search

ctlab / fgsea

Fast Gene Set Enrichment Analysis
Other
376 stars 67 forks source link

BPPARAM error #69

Closed andrewbcaldwell closed 4 years ago

andrewbcaldwell commented 4 years ago

I recently updated to R 4.4.0 and reinstalled fgsea, however I have ran into an issue when running fgsea or fgseaMultilevel:

Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) ==  : 
  missing value where TRUE/FALSE needed

I've tried reinstalling both via GitHub or Bioconductor and I have the same issue. Thanks!

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] devtools_2.3.0                          usethis_1.6.1                          
 [3] fgsea_1.14.0                            BiocParallel_1.22.0                    
 [5] msigdbr_7.1.1                           dplyr_1.0.0                            
 [7] data.table_1.12.8                       topconfects_1.4.0                      
 [9] enrichR_2.1                             tmod_0.40                              
[11] hugene11sttranscriptcluster.db_8.7.0    org.Hs.eg.db_3.11.4                    
[13] pd.hugene.1.1.st.v1_3.14.1              DBI_1.1.0                              
[15] oligo_1.52.0                            oligoClasses_1.50.0                    
[17] RSQLite_2.2.0                           Biostrings_2.56.0                      
[19] XVector_0.28.0                          annotate_1.66.0                        
[21] XML_3.99-0.3                            limma_3.44.1                           
[23] RColorBrewer_1.1-2                      plyranges_1.8.0                        
[25] DiffBind_2.16.0                         SummarizedExperiment_1.18.1            
[27] DelayedArray_0.14.0                     matrixStats_0.56.0                     
[29] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.40.0                 
[31] AnnotationDbi_1.50.0                    Biobase_2.48.0                         
[33] GenomicRanges_1.40.0                    GenomeInfoDb_1.24.0                    
[35] IRanges_2.22.2                          S4Vectors_0.26.1                       
[37] BiocGenerics_0.34.0                     ChIPseeker_1.24.0                      

loaded via a namespace (and not attached):
  [1] estimability_1.3         rappdirs_0.3.1           rtracklayer_1.48.0       AnnotationForge_1.30.1  
  [5] tidyr_1.1.0              ggplot2_3.3.1            bit64_0.9-7              hwriter_1.3.2           
  [9] RCurl_1.98-1.2           generics_0.0.2           preprocessCore_1.50.0    callr_3.4.3             
 [13] cowplot_1.0.0            europepmc_0.4            bit_1.1-15.2             enrichplot_1.8.1        
 [17] base64url_1.4            xml2_1.3.2               assertthat_0.2.1         batchtools_0.9.13       
 [21] viridis_0.5.1            amap_0.8-18              hms_0.5.3                plotwidgets_0.4         
 [25] fansi_0.4.1              progress_1.2.2           caTools_1.18.0           dbplyr_1.4.4            
 [29] Rgraphviz_2.32.0         igraph_1.2.5             geneplotter_1.66.0       htmlwidgets_1.5.1       
 [33] purrr_0.3.4              ellipsis_0.3.1           backports_1.1.7          V8_3.1.0                
 [37] biomaRt_2.44.0           vctrs_0.3.0              remotes_2.1.1            withr_2.2.0             
 [41] ggforce_0.3.1            triebeard_0.3.0          DOT_0.1                  BSgenome_1.56.0         
 [45] checkmate_2.0.0          emmeans_1.4.7            GenomicAlignments_1.24.0 prettyunits_1.1.1       
 [49] DOSE_3.14.0              crayon_1.3.4             genefilter_1.70.0        edgeR_3.30.3            
 [53] pkgconfig_2.0.3          tweenr_1.0.1             nlme_3.1-148             pkgload_1.1.0           
 [57] rlang_0.4.6              lifecycle_0.2.0          affyio_1.58.0            BiocFileCache_1.12.0    
 [61] qusage_2.22.0            GOstats_2.54.0           rsvg_2.1                 rprojroot_1.3-2         
 [65] polyclip_1.10-0          graph_1.66.0             Matrix_1.2-18            urltools_1.7.3          
 [69] boot_1.3-25              beeswarm_0.2.3           ggridges_0.5.2           processx_3.4.2          
 [73] pheatmap_1.0.12          png_0.1-7                viridisLite_0.3.0        rjson_0.2.20            
 [77] bitops_1.0-6             KernSmooth_2.23-17       blob_1.2.1               stringr_1.4.0           
 [81] qvalue_2.20.0            ShortRead_1.46.0         brew_1.0-6               jpeg_0.1-8.1            
 [85] gridGraphics_0.5-0       scales_1.1.1             memoise_1.1.0            GSEABase_1.50.1         
 [89] magrittr_1.5             plyr_1.8.6               gplots_3.0.3             gdata_2.18.0            
 [93] zlibbioc_1.34.0          compiler_4.0.0           scatterpie_0.1.4         plotrix_3.7-8           
 [97] DESeq2_1.28.1            Rsamtools_2.4.0          cli_2.0.2                systemPipeR_1.22.0      
[101] Category_2.54.0          ps_1.3.3                 MASS_7.3-51.6            tidyselect_1.1.0        
[105] fftw_1.0-6               stringi_1.4.6            yaml_2.2.1               GOSemSim_2.14.0         
[109] askpass_1.1              locfit_1.5-9.4           latticeExtra_0.6-29      ggrepel_0.8.2           
[113] grid_4.0.0               VariantAnnotation_1.34.0 fastmatch_1.1-0          tools_4.0.0             
[117] rstudioapi_0.11          foreach_1.5.0            tagcloud_0.6             gridExtra_2.3           
[121] farver_2.0.3             ggraph_2.0.3             digest_0.6.25            rvcheck_0.1.8           
[125] BiocManager_1.30.10      ff_2.2-14.2              Rcpp_1.0.4.6             httr_1.4.1              
[129] colorspace_1.4-1         fs_1.4.1                 splines_4.0.0            RBGL_1.64.0             
[133] graphlayouts_0.7.0       ggplotify_0.0.5          sessioninfo_1.1.1        xtable_1.8-4            
[137] jsonlite_1.6.1           tidygraph_1.2.0          testthat_2.3.2           R6_2.4.1                
[141] pillar_1.4.4             htmltools_0.4.0          affxparser_1.60.0        glue_1.4.1              
[145] DT_0.13                  codetools_0.2-16         pkgbuild_1.0.8           mvtnorm_1.1-0           
[149] utf8_1.1.4               lattice_0.20-41          tibble_3.0.1             curl_4.3                
[153] gtools_3.8.2             GO.db_3.11.4             openssl_1.4.1            survival_3.1-12         
[157] desc_1.2.0               munsell_0.5.0            DO.db_2.9                GenomeInfoDbData_1.2.3  
[161] iterators_1.0.12         reshape2_1.4.4           gtable_0.3.0
assaron commented 4 years ago

Hi,

It seems to be a BiocParallel related issue. There are serveral things you could try. 1) Add nproc=1 parameter. This effectively should turn off any parallelization. 2) Check, that BiocParallel is properly working by running library(BiocParallel); example("bplapply"). 3) Update BiocParallel to a more recent version (you probably need to upgrade Bioconductor as well).

andrewbcaldwell commented 4 years ago

Thank you for the response! nproc=1 seems to have solved the issue.