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KrishnaswamyLab / phateR

PHATE dimensionality reduction method implemented in R
GNU General Public License v2.0
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Phate does not finish after update #39

Closed jibsch closed 4 years ago

jibsch commented 4 years ago

Hi, Thanks for the software - I appreciate the results obtained with Phate. I've recently updated the R package and the code that used to run, does now throw an error.

Describe the bug The program's Python backend seems to throw an error.

To Reproduce phate = phate(rna, mds.solver = "smacof")

System information:

Output of phate.0.4.5:

Calculating PHATE... Running PHATE on 5325 cells and 16346 genes. Calculating graph and diffusion operator... Calculating PCA... Calculated PCA in 27.71 seconds. Calculating KNN search... Calculated KNN search in 4.74 seconds. Calculating affinities... Calculated affinities in 0.13 seconds. Calculated graph and diffusion operator in 32.59 seconds. Calculated PHATE in 32.59 seconds. Error in py_call_impl(callable, dots$args, dots$keywords) : TypeError: init() got an unexpected keyword argument 'mds_solver'

Output of pd.show_versions():

``` INSTALLED VERSIONS ------------------ commit : None python : 3.6.8.final.0 python-bits : 64 OS : Linux OS-release : 4.15.0-23-generic machine : x86_64 processor : x86_64 byteorder : little LC_ALL : None LANG : en_AU.UTF-8 LOCALE : en_AU.UTF-8 pandas : 0.25.0 numpy : 1.16.4 pytz : 2019.1 dateutil : 2.8.0 pip : 19.0.1 setuptools : 40.7.1 Cython : 0.29.3 pytest : 4.1.0 hypothesis : None sphinx : None blosc : None feather : None xlsxwriter : None lxml.etree : None html5lib : None pymysql : None psycopg2 : None jinja2 : None IPython : None pandas_datareader: None bs4 : None bottleneck : None fastparquet : None gcsfs : None lxml.etree : None matplotlib : 3.1.1 numexpr : 2.7.0 odfpy : None openpyxl : None pandas_gbq : None pyarrow : None pytables : None s3fs : None scipy : 1.3.0 sqlalchemy : None tables : 3.6.1 xarray : None xlrd : None xlwt : None xlsxwriter : None ```

Output of sessionInfo():

``` R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] phateR_1.0.0.999 Matrix_1.2-14 SingleCellExperiment_1.4.1 [4] SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.6 [7] matrixStats_0.55.0 Biobase_2.42.0 GenomicRanges_1.34.0 [10] GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1 [13] BiocGenerics_0.28.0 edgeR_3.24.3 limma_3.38.3 loaded via a namespace (and not attached): [1] Seurat_3.1.2 TH.data_1.0-10 Rtsne_0.15 colorspace_1.4-1 [5] ggridges_0.5.2 XVector_0.22.0 rstudioapi_0.10 leiden_0.3.1 [9] listenv_0.8.0 npsurv_0.4-0 ggrepel_0.8.1 fansi_0.4.1 [13] mvtnorm_1.0-12 codetools_0.2-15 splines_3.5.1 R.methodsS3_1.7.1 [17] mnormt_1.5-5 lsei_1.2-0 knitr_1.23 TFisher_0.2.0 [21] zeallot_0.1.0 jsonlite_1.6 ica_1.0-2 cluster_2.0.7-1 [25] png_0.1-7 R.oo_1.23.0 uwot_0.1.5 sctransform_0.2.1 [29] compiler_3.5.1 httr_1.4.1 backports_1.1.5 assertthat_0.2.1 [33] lazyeval_0.2.2 cli_2.0.1 htmltools_0.3.6 tools_3.5.1 [37] rsvd_1.0.2 igraph_1.2.4.2 GenomeInfoDbData_1.2.0 gtable_0.3.0 [41] glue_1.3.1 RANN_2.6.1 reshape2_1.4.3 dplyr_0.8.3 [45] rappdirs_0.3.1 Rcpp_1.0.3 vctrs_0.2.1 multtest_2.38.0 [49] gdata_2.18.0 ape_5.3 nlme_3.1-137 gbRd_0.4-11 [53] lmtest_0.9-37 xfun_0.8 stringr_1.4.0 globals_0.12.5 [57] lifecycle_0.1.0 irlba_2.3.3 gtools_3.8.1 future_1.15.1 [61] zlibbioc_1.28.0 MASS_7.3-50 zoo_1.8-7 scales_1.1.0 [65] sandwich_2.5-1 RColorBrewer_1.1-2 yaml_2.2.0 reticulate_1.14 [69] pbapply_1.4-2 gridExtra_2.3 ggplot2_3.2.1 stringi_1.4.5 [73] mutoss_0.1-12 plotrix_3.7-7 caTools_1.17.1.3 bibtex_0.4.2.2 [77] Rdpack_0.11-1 SDMTools_1.1-221.2 rlang_0.4.2 pkgconfig_2.0.3 [81] bitops_1.0-6 lattice_0.20-35 ROCR_1.0-7 purrr_0.3.3 [85] htmlwidgets_1.5.1 cowplot_1.0.0 tidyselect_0.2.5 RcppAnnoy_0.0.14 [89] plyr_1.8.5 magrittr_1.5 R6_2.4.1 gplots_3.0.1.2 [93] multcomp_1.4-12 pillar_1.4.3 sn_1.5-4 fitdistrplus_1.0-14 [97] RCurl_1.95-4.12 survival_2.42-6 tsne_0.1-3 tibble_2.1.3 [101] future.apply_1.4.0 crayon_1.3.4 KernSmooth_2.23-15 plotly_4.9.1 [105] locfit_1.5-9.1 grid_3.5.1 data.table_1.12.8 metap_1.2 [109] digest_0.6.23 tidyr_1.0.0 numDeriv_2016.8-1.1 R.utils_2.9.2 [113] RcppParallel_4.4.4 munsell_0.5.0 viridisLite_0.3.0 ```

Output of reticulate::py_discover_config(required_module = "phate"):

``` python: /mnt/data/home/jsch0032/tools/Miniconda3/bin/python3 libpython: /home/jsch0032/tools/Miniconda3/lib/libpython3.6m.so pythonhome: /mnt/data/home/jsch0032/tools/Miniconda3:/mnt/data/home/jsch0032/tools/Miniconda3 version: 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34) [GCC 7.3.0] numpy: /mnt/data/home/jsch0032/.local/lib/python3.6/site-packages/numpy numpy_version: 1.16.4 phate: /home/jsch0032/.local/lib/python3.6/site-packages/phate NOTE: Python version was forced by RETICULATE_PYTHON ```

Additional context Add any other context about the problem here.

scottgigante commented 4 years ago

Hi @jibsch, you can solve this issue by updating the PHATE python package. /mnt/data/home/jsch0032/tools/Miniconda3/bin/python -m pip install --upgrade phate. I will investigate why this didn't show as an error.

jibsch commented 4 years ago

Thanks, Scott. I had tried updating the Python package, but maybe on the wrong version. Either way, this worked. Cheers!