Hello,

I am trying to run ChIPQC on 83 samples. I am using the following line to make the DBA object:

CHIPQC_DBA = ChIPQC(samples,consensus = TRUE, bCount=TRUE, summits=250, annotation="hg38", blacklist = blacklist.hg38)

It is running until this point and crashing with the following error:

Checking chromosomes:
[1] "chr1"
Compiling annotation...
Adding controls...
Counting reads in consensus peakset...
Re-centering peaks...
Computing metrics for 83 samples...
'BiocParallel' did not register default BiocParallelParam:
  comparison of these types is not implemented
Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) ==  :
  missing value where TRUE/FALSE needed
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply
Execution halted

I would really appreciate if Rory or Thomas could help me on thise!

Here is my session info:

 R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS/LAPACK: /fshare/users/sakibs/miniconda3/envs/latest_R_3.6/lib/R/lib/libRblas.so

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

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

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
 [2] GenomicFeatures_1.38.2
 [3] AnnotationDbi_1.48.0
 [4] ChIPQC_1.22.0
 [5] DiffBind_2.14.0
 [6] SummarizedExperiment_1.16.1
 [7] DelayedArray_0.12.3
 [8] BiocParallel_1.20.1
 [9] matrixStats_0.56.0
[10] Biobase_2.46.0
[11] GenomicRanges_1.38.0
[12] GenomeInfoDb_1.22.1
[13] IRanges_2.20.2
[14] S4Vectors_0.24.4
[15] BiocGenerics_0.32.0
[16] ggplot2_3.3.0

loaded via a namespace (and not attached):
  [1] amap_0.8-18
  [2] colorspace_1.4-1
  [3] rjson_0.2.20
  [4] hwriter_1.3.2
  [5] ellipsis_0.3.0
  [6] XVector_0.26.0
  [7] ggrepel_0.8.2
  [8] bit64_0.9-7
  [9] fansi_0.4.1
 [10] splines_3.6.1
 [11] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2
 [12] Nozzle.R1_1.1-1
 [13] Rsamtools_2.2.3
 [14] annotate_1.64.0
 [15] GO.db_3.10.0
 [16] dbplyr_1.4.3
 [17] png_0.1-7
 [18] pheatmap_1.0.12
 [19] graph_1.64.0
 [20] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
 [21] compiler_3.6.1
 [22] httr_1.4.1
 [23] GOstats_2.52.0
 [24] backports_1.1.6
 [25] assertthat_0.2.1
 [26] Matrix_1.2-18
 [27] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [28] limma_3.42.2
 [29] cli_2.0.2
 [30] prettyunits_1.1.1
 [31] tools_3.6.1
 [32] gtable_0.3.0
 [33] glue_1.4.0
 [34] GenomeInfoDbData_1.2.2
 [35] Category_2.52.1
 [36] reshape2_1.4.4
 [37] systemPipeR_1.20.0
 [38] dplyr_0.8.5
 [39] batchtools_0.9.13
 [40] rappdirs_0.3.1
 [41] ShortRead_1.44.3
 [42] Rcpp_1.0.4.6
 [43] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [44] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
 [45] vctrs_0.2.4
 [46] Biostrings_2.54.0
 [47] gdata_2.18.0
 [48] rtracklayer_1.46.0
 [49] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
 [50] stringr_1.4.0
 [51] lifecycle_0.2.0
 [52] gtools_3.8.2
 [53] XML_3.99-0.3
 [54] edgeR_3.28.1
 [55] zlibbioc_1.32.0
 [56] scales_1.1.0
 [57] BSgenome_1.54.0
 [58] VariantAnnotation_1.32.0
 [59] hms_0.5.3
 [60] RBGL_1.62.1
 [61] RColorBrewer_1.1-2
 [62] yaml_2.2.1
 [63] curl_4.3
 [64] memoise_1.1.0
 [65] biomaRt_2.42.1
 [66] latticeExtra_0.6-29
 [67] stringi_1.4.6
 [68] RSQLite_2.2.0
 [69] genefilter_1.68.0
 [70] checkmate_2.0.0
 [71] caTools_1.18.0
 [72] chipseq_1.36.0
 [73] rlang_0.4.5
 [74] pkgconfig_2.0.3
 [75] bitops_1.0-6
 [76] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
 [77] lattice_0.20-41
 [78] purrr_0.3.4
 [79] GenomicAlignments_1.22.1
 [80] bit_1.1-15.2
 [81] tidyselect_1.0.0
 [82] GSEABase_1.48.0
 [83] AnnotationForge_1.28.0
 [84] plyr_1.8.6
 [85] magrittr_1.5
 [86] R6_2.4.1
 [87] gplots_3.0.3
 [88] base64url_1.4
 [89] DBI_1.1.0
 [90] pillar_1.4.3
 [91] withr_2.1.2
 [92] survival_3.1-12
 [93] RCurl_1.98-1.2
 [94] tibble_3.0.0
 [95] crayon_1.3.4
 [96] KernSmooth_2.23-16
 [97] BiocFileCache_1.10.2
 [98] jpeg_0.1-8.1
 [99] progress_1.2.2
[100] locfit_1.5-9.4
[101] grid_3.6.1
[102] data.table_1.12.8
[103] blob_1.2.1
[104] Rgraphviz_2.30.0
[105] digest_0.6.25
[106] xtable_1.8-4
[107] brew_1.0-6
[108] openssl_1.4.1
[109] munsell_0.5.0
[110] askpass_1.1`

I have submitted a fix for ChIPQC that makes the use of BiocParallel more explicit, checking for installed backends and reporting information on how ChIPQC will be executed.

This fix will be in effect from version ChIPQC_1.32.1 in the main Release branch. There are related fixes in DiffBind_3.6.2 so these should be updated together.