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neurorestore / Augur

Cell type prioritization in single-cell data
MIT License
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Does Augur run with yardstick (1.1.0)? #22

Open amissarova opened 1 year ago

amissarova commented 1 year ago

Hi, It seems to me that Augur might not be working properly when yardstick==1.1.0 - is that correct (it works with a different environment, in which yardstick==1.0.0)? The intuition here is based on the error message:

Error in `mutate()`:
! Problem while computing `metrics = pred %>% map(metric_fun)`.
Caused by error in `metric_set()`:
! Failed to compute `roc_auc()`.
Caused by error in `parse()`:
! <text>:1:7: unexpected symbol
1: Using an
          ^
Run `rlang::last_error()` to see where the error occurred.

Session Info in which Augur doesn't run:

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        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               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] EssReg_0.1.0                doParallel_1.0.17           iterators_1.0.14            SLIDE_0.1.0                 BiocParallel_1.30.3        
 [6] knitr_1.39                  foreach_1.5.2               plyr_1.8.7                  stringr_1.4.1               SeuratObject_4.1.3         
[11] Seurat_4.3.0                patchwork_1.1.2             dplyr_1.0.10                scater_1.24.0               ggplot2_3.3.6              
[16] scuttle_1.6.0               SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1 Biobase_2.56.0              GenomicRanges_1.48.0       
[21] GenomeInfoDb_1.32.4         IRanges_2.30.1              S4Vectors_0.34.0            BiocGenerics_0.42.0         MatrixGenerics_1.8.0       
[26] matrixStats_0.63.0          miloR_1.4.0                 edgeR_3.38.0                limma_3.52.4                miloDE_0.0.0.9000          

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                spatstat.explore_3.0-5    reticulate_1.26           tidyselect_1.2.0          htmlwidgets_1.5.4         grid_4.2.0               
  [7] Rtsne_0.16                munsell_0.5.0             ScaledMatrix_1.4.0        codetools_0.2-18          ica_1.0-3                 statmod_1.4.36           
 [13] scran_1.24.0              future_1.29.0             miniUI_0.1.1.1            withr_2.5.0               tester_0.1.7              spatstat.random_3.0-1    
 [19] colorspace_2.0-3          progressr_0.11.0          highr_0.9                 rstudioapi_0.13           ROCR_1.0-11               tensor_1.5               
 [25] ggsignif_0.6.3            pbmcapply_1.5.1           listenv_0.8.0             labeling_0.4.2            GenomeInfoDbData_1.2.8    polyclip_1.10-4          
 [31] farver_2.1.1              parallelly_1.32.1         vctrs_0.4.1               generics_0.1.3            xfun_0.31                 ipred_0.9-12             
 [37] randomForest_4.7-1        R6_2.5.1                  ggbeeswarm_0.6.0          graphlayouts_0.8.3        rsvd_1.0.5                locfit_1.5-9.5           
 [43] pals_1.7                  bitops_1.0-7              spatstat.utils_3.0-1      DelayedArray_0.22.0       assertthat_0.2.1          promises_1.2.0.1         
 [49] scales_1.2.1              ggraph_2.1.0              nnet_7.3-17               beeswarm_0.4.0            gtable_0.3.1              beachmat_2.12.0          
 [55] globals_0.16.2            goftest_1.2-3             tidygraph_1.2.2           timeDate_3043.102         rlang_1.0.6               splines_4.2.0            
 [61] rstatix_0.7.0             lazyeval_0.2.2            yardstick_1.1.0           dichromat_2.0-0.1         spatstat.geom_3.0-3       broom_1.0.0              
 [67] reshape2_1.4.4            abind_1.4-5               backports_1.4.1           httpuv_1.6.6              tools_4.2.0               lava_1.6.10              
 [73] Augur_1.0.3               ellipsis_0.3.2            RColorBrewer_1.1-3        ggridges_0.5.4            Rcpp_1.0.9                parsnip_1.0.4            
 [79] sparseMatrixStats_1.8.0   zlibbioc_1.42.0           purrr_0.3.5               RCurl_1.98-1.8            deldir_1.0-6              ggpubr_0.4.0             
 [85] rpart_4.1.16              pbapply_1.6-0             viridis_0.6.2             cowplot_1.1.1             zoo_1.8-11                ggrepel_0.9.2            
 [91] cluster_2.1.3             furrr_0.2.3               magrittr_2.0.3            data.table_1.14.6         scattermore_0.8           lmtest_0.9-40            
 [97] RANN_2.6.1                fitdistrplus_1.1-8        mime_0.12                 xtable_1.8-4              gridExtra_2.3             compiler_4.2.0           
[103] tibble_3.1.8              maps_3.4.0                crayon_1.5.2              KernSmooth_2.23-20        htmltools_0.5.3           later_1.3.0              
[109] tidyr_1.2.1               lubridate_1.8.0           DBI_1.1.3                 tweenr_2.0.2              MASS_7.3-57               Matrix_1.5-1             
[115] car_3.1-0                 cli_3.4.1                 metapod_1.4.0             gower_1.0.0               igraph_1.3.5              pkgconfig_2.0.3          
[121] RcppGreedySetCover_0.1.0  sp_1.5-1                  plotly_4.10.1             spatstat.sparse_3.0-0     recipes_0.2.0             vipor_0.4.5              
[127] hardhat_1.2.0             dqrng_0.3.0               XVector_0.36.0            prodlim_2019.11.13        digest_0.6.30             sctransform_0.3.5        
[133] RcppAnnoy_0.0.20          spatstat.data_3.0-0       leiden_0.4.3              uwot_0.1.14               DelayedMatrixStats_1.18.0 shiny_1.7.3              
[139] gtools_3.9.4              nlme_3.1-157              lifecycle_1.0.1           jsonlite_1.8.3            carData_3.0-5             BiocNeighbors_1.14.0     
[145] mapproj_1.2.8             viridisLite_0.4.1         fansi_1.0.3               pillar_1.8.1              lattice_0.20-45           fastmap_1.1.0            
[151] httr_1.4.4                survival_3.3-1            glue_1.6.2                png_0.1-7                 bluster_1.6.0             ggforce_0.4.1            
[157] class_7.3-20
jordansquair commented 1 year ago

Are you reproducing this error with our toy dataset? Can you provide a reproducible example please?