Hi all, I am having trouble getting DiffBind's dba.counts to run to completion. I am frequently met with the following error:

Reads will be counted as Paired-end.
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
  element index: 1
  first error: cannot allocate vector of size 163.4 Mb

From what I understand, this is a memory issue. I have tried running gc() and I have also tried chainging the DBA$config$yieldSize to a lower number, although I am not sure if I have actually done that correctly. Below I have my various attempts at dba.count(), all of which eventually give the "cannot allocate vector size" error, never at the same sample and always a different size vector. Am I changing the yieldSize correctly, and if I am is there anything else I can do to lower the memory usage (even if it takes longer to run?)

For computer specs, I do only have 8GB of RAM which I suspect is problematic.

Code should be placed in three backticks as shown below

library(DiffBind)

#Read in meta data which directs to bam and peak files
samples2 <- read.csv("meta.csv") 
samples2

#####################
#Create a dba object#
#####################
dba <- dba(sampleSheet = samples2)
dba2 <- dba(sampleSheet=samples2)
dba3 <- dba(sampleSheet = samples2)
dba4 <- dba(sampleSheet = samples2)

################
#Counting Reads#
################
dba <- dba.count(dba, bUseSummarizeOverlaps = TRUE)
dba2$config$yieldSize <- 2500000
dba2 <- dba.count(dba2, bUseSummarizeOverlaps = dba2$config$yieldSize, bParallel = FALSE) 
dba3$config$yieldSize <- 50000
dba3 <- dba.count(dba3, bUseSummarizeOverlaps = dba3$config$yieldSize, bParallel = FALSE)
dba4 <- dba.count(dba4, bParallel = FALSE)

sessionInfo( )
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

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DiffBind_3.2.7              SummarizedExperiment_1.22.0
 [3] Biobase_2.52.0              MatrixGenerics_1.4.3       
 [5] matrixStats_0.61.0          GenomicRanges_1.44.0       
 [7] GenomeInfoDb_1.28.4         IRanges_2.26.0             
 [9] S4Vectors_0.30.1            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.1          GOstats_2.58.0           BiocFileCache_2.0.0     
  [4] plyr_1.8.6               GSEABase_1.54.0          splines_4.1.1           
  [7] BiocParallel_1.26.2      ggplot2_3.3.5            amap_0.8-18             
 [10] digest_0.6.28            invgamma_1.1             GO.db_3.13.0            
 [13] SQUAREM_2021.1           fansi_0.5.0              magrittr_2.0.1          
 [16] checkmate_2.0.0          memoise_2.0.0            BSgenome_1.60.0         
 [19] base64url_1.4            limma_3.48.3             Biostrings_2.60.2       
 [22] annotate_1.70.0          systemPipeR_1.26.3       bdsmatrix_1.3-4         
 [25] prettyunits_1.1.1        jpeg_0.1-9               colorspace_2.0-2        
 [28] blob_1.2.2               rappdirs_0.3.3           apeglm_1.14.0           
 [31] ggrepel_0.9.1            dplyr_1.0.7              crayon_1.4.1            
 [34] RCurl_1.98-1.5           jsonlite_1.7.2           graph_1.70.0            
 [37] genefilter_1.74.0        brew_1.0-6               survival_3.2-11         
 [40] VariantAnnotation_1.38.0 glue_1.4.2               gtable_0.3.0            
 [43] zlibbioc_1.38.0          XVector_0.32.0           DelayedArray_0.18.0     
 [46] V8_3.4.2                 Rgraphviz_2.36.0         scales_1.1.1            
 [49] pheatmap_1.0.12          mvtnorm_1.1-2            DBI_1.1.1               
 [52] edgeR_3.34.1             Rcpp_1.0.7               xtable_1.8-4            
 [55] progress_1.2.2           emdbook_1.3.12           bit_4.0.4               
 [58] rsvg_2.1.2               AnnotationForge_1.34.0   truncnorm_1.0-8         
 [61] httr_1.4.2               gplots_3.1.1             RColorBrewer_1.1-2      
 [64] ellipsis_0.3.2           pkgconfig_2.0.3          XML_3.99-0.8            
 [67] dbplyr_2.1.1             locfit_1.5-9.4           utf8_1.2.2              
 [70] tidyselect_1.1.1         rlang_0.4.11             AnnotationDbi_1.54.1    
 [73] munsell_0.5.0            tools_4.1.1              cachem_1.0.6            
 [76] generics_0.1.0           RSQLite_2.2.8            stringr_1.4.0           
 [79] fastmap_1.1.0            yaml_2.2.1               bit64_4.0.5             
 [82] caTools_1.18.2           purrr_0.3.4              KEGGREST_1.32.0         
 [85] RBGL_1.68.0              xml2_1.3.2               biomaRt_2.48.3          
 [88] compiler_4.1.1           rstudioapi_0.13          filelock_1.0.2          
 [91] curl_4.3.2               png_0.1-7                tibble_3.1.4            
 [94] stringi_1.7.4            GenomicFeatures_1.44.2   lattice_0.20-44         
 [97] Matrix_1.3-4             vctrs_0.3.8              pillar_1.6.3            
[100] lifecycle_1.0.1          irlba_2.3.3              data.table_1.14.0       
[103] bitops_1.0-7             rtracklayer_1.52.1       R6_2.5.1                
[106] BiocIO_1.2.0             latticeExtra_0.6-29      hwriter_1.3.2           
[109] ShortRead_1.50.0         KernSmooth_2.23-20       MASS_7.3-54             
[112] gtools_3.9.2             assertthat_0.2.1         Category_2.58.0         
[115] rjson_0.2.20             withr_2.4.2              GenomicAlignments_1.28.0
[118] batchtools_0.9.15        Rsamtools_2.8.0          GenomeInfoDbData_1.2.6  
[121] hms_1.1.1                grid_4.1.1               DOT_0.1                 
[124] coda_0.19-4              GreyListChIP_1.24.0      ashr_2.2-47             
[127] mixsqp_0.3-43            bbmle_1.0.24             numDeriv_2016.8-1.1     
[130] restfulr_0.0.13