DiffBind (Error in if (DBA$config$parallelPackage))
Entering edit mode
eggrandio • 0
Last seen 4 months ago
United States


I am trying to use the DiffBind package but I get the following error:

wtvspq.count = dba.count(wtvspq[1:2], bParallel = FALSE)
Computing summits...
Error in if (DBA$config$parallelPackage == DBA_PARALLEL_MULTICORE) { : 
  argument is of length zero

I am able to create a dba object, and even changing the config to RunParallel=FALSE, I get the same error. I had problems in the past using DiffBind on Windows, but at least I was able to run it serially.

wtvspq = dba(sampleSheet="reduced.csv", dir="C:/DATA/BAM_as_BED/",
                      DataType=DBA_DATA_GRANGES, RunParallel=FALSE, 
                      minQCth=15, fragmentSize=125, 
                      bCorPlot=FALSE, reportInit="DBA", 
                      bUsePval=FALSE, design=TRUE,
                      doBlacklist=TRUE, doGreylist=TRUE))

Here is my sessionInfo in case it helps:

R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DiffBind_3.2.5              SummarizedExperiment_1.22.0 Biobase_2.52.0              MatrixGenerics_1.4.2       
 [5] matrixStats_0.60.0          GenomicRanges_1.44.0        GenomeInfoDb_1.28.1         IRanges_2.26.0             
 [9] S4Vectors_0.30.0            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.1          GOstats_2.58.0           BiocFileCache_2.0.0      plyr_1.8.6               GSEABase_1.54.0         
  [6] splines_4.1.1            BiocParallel_1.26.1      ggplot2_3.3.5            amap_0.8-18              digest_0.6.27           
 [11] invgamma_1.1             htmltools_0.5.1.1        viridis_0.6.1            GO.db_3.13.0             SQUAREM_2021.1          
 [16] fansi_0.5.0              magrittr_2.0.1           checkmate_2.0.0          memoise_2.0.0            BSgenome_1.60.0         
 [21] base64url_1.4            limma_3.48.3             Biostrings_2.60.1        annotate_1.70.0          systemPipeR_1.26.3      
 [26] bdsmatrix_1.3-4          prettyunits_1.1.1        jpeg_0.1-9               colorspace_2.0-2         blob_1.2.2              
 [31] rappdirs_0.3.3           apeglm_1.14.0            ggrepel_0.9.1            xfun_0.24                dplyr_1.0.7             
 [36] crayon_1.4.1             RCurl_1.98-1.3           jsonlite_1.7.2           graph_1.70.0             genefilter_1.74.0       
 [41] brew_1.0-6               survival_3.2-12          VariantAnnotation_1.38.0 glue_1.4.2               gtable_0.3.0            
 [46] zlibbioc_1.38.0          XVector_0.32.0           DelayedArray_0.18.0      V8_3.4.2                 Rgraphviz_2.36.0        
 [51] scales_1.1.1             mvtnorm_1.1-2            pheatmap_1.0.12          DBI_1.1.1                edgeR_3.34.0            
 [56] Rcpp_1.0.7               viridisLite_0.4.0        xtable_1.8-4             progress_1.2.2           emdbook_1.3.12          
 [61] bit_4.0.4                rsvg_2.1.2               truncnorm_1.0-8          AnnotationForge_1.34.0   httr_1.4.2              
 [66] gplots_3.1.1             RColorBrewer_1.1-2       ellipsis_0.3.2           pkgconfig_2.0.3          XML_3.99-0.6            
 [71] dbplyr_2.1.1             locfit_1.5-9.4           utf8_1.2.1               tidyselect_1.1.1         rlang_0.4.11            
 [76] AnnotationDbi_1.54.1     munsell_0.5.0            tools_4.1.1              cachem_1.0.5             generics_0.1.0          
 [81] RSQLite_2.2.7            broom_0.7.9              evaluate_0.14            stringr_1.4.0            fastmap_1.1.0           
 [86] yaml_2.2.1               knitr_1.33               bit64_4.0.5              caTools_1.18.2           purrr_0.3.4             
 [91] KEGGREST_1.32.0          dendextend_1.15.1        RBGL_1.68.0              xml2_1.3.2               biomaRt_2.48.3          
 [96] compiler_4.1.1           rstudioapi_0.13          filelock_1.0.2           curl_4.3.2               png_0.1-7               
[101] tibble_3.1.2             stringi_1.7.3            GenomicFeatures_1.44.1   lattice_0.20-44          Matrix_1.3-4            
[106] vctrs_0.3.8              pillar_1.6.2             lifecycle_1.0.0          irlba_2.3.3              data.table_1.14.0       
[111] bitops_1.0-7             rtracklayer_1.52.1       R6_2.5.1                 BiocIO_1.2.0             latticeExtra_0.6-29     
[116] hwriter_1.3.2            ShortRead_1.50.0         KernSmooth_2.23-20       gridExtra_2.3            MASS_7.3-54             
[121] gtools_3.9.2             assertthat_0.2.1         Category_2.58.0          rjson_0.2.20             withr_2.4.2             
[126] GenomicAlignments_1.28.0 batchtools_0.9.15        Rsamtools_2.8.0          GenomeInfoDbData_1.2.6   hms_1.1.0               
[131] grid_4.1.1               coda_0.19-4              tidyr_1.1.3              DOT_0.1                  rmarkdown_2.10          
[136] GreyListChIP_1.24.0      ashr_2.2-47              mixsqp_0.3-43            bbmle_1.0.24             numDeriv_2016.8-1.1     
[141] tinytex_0.33             restfulr_0.0.13
parallel R DiffBind • 307 views
Entering edit mode
Rory Stark ★ 4.2k
Last seen 1 day ago
CRUK, Cambridge, UK

I am checking in a fix for this case where a config record is specified without a value for parallelPackage. It will then run in serial mode from version 3.2.6 onwards.

You can workaround this by adding a value for config$parallelPackage to your config data.frame. For example, add parallelPackage=0 to aways run serially, or parallelPackage=1 to enable parallel execution, in your call to dba() where you specify the config values.

Entering edit mode

That sounds good. Although I do not know why, I was getting that error message also without specifying a config file. That's why I tried RunParallel=FALSE, but I guess parallelPackage still needs a value.

Entering edit mode

Hi Rory,

Thank you for clarifying and for the awesome R package! I was just wondering if there is any update on this as I seem to still be experiencing this issue in 3.4.0.

Entering edit mode

I added some more checks in DiffBind_3.4.2 to make sure it runs correctly on Windows.


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