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Library loading issue #238

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rytpark opened this issue May 1, 2023 · 1 comment
Open

Library loading issue #238

rytpark opened this issue May 1, 2023 · 1 comment

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@rytpark
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rytpark commented May 1, 2023

Dear SingleR community,

I've recently installed SingleR for annotation of various T-cell subtypes. Although I was able to install via the bioconductor command
BiocManager::install("SingleR")
I haven't been able to load it into R yet. Whenever i run
library(SingleR)
I am faced with the following error:
Error: package or namespace load failed for ‘SingleR’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocParallel/libs/BiocParallel.so': dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocParallel/libs/BiocParallel.so, 0x0006): Library not loaded: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib Referenced from: <BE9EB1DB-DF61-3612-B689-0B341783A2EC> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BiocParallel/libs/BiocParallel.so Reason: tried: '/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' (no such file), '/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libR.dylib' (no such file), '/usr/local/lib/libR.dylib' (no such file), '/usr/lib/libR.dylib' (no

I have already attempted updating BiocParallel but it unfortunately did not resolve the issue.

Has anyone experienced this error before? Any insight would be greatly appreciated!

@rytpark
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rytpark commented May 1, 2023

For context, here is my session Info:

Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2

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-x86_64/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: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] celldex_1.10.0              SummarizedExperiment_1.30.0 Biobase_2.60.0              GenomicRanges_1.52.0       
 [5] GenomeInfoDb_1.36.0         IRanges_2.34.0              S4Vectors_0.38.0            BiocGenerics_0.46.0        
 [9] MatrixGenerics_1.12.0       matrixStats_0.63.0          EnhancedVolcano_1.18.0      ggrepel_0.9.3              
[13] ggpubr_0.6.0                harmony_0.1.1               Rcpp_1.0.10                 lubridate_1.9.2            
[17] forcats_1.0.0               stringr_1.5.0               dplyr_1.1.2                 purrr_1.0.1                
[21] readr_2.1.4                 tidyr_1.3.0                 tibble_3.2.1                ggplot2_3.4.2              
[25] tidyverse_2.0.0             SeuratObject_4.1.3          Seurat_4.3.0               

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.20              splines_4.3.0                 later_1.3.0                   filelock_1.0.2               
  [5] bitops_1.0-7                  polyclip_1.10-4               lifecycle_1.0.3               rstatix_0.7.2                
  [9] globals_0.16.2                lattice_0.21-8                MASS_7.3-59                   backports_1.4.1              
 [13] magrittr_2.0.3                plotly_4.10.1                 yaml_2.3.7                    httpuv_1.6.9                 
 [17] sctransform_0.3.5             sp_1.6-0                      spatstat.sparse_3.0-1         reticulate_1.28              
 [21] cowplot_1.1.1                 pbapply_1.7-0                 DBI_1.1.3                     RColorBrewer_1.1-3           
 [25] abind_1.4-5                   zlibbioc_1.46.0               Rtsne_0.16                    RCurl_1.98-1.12              
 [29] rappdirs_0.3.3                GenomeInfoDbData_1.2.10       irlba_2.3.5.1                 listenv_0.9.0                
 [33] spatstat.utils_3.0-2          goftest_1.2-3                 spatstat.random_3.1-4         fitdistrplus_1.1-11          
 [37] parallelly_1.35.0             DelayedMatrixStats_1.22.0     leiden_0.4.3                  codetools_0.2-19             
 [41] DelayedArray_0.25.0           tidyselect_1.2.0              BiocFileCache_2.8.0           spatstat.explore_3.1-0       
 [45] jsonlite_1.8.4                ellipsis_0.3.2                progressr_0.13.0              ggridges_0.5.4               
 [49] survival_3.5-5                tools_4.3.0                   ica_1.0-3                     glue_1.6.2                   
 [53] gridExtra_2.3                 withr_2.5.0                   BiocManager_1.30.20           fastmap_1.1.1                
 [57] fansi_1.0.4                   digest_0.6.31                 timechange_0.2.0              R6_2.5.1                     
 [61] mime_0.12                     colorspace_2.1-0              scattermore_0.8               tensor_1.5                   
 [65] spatstat.data_3.0-1           RSQLite_2.3.1                 utf8_1.2.3                    generics_0.1.3               
 [69] data.table_1.14.8             httr_1.4.5                    htmlwidgets_1.6.2             uwot_0.1.14                  
 [73] pkgconfig_2.0.3               gtable_0.3.3                  blob_1.2.4                    lmtest_0.9-40                
 [77] XVector_0.40.0                htmltools_0.5.5               carData_3.0-5                 scales_1.2.1                 
 [81] png_0.1-8                     rstudioapi_0.14               tzdb_0.3.0                    reshape2_1.4.4               
 [85] curl_5.0.0                    nlme_3.1-162                  zoo_1.8-12                    cachem_1.0.7                 
 [89] BiocVersion_3.17.1            KernSmooth_2.23-20            parallel_4.3.0                miniUI_0.1.1.1               
 [93] AnnotationDbi_1.62.0          pillar_1.9.0                  grid_4.3.0                    vctrs_0.6.2                  
 [97] RANN_2.6.1                    promises_1.2.0.1              car_3.1-2                     dbplyr_2.3.2                 
[101] xtable_1.8-4                  cluster_2.1.4                 cli_3.6.1                     compiler_4.3.0               
[105] rlang_1.1.1                   crayon_1.5.2                  future.apply_1.10.0           ggsignif_0.6.4               
[109] plyr_1.8.8                    stringi_1.7.12                viridisLite_0.4.1             deldir_1.0-6                 
[113] munsell_0.5.0                 Biostrings_2.68.0             lazyeval_0.2.2                spatstat.geom_3.1-0          
[117] Matrix_1.5-4                  ExperimentHub_2.8.0           hms_1.1.3                     patchwork_1.1.2              
[121] sparseMatrixStats_1.12.0      bit64_4.0.5                   future_1.32.0                 KEGGREST_1.40.0              
[125] shiny_1.7.4                   interactiveDisplayBase_1.38.0 AnnotationHub_3.8.0           ROCR_1.0-11                  
[129] igraph_1.4.2                  broom_1.0.4                   memoise_2.0.1                 bit_4.0.5       ```

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