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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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Error with future package #194

Closed Goultard59 closed 1 year ago

Goultard59 commented 4 years ago

Hi,

I get the following error : "UNRELIABLE VALUE: Future ('future_lapply-1') unexpectedly generated random numbers without specifying argument '[future.]seed'. There is a risk that those random numbers are not statistically sound and the overall results might be invalid. To fix this, specify argument '[future.]seed', e.g. 'seed=TRUE'. This ensures that proper, parallel-safe random numbers are produced via the L'Ecuyer-CMRG method. To disable this check, use [future].seed=NULL, or set option 'future.rng.onMisuse' to "ignore".

Th error happening at those steps :
immune.integrated <- RunOptimizeALS(immune, k = 20, lambda = 5, split.by = "SAMP") immune.integrated <- RunQuantileNorm(immune.integrated, split.by = "SAMP")

I'm using Seurat who uses the future package for parallelisation (https://satijalab.org/seurat/v3.2/future_vignette.html)

I get an error when I load future packages first if I load it later it changes the integration result without any error message.

For now I have deactivated the usage of future package and the result work properly.

Thanks, Adrien.

R version 3.6.0 (2019-04-26)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/miniconda3/lib/R/lib/libRblas.so

locale:
[1] C

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

other attached packages:
 [1] SeuratWrappers_0.2.0        magrittr_1.5               
 [3] monocle3_0.2.2              Seurat_3.2.2               
 [5] SingleR_1.0.6               AnnotationHub_2.18.0       
 [7] BiocFileCache_1.10.2        dbplyr_1.4.4               
 [9] tibble_3.0.3                biomaRt_2.42.1             
[11] scran_1.14.6                SingleCellExperiment_1.8.0 
[13] SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
[15] BiocParallel_1.20.1         matrixStats_0.57.0         
[17] Biobase_2.46.0              GenomicRanges_1.38.0       
[19] GenomeInfoDb_1.22.1         IRanges_2.20.2             
[21] S4Vectors_0.24.4            BiocGenerics_0.32.0        
[23] openxlsx_4.2.2              dplyr_1.0.2                
[25] liger_0.5.0                 patchwork_1.0.1            
[27] Matrix_1.2-18               cowplot_1.1.0              
[29] ggplot2_3.3.2               future_1.19.1              

loaded via a namespace (and not attached):
  [1] reticulate_1.16               tidyselect_1.1.0             
  [3] RSQLite_2.2.1                 AnnotationDbi_1.48.0         
  [5] htmlwidgets_1.5.2             grid_3.6.0                   
  [7] Rtsne_0.15                    munsell_0.5.0                
  [9] codetools_0.2-16              ica_1.0-2                    
 [11] statmod_1.4.34                pbdZMQ_0.3-3                 
 [13] miniUI_0.1.1.1                withr_2.3.0                  
 [15] colorspace_1.4-1              riverplot_0.6                
 [17] uuid_0.1-2                    ROCR_1.0-11                  
 [19] tensor_1.5                    listenv_0.8.0                
 [21] repr_0.19.2                   GenomeInfoDbData_1.2.2       
 [23] polyclip_1.10-0               bit64_0.9-7.1                
 [25] vctrs_0.3.4                   generics_0.0.2               
 [27] R6_2.4.1                      ggbeeswarm_0.6.0             
 [29] rsvd_1.0.3                    locfit_1.5-9.4               
 [31] bitops_1.0-6                  spatstat.utils_1.17-0        
 [33] assertthat_0.2.1              promises_1.1.1               
 [35] scales_1.1.1                  beeswarm_0.2.3               
 [37] gtable_0.3.0                  globals_0.13.0               
 [39] goftest_1.2-2                 rlang_0.4.7                  
 [41] splines_3.6.0                 lazyeval_0.2.2               
 [43] BiocManager_1.30.10           yaml_2.2.1                   
 [45] reshape2_1.4.4                abind_1.4-5                  
 [47] httpuv_1.5.4                  tools_3.6.0                  
 [49] ellipsis_0.3.1                RColorBrewer_1.1-2           
 [51] ggridges_0.5.2                Rcpp_1.0.1                   
 [53] plyr_1.8.6                    base64enc_0.1-3              
 [55] progress_1.2.2                zlibbioc_1.32.0              
 [57] purrr_0.3.4                   RCurl_1.98-1.1               
 [59] prettyunits_1.1.1             rpart_4.1-15                 
 [61] openssl_1.4.3                 deldir_0.1-29                
 [63] pbapply_1.4-3                 viridis_0.5.1                
 [65] zoo_1.8-8                     ggrepel_0.8.2                
 [67] cluster_2.1.0                 data.table_1.13.0            
 [69] lmtest_0.9-38                 RANN_2.6.1                   
 [71] fitdistrplus_1.1-1            hms_0.5.2                    
 [73] mime_0.9                      evaluate_0.13                
 [75] xtable_1.8-4                  XML_3.98-1.20                
 [77] mclust_5.4.6                  gridExtra_2.3                
 [79] compiler_3.6.0                scater_1.14.6                
 [81] KernSmooth_2.23-17            crayon_1.3.4                 
 [83] htmltools_0.3.6               mgcv_1.8-33                  
 [85] later_1.1.0.1                 snow_0.4-3                   
 [87] tidyr_1.1.2                   DBI_1.1.0                    
 [89] ExperimentHub_1.12.0          MASS_7.3-53                  
 [91] rappdirs_0.3.1                igraph_1.2.4.1               
 [93] pkgconfig_2.0.3               IRdisplay_0.7.0              
 [95] plotly_4.9.2.1                foreach_1.5.0                
 [97] vipor_0.4.5                   dqrng_0.2.1                  
 [99] XVector_0.26.0                stringr_1.4.0                
[101] digest_0.6.18                 sctransform_0.3              
[103] RcppAnnoy_0.0.16              spatstat.data_1.4-3          
[105] leiden_0.3.3                  uwot_0.1.8                   
[107] edgeR_3.28.1                  DelayedMatrixStats_1.8.0     
[109] curl_4.3                      shiny_1.3.2                  
[111] lifecycle_0.2.0               nlme_3.1-149                 
[113] jsonlite_1.6                  BiocNeighbors_1.4.2          
[115] viridisLite_0.3.0             askpass_1.1                  
[117] limma_3.42.2                  pillar_1.4.6                 
[119] lattice_0.20-41               httr_1.4.2                   
[121] survival_3.2-7                interactiveDisplayBase_1.24.0
[123] glue_1.4.2                    remotes_2.1.0                
[125] zip_2.1.1                     FNN_1.1.3                    
[127] spatstat_1.64-1               png_0.1-7                    
[129] iterators_1.0.12              BiocVersion_3.10.1           
[131] bit_1.1-15.2                  stringi_1.4.3                
[133] blob_1.2.1                    BiocSingular_1.2.2           
[135] doSNOW_1.0.18                 memoise_1.1.0                
[137] IRkernel_0.8.15               irlba_2.3.3                  
[139] future.apply_1.6.0
samuel-marsh commented 4 years ago

Hi,

Not member of dev team but hopefully this is helpful. So this isn't really a LIGER issue if you are running LIGER through the Seurat wrapper and using future package for Seurat functions that support it, so it would be more appropriate on the Seurat GitHub. Someone else has recently raised this issue on their GitHub so hopefully fix is applied soon. https://github.com/satijalab/seurat/issues/3622.

Best, Sam