 [69] cluster_2.1.0 repmis_0.5 [71] ape_5.4-1 lazyeval_0.2.2 [73] laeken_0.5.1 crayon_1.4.1 [75] pkgconfig_2.0.3 nlme_3.1-152 [77] pkgload_1.1.0 seriation_1.2-9 [79] pals_1.6 nnet_7.3-15 [81] devtools_2.3.2 rlang_0.4.10 [83] globals_0.14.0 lifecycle_1.0.0 [85] miniUI_0.1.1.1 SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 [87] registry_0.5-1 SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20 [89] BiocFileCache_1.14.0 dichromat_2.0-0 [91] cellranger_1.1.0 rprojroot_2.0.2 [93] polyclip_1.10-0 RcppHNSW_0.3.0 [95] lmtest_0.9-38 Matrix_1.3-2 [97] carData_3.0-4 Rhdf5lib_1.12.1 [99] boot_1.3-27 zoo_1.8-8 [101] ggridges_0.5.3 processx_3.4.5 [103] png_0.1-7 viridisLite_0.3.0 [105] bitops_1.0-6 R.oo_1.24.0 [107] rhdf5filters_1.2.0 KernSmooth_2.23-18 [109] Biostrings_2.58.0 anndata_0.7.5.1 [111] blob_1.2.1 stringr_1.4.0 [113] parallelly_1.23.0 R.cache_0.14.0 [115] MAGMA.Celltyping_1.0.0 scales_1.1.1 [117] memoise_2.0.0 magrittr_2.0.1 [119] plyr_1.8.6 hexbin_1.28.2 [121] ica_1.0-2 gplots_3.1.1 [123] zlibbioc_1.36.0 compiler_4.0.3 [125] RColorBrewer_1.1-2 pcaMethods_1.82.0 [127] fitdistrplus_1.1-3 Rsamtools_2.6.0 [129] homologene_1.4.68.19.3.27 cli_2.3.0 [131] XVector_0.30.0 listenv_0.8.0 [133] patchwork_1.1.0.9000 pbapply_1.4-3 [135] ps_1.5.0 ggplot.multistats_1.0.0 [137] MASS_7.3-53.1 mgcv_1.8-33 [139] tidyselect_1.1.0 stringi_1.5.3 [141] forcats_0.5.1 yaml_2.2.1 [143] askpass_1.1 ggrepel_0.9.1 [145] grid_4.0.3 tools_4.0.3 [147] future.apply_1.7.0 rio_0.5.16 [149] rstudioapi_0.13 RNOmni_1.0.0 [151] foreach_1.5.1 foreign_0.8-81 [153] gridExtra_2.3 smoother_1.1 [155] scatterplot3d_0.3-41 Rtsne_0.15 [157] HGNChelper_0.8.1 digest_0.6.27 [159] shiny_1.6.0 Rcpp_1.0.6 [161] car_3.0-10 later_1.1.0.1 [163] RcppAnnoy_0.0.18 httr_1.4.2 [165] ggdendro_0.1.22 AnnotationDbi_1.52.0 [167] colorspace_2.0-0 XML_3.99-0.5 [169] fs_1.5.0 tensor_1.5 [171] ranger_0.12.1 splines_4.0.3 [173] uwot_0.1.10 spatstat.utils_2.0-0 [175] sp_1.4-5 mapproj_1.2.7 [177] plotly_4.9.3 sessioninfo_1.1.1 [179] xtable_1.8-4 jsonlite_1.7.2 [181] heatmaply_1.2.1 spatstat_1.64-1 [183] sceasy_0.0.6 testthat_3.0.2 [185] destiny_3.4.0 R6_2.5.0 [187] EWCE_0.99.2 pillar_1.4.7 [189] htmltools_0.5.1.1 mime_0.10 [191] BiocParallel_1.24.1 glue_1.4.2 [193] fastmap_1.1.0 VIM_6.1.0 [195] class_7.3-18 codetools_0.2-18 [197] maps_3.3.0 pkgbuild_1.2.0 [199] lattice_0.20-41 tibble_3.0.6 [201] curl_4.3 leiden_0.3.7 [203] gtools_3.8.2 zip_2.1.1 [205] openxlsx_4.2.3 openssl_1.4.3 [207] survival_3.2-7 limma_3.46.0 [209] rmarkdown_2.6 desc_1.2.0 [211] munsell_0.5.0 e1071_1.7-4 [213] rhdf5_2.34.0 GenomeInfoDbData_1.2.4 [215] iterators_1.0.13 HDF5Array_1.18.1 [217] haven_2.3.1 reshape2_1.4.4 [219] gtable_0.3.0 ```