RunHarmony() Error on macOS: “Invalid number of ncores provided: 0. Maximum available cores: NA”

[Krystalkeke]

System Information

• OS: macOS (please specify your version, e.g., macOS 14.5 Sonoma)
• R version: 4.3.3 Patched (2024-04-09 r86847)
• Harmony version: 1.2.4
• Seurat version: 5.1.0

Reproducible Code

# Attempt to run Harmony on a Seurat object
sub <- sub %>% 
  RunHarmony(group.by.vars = "sample", plot_convergence = TRUE, ncores = 1)

Observed Error
Warning: HarmonyMatrix is deprecated and will be removed in the future from the API
Error in value[3L] : Invalid number of ncores provided: 0.
Maximum available cores: NA

[pati-ni]

Hi @Krystalkeke

Can you please provide the output of this command on you MacOS system?

RhpcBLASctl::omp_get_max_threads()

I am also confused why you the HarmonyMatrix warning because this function is deprecated...

Can you also confirm what type is the sub variable? A seurat object?

[pati-ni]

@Krystalkeke

also please share a sessionInfo() :)

[Krystalkeke]

Thank you very much for your reply! I encountered the same Harmony error on both macOS and Linux systems using R 4.3.3, which occurred after installing certain R packages.

Error Message

Error in value[[3L]](cond) : Invalid number of ncores provided: 0.
Maximum available cores: 56
Calls: %>% ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
HarmonyMatrix is deprecated and will be removed in the future from the API in the future
Execution halted

System 1: macOS

> RhpcBLASctl::omp_get_max_threads()
[1] NA

Complete sessionInfo() (macOS):

R version 4.3.3 Patched (2024-04-09 r86847)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] ggpubr_0.6.0                scCustomize_2.1.2           clustree_0.5.1              ggraph_2.2.1                org.Mm.eg.db_3.17.0        
 [6] AnnotationDbi_1.64.1        clusterProfiler_4.10.1      ggplotify_0.1.2             CellChat_2.1.2              igraph_2.0.3               
[11] openxlsx_4.2.7.1            scales_1.4.0                base64enc_0.1-3             SingleCellExperiment_1.24.0 RColorBrewer_1.1-3         
[16] celldex_1.10.1              SingleR_2.4.1               SummarizedExperiment_1.32.0 GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        
[21] IRanges_2.36.0              S4Vectors_0.40.2            MatrixGenerics_1.14.0       matrixStats_1.4.1           gridExtra_2.3              
[26] SCP_0.5.6                   scRNAtoolVis_0.1.0          lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1              
[31] purrr_1.0.2                 readr_2.1.5                 tibble_3.2.1                tidyverse_2.0.0             monocle_2.30.1             
[36] DDRTree_0.1.5               irlba_2.3.5.1               VGAM_1.1-12                 Biobase_2.62.0              BiocGenerics_0.48.1        
[41] Matrix_1.6-5                ggsci_3.2.0                 Nebulosa_1.12.1             ggplot2_3.5.2               dplyr_1.1.4                
[46] tidyr_1.3.1                 harmony_1.2.4               Rcpp_1.0.13                 patchwork_1.3.0             Seurat_5.1.0               
[51] SeuratObject_5.0.2          sp_2.1-4                   

loaded via a namespace (and not attached):
  [1] ica_1.0-3                     plotly_4.10.4                 rematch2_2.1.2                devtools_2.4.5                zlibbioc_1.48.2              
  [6] tidyselect_1.2.1              bit_4.5.0                     doParallel_1.0.17             clue_0.3-65                   lattice_0.22-6               
 [11] rjson_0.2.23                  blob_1.2.4                    urlchecker_1.0.1              rngtools_1.5.2                S4Arrays_1.2.1               
 [16] parallel_4.3.3                dichromat_2.0-0.1             png_0.1-8                     registry_0.5-1                cli_3.6.3                    
 [21] goftest_1.2-3                 ggnetwork_0.5.13              BiocNeighbors_1.20.2          Signac_1.14.0                 uwot_0.1.16                  
 [26] shadowtext_0.1.4              curl_5.2.3                    mime_0.12                     evaluate_1.0.0                tidytree_0.4.6               
 [31] leiden_0.4.3.1                ComplexHeatmap_2.18.0         stringi_1.8.4                 backports_1.5.0               XML_3.99-0.17                
 [36] slingshot_2.16.0              httpuv_1.6.15                 paletteer_1.6.0               magrittr_2.0.3                rappdirs_0.3.3               
 [41] RcppRoll_0.3.1                mclust_6.1.1                  CIBERSORT_0.1.0               sctransform_0.4.1             ggbeeswarm_0.7.2             
 [46] sessioninfo_1.2.2             DBI_1.2.3                     HDF5Array_1.30.1              jquerylib_0.1.4               withr_3.0.1                  
 [51] systemfonts_1.1.0             class_7.3-22                  enrichplot_1.22.0             lmtest_0.9-40                 ggnewscale_0.5.0             
 [56] tidygraph_1.3.1               BiocManager_1.30.25           htmlwidgets_1.6.4             splancs_2.01-45               fs_1.6.4                     
 [61] biomaRt_2.58.2                ggrepel_0.9.6                 princurve_2.1.6               statnet.common_4.9.0          SparseArray_1.2.4            
 [66] reticulate_1.39.0             zoo_1.8-12                    XVector_0.42.0                knitr_1.48                    network_1.18.2               
 [71] RhpcBLASctl_0.23-42           timechange_0.3.0              foreach_1.5.2                 fansi_1.0.6                   grid_4.3.3                   
 [76] data.table_1.16.0             ggtree_3.10.1                 rhdf5_2.46.1                  R.oo_1.26.0                   RSpectra_0.16-2              
 [81] ggrastr_1.0.2                 fastDummies_1.7.4             gridGraphics_0.5-1            ellipsis_0.3.2                lazyeval_0.2.2               
 [86] yaml_2.3.10                   survival_3.7-0                scattermore_1.2               BiocVersion_3.18.1            crayon_1.5.3                 
 [91] RcppAnnoy_0.0.22              progressr_0.14.0              tweenr_2.0.3                  later_1.3.2                   ggridges_0.5.6               
 [96] codetools_0.2-20              GlobalOptions_0.1.2           profvis_0.4.0                 HSMMSingleCell_1.22.0         alphahull_2.5                
[101] KEGGREST_1.42.0               Rtsne_0.17                    shape_1.4.6.1                 fastICA_1.2-5.1               limma_3.58.1                 
[106] Rsamtools_2.18.0              filelock_1.0.3                pkgconfig_2.0.3               xml2_1.3.6                    spatstat.univar_3.0-1        
[111] aplot_0.2.3                   gridBase_0.4-7                spatstat.sparse_3.1-0         ape_5.8                       viridisLite_0.4.2            
[116] xtable_1.8-4                  interp_1.1-6                  car_3.1-2                     plyr_1.8.9                    httr_1.4.7                   
[121] tools_4.3.3                   globals_0.16.3                pkgbuild_1.4.4                broom_1.0.6                   beeswarm_0.4.0               
[126] nlme_3.1-166                  HDO.db_0.99.1                 dbplyr_2.5.0                  ExperimentHub_2.10.0          ggunchull_1.0.1              
[131] digest_0.6.37                 furrr_0.3.1                   farver_2.1.2                  tzdb_0.4.0                    reshape2_1.4.4               
[136] TrajectoryUtils_1.16.1        ks_1.14.3                     yulab.utils_0.1.7             viridis_0.6.5                 glue_1.7.0                   
[141] cachem_1.1.0                  BiocFileCache_2.10.2          polyclip_1.10-7               generics_0.1.3                proxyC_0.5.2                 
[146] Biostrings_2.70.3             ggalluvial_0.12.5             mvtnorm_1.3-1                 parallelly_1.38.0             pkgload_1.4.0                
[151] statmod_1.5.0                 R.cache_0.16.0                RcppHNSW_0.6.0                ScaledMatrix_1.10.0           carData_3.0-5                
[156] pbapply_1.7-2                 spam_2.11-0                   gson_0.1.0                    utf8_1.2.4                    graphlayouts_1.2.0           
[161] preprocessCore_1.64.0         ggsignif_0.6.4                shiny_1.9.1                   GenomeInfoDbData_1.2.10       R.utils_2.12.3               
[166] rhdf5filters_1.14.1           RCurl_1.98-1.16               memoise_2.0.1                 rmarkdown_2.28                pheatmap_1.0.12              
[171] R.methodsS3_1.8.2             svglite_2.1.3                 future_1.34.0                 RANN_2.6.2                    spatstat.data_3.1-2          
[176] rstudioapi_0.16.0             janitor_2.2.0                 cluster_2.1.6                 spatstat.utils_3.1-0          hms_1.1.3                    
[181] fitdistrplus_1.2.1            sgeostat_1.0-27               cowplot_1.1.3                 colorspace_2.1-1              FNN_1.1.4.1                  
[186] rlang_1.1.4                   ggdendro_0.2.0                DelayedMatrixStats_1.24.0     sparseMatrixStats_1.14.0      dotCall64_1.1-1              
[191] ggforce_0.4.2                 circlize_0.4.16               dbscan_1.2.2                  xfun_0.47                     coda_0.19-4.1                
[196] sna_2.8                       e1071_1.7-16                  remotes_2.5.0                 iterators_1.0.14              abind_1.4-8                  
[201] GOSemSim_2.28.1               interactiveDisplayBase_1.40.0 treeio_1.26.0                 Rhdf5lib_1.24.2               bitops_1.0-8                 
[206] promises_1.3.0                scatterpie_0.2.4              RSQLite_2.3.7                 leidenbase_0.1.27             qvalue_2.34.0                
[211] fgsea_1.28.0                  DelayedArray_0.28.0           proxy_0.4-27                  GO.db_3.17.0                  compiler_4.3.3               
[216] prettyunits_1.2.0             beachmat_2.18.1               listenv_0.9.1                 AnnotationHub_3.10.1          BiocSingular_1.18.0          
[221] tensor_1.5                    usethis_3.0.0                 MASS_7.3-60.0.1               progress_1.2.3                BiocParallel_1.36.0          
[226] spatstat.random_3.3-2         R6_2.5.1                      rstatix_0.7.2                 fastmap_1.2.0                 fastmatch_1.1-4              
[231] vipor_0.4.7                   ROCR_1.0-11                   rsvd_1.0.5                    gtable_0.3.6                  KernSmooth_2.23-24           
[236] miniUI_0.1.1.1                deldir_2.0-4                  htmltools_0.5.8.1             bit64_4.5.2                   ggprism_1.0.5                
[241] spatstat.explore_3.3-2        lifecycle_1.0.4               zip_2.3.1                     sass_0.4.9                    vctrs_0.6.5                  
[246] snakecase_0.11.1              slam_0.1-53                   spatstat.geom_3.3-3           DOSE_3.28.2                   NMF_0.28                     
[251] ggfun_0.1.6                   future.apply_1.11.2           pracma_2.4.4                  bslib_0.8.0                   pillar_1.9.0                 
[256] combinat_0.0-8                jsonlite_1.8.9                GetoptLong_1.0.5

System 2: Linux

> RhpcBLASctl::omp_get_max_threads()
[1] 56  # OpenMP is available but still fails!

sessionInfo() (Linux):

R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS/LAPACK: /data4/zhouke/anaconda3/envs/r-4.3.3/lib/libopenblasp-r0.3.21.so;  LAPACK version 3.9.0

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       

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] compiler_4.3.3      RhpcBLASctl_0.23-42

Reproducible Code

# Both seurat_rmbatch and sub are Seurat objects
seurat_rmbatch <- seurat_rmbatch %>% 
  RunHarmony(group.by.vars = "sample", plot_convergence = TRUE)

Key Points

1. Previously working code now fails after installing additional R packages
2. Same error occurs on both macOS and Linux
3. Problem is package conflict
4. Error appears consistently: "Invalid number of ncores provided: 0"

Important Context

• The data and code have previously run without any problems
• This issue almost certainly results from installing certain R packages that caused Harmony to report errors
• Since many R packages were installed, I'm not sure which specific ones caused the issue