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Error when running graph_test() with devel version #679

Closed abspangler13 closed 9 months ago

abspangler13 commented 10 months ago

Describe the bug I'm running the development version of monocle3.

> packageVersion("monocle3") [1] ‘1.4.1’

I'm getting an error when trying to run graph_test()

To Reproduce deg_bcells <- graph_test(cds, neighbor_graph = 'principal_graph', cores = 4)

Error

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/sysapps/cluster/software/Anaconda3/2022.05/envs/R-4.2.1/lib/R/library/sf/libs/sf.so':
  libproj.so.15: cannot open shared object file: No such file or directory

traceback()

> traceback()
7: dyn.load(file, DLLpath = DLLpath, ...)
6: library.dynam(lib, package, package.lib)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(x)
2: calculateLW(cds = cds, k = k, neighbor_graph = neighbor_graph, 
       reduction_method = reduction_method, verbose = verbose, nn_control = nn_control)
1: graph_test(cds, neighbor_graph = "principal_graph", cores = 4)

Expected behavior Expected the dataframe output of the this function.

sessionInfo():

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS/LAPACK: /sysapps/cluster/software/Anaconda3/2022.05/envs/R-4.2.1/lib/libopenblasp-r0.3.23.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] reprex_2.0.2                RColorBrewer_1.1-3         
 [3] magrittr_2.0.3              patchwork_1.1.2            
 [5] ggplot2_3.4.0               SeuratWrappers_0.3.1       
 [7] SeuratData_0.2.2            sp_2.0-0                   
 [9] SeuratObject_4.1.2          Seurat_4.2.0               
[11] monocle3_1.4.1              SingleCellExperiment_1.20.1
[13] SummarizedExperiment_1.28.0 GenomicRanges_1.49.1       
[15] GenomeInfoDb_1.34.9         IRanges_2.31.2             
[17] S4Vectors_0.36.2            MatrixGenerics_1.9.1       
[19] matrixStats_0.62.0          Biobase_2.57.1             
[21] BiocGenerics_0.44.0        

loaded via a namespace (and not attached):
  [1] utf8_1.2.2             clipr_0.8.0            reticulate_1.26       
  [4] R.utils_2.12.0         tidyselect_1.1.2       lme4_1.1-34           
  [7] htmlwidgets_1.5.4      grid_4.2.1             Rtsne_0.16            
 [10] munsell_0.5.0          codetools_0.2-18       ica_1.0-3             
 [13] units_0.8-3            future_1.28.0          miniUI_0.1.1.1        
 [16] withr_2.5.0            spatstat.random_3.1-3  colorspace_2.0-3      
 [19] progressr_0.11.0       highr_0.9              knitr_1.40            
 [22] rstudioapi_0.14        ROCR_1.0-11            tensor_1.5            
 [25] listenv_0.8.0          labeling_0.4.2         slam_0.1-50           
 [28] GenomeInfoDbData_1.2.8 polyclip_1.10-0        farver_2.1.1          
 [31] rprojroot_2.0.3        parallelly_1.32.1      vctrs_0.5.2           
 [34] generics_0.1.3         xfun_0.33              R6_2.5.1              
 [37] rsvd_1.0.5             bitops_1.0-7           spatstat.utils_3.0-1  
 [40] DelayedArray_0.24.0    assertthat_0.2.1       promises_1.2.0.1      
 [43] scales_1.2.1           rgeos_0.6-4            gtable_0.3.1          
 [46] globals_0.16.1         processx_3.7.0         goftest_1.2-3         
 [49] rlang_1.0.6            splines_4.2.1          lazyeval_0.2.2        
 [52] spatstat.geom_3.0-6    BiocManager_1.30.18    yaml_2.3.5            
 [55] reshape2_1.4.4         abind_1.4-5            httpuv_1.6.6          
 [58] tools_4.2.1            spData_2.2.0           ellipsis_0.3.2        
 [61] spatstat.core_2.4-4    proxy_0.4-27           ggridges_0.5.3        
 [64] Rcpp_1.0.11            plyr_1.8.7             zlibbioc_1.43.0       
 [67] classInt_0.4-7         purrr_0.3.4            RCurl_1.98-1.8        
 [70] ps_1.7.1               rpart_4.1.16           deldir_1.0-6          
 [73] pbapply_1.5-0          viridis_0.6.2          cowplot_1.1.1         
 [76] zoo_1.8-12             ggrepel_0.9.1          cluster_2.1.4         
 [79] fs_1.5.2               here_1.0.1             data.table_1.14.2     
 [82] scattermore_0.8        lmtest_0.9-40          RANN_2.6.1            
 [85] fitdistrplus_1.1-8     R.cache_0.16.0         mime_0.12             
 [88] evaluate_0.16          xtable_1.8-4           gridExtra_2.3         
 [91] compiler_4.2.1         tibble_3.1.8           KernSmooth_2.23-20    
 [94] crayon_1.5.1           minqa_1.2.4            R.oo_1.25.0           
 [97] htmltools_0.5.3        mgcv_1.8-40            later_1.3.0           
[100] tidyr_1.2.1            DBI_1.1.3              MASS_7.3-58.1         
[103] rappdirs_0.3.3         boot_1.3-28            Matrix_1.5-1          
[106] cli_3.4.1              R.methodsS3_1.8.2      parallel_4.2.1        
[109] igraph_1.5.1           pkgconfig_2.0.3        plotly_4.10.0         
[112] spatstat.sparse_3.0-0  XVector_0.37.1         stringr_1.5.0         
[115] callr_3.7.2            digest_0.6.29          sctransform_0.3.5     
[118] RcppAnnoy_0.0.19       spatstat.data_3.0-0    rmarkdown_2.16        
[121] leiden_0.4.3           uwot_0.1.14            shiny_1.7.2           
[124] nloptr_2.0.3           lifecycle_1.0.3        nlme_3.1-159          
[127] jsonlite_1.8.0         viridisLite_0.4.1      fansi_1.0.3           
[130] pillar_1.8.1           lattice_0.20-45        fastmap_1.1.0         
[133] httr_1.4.4             survival_3.4-0         glue_1.6.2            
[136] remotes_2.4.2          png_0.1-7              class_7.3-20          
[139] stringi_1.7.6          styler_1.7.0           dplyr_1.0.10          
[142] irlba_2.3.5            e1071_1.7-11           future.apply_1.9.1

Additional context I'm not sure if this is a bug with the development version or an installation issue on my end.

brgew commented 9 months ago

Hi Abby,

That error says that the 'sf' package cannot find the Unix/Linux object library called 'proj'. The 'sf' package page on CRAN lists PROJ as a system requirement

SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3

You might try reinstalling 'sf'.

Best Wishes, Brent