BiocParallel Error in Findpeaks()

[mbilgic4]

Hi, thank you for developing this useful package.

I'm getting this error when trying to run peak finding step. It goes until chr3, then gives this error. I am not sure what causes this error in BiocParallel. A similar error seems to happen on another package here https://github.com/sneumann/xcms/issues/384

chrs <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chrX", "chrY") maxwidth <- 1000 readlength <- 100 fullcovF1 <- loadBpCoverages(nextinput1[1],chrs) fullcovR1 <- loadBpCoverages(nextinput1[2],chrs) forwardPeaks1 <-findPeaks(fullcovF1, '+', readlength, maxwidth) Error: BiocParallel errors 1 remote errors, element index: 3 18 unevaluated and other errors first remote error: Error in h(simpleError(msg, call)): error in evaluating the argument 'values' in selecting a method for function 'Rle': only 0's may be mixed with negative subscripts

traceback() 8: stop(.error_bplist(res)) 7: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO) 6: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS) 5: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS) 4: bpmapply(.regionMatrixByChr, fullCov, names(fullCov), MoreArgs = moreArgs, SIMPLIFY = FALSE, BPPARAM = BPPARAM) 3: bpmapply(.regionMatrixByChr, fullCov, names(fullCov), MoreArgs = moreArgs, SIMPLIFY = FALSE, BPPARAM = BPPARAM) 2: derfinder::regionMatrix(fullCov = fullCov, L = L, cutoff = cutoff) 1: findPeaks(fullcovF1, "+", readlength, maxwidth)

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8 (Core)

Matrix products: default BLAS: /opt/R/4.2.0/lib64/R/lib/libRblas.so LAPACK: /opt/R/4.2.0/lib64/R/lib/libRlapack.so

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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 methods base

other attached packages: [1] doParallel_1.0.17 scAPAtrap_0.1.0 regioneR_1.28.0 bumphunter_1.38.0 locfit_1.5-9.5
[6] iterators_1.0.14 foreach_1.5.2 derfinder_1.30.0 GenomicAlignments_1.32.0 Rsamtools_2.12.0
[11] movAPA_0.1.0 DEXSeq_1.42.0 BiocParallel_1.30.2 DESeq2_1.36.0 SummarizedExperiment_1.26.1 [16] MatrixGenerics_1.8.0 matrixStats_0.62.0 GenomicFeatures_1.48.1 AnnotationDbi_1.58.0 Biobase_2.56.0
[21] ggbio_1.44.0 BSgenome_1.64.0 rtracklayer_1.56.0 Biostrings_2.64.0 XVector_0.36.0
[26] ggplot2_3.3.6 data.table_1.14.2 RColorBrewer_1.1-3 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[31] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 reshape2_1.4.4 dplyr_1.0.9

loaded via a namespace (and not attached): [1] snow_0.4-4 backports_1.4.1 Hmisc_4.7-0 BiocFileCache_2.4.0 plyr_1.8.7
[6] lazyeval_0.2.2 splines_4.2.0 digest_0.6.29 ensembldb_2.20.1 htmltools_0.5.2
[11] fansi_1.0.3 magrittr_2.0.3 checkmate_2.1.0 memoise_2.0.1 cluster_2.1.3
[16] annotate_1.74.0 prettyunits_1.1.1 jpeg_0.1-9 colorspace_2.0-3 blob_1.2.3
[21] rappdirs_0.3.3 xfun_0.31 crayon_1.5.1 RCurl_1.98-1.6 graph_1.74.0
[26] genefilter_1.78.0 survival_3.3-1 VariantAnnotation_1.42.1 glue_1.6.2 gtable_0.3.0
[31] zlibbioc_1.42.0 DelayedArray_0.22.0 scales_1.2.0 DBI_1.1.2 GGally_2.1.2
[36] rngtools_1.5.2 derfinderHelper_1.30.0 Rcpp_1.0.8.3 xtable_1.8-4 progress_1.2.2
[41] htmlTable_2.4.0 foreign_0.8-82 bit_4.0.4 OrganismDbi_1.38.0 Formula_1.2-4
[46] htmlwidgets_1.5.4 httr_1.4.3 ellipsis_0.3.2 pkgconfig_2.0.3 reshape_0.8.9
[51] XML_3.99-0.9 nnet_7.3-17 dbplyr_2.1.1 utf8_1.2.2 tidyselect_1.1.2
[56] rlang_1.0.2 munsell_0.5.0 tools_4.2.0 cachem_1.0.6 cli_3.3.0
[61] generics_0.1.2 RSQLite_2.2.14 stringr_1.4.0 fastmap_1.1.0 yaml_2.3.5
[66] knitr_1.39 bit64_4.0.5 purrr_0.3.4 KEGGREST_1.36.0 AnnotationFilter_1.20.0 [71] RBGL_1.72.0 doRNG_1.8.2 xml2_1.3.3 biomaRt_2.52.0 compiler_4.2.0
[76] rstudioapi_0.13 filelock_1.0.2 curl_4.3.2 png_0.1-7 tibble_3.1.7
[81] statmod_1.4.36 geneplotter_1.74.0 stringi_1.7.6 GenomicFiles_1.32.1 lattice_0.20-45
[86] ProtGenerics_1.28.0 Matrix_1.4-1 vctrs_0.4.1 pillar_1.7.0 lifecycle_1.0.1
[91] BiocManager_1.30.18 bitops_1.0-7 qvalue_2.28.0 R6_2.5.1 BiocIO_1.6.0
[96] latticeExtra_0.6-29 hwriter_1.3.2.1 gridExtra_2.3 codetools_0.2-18 dichromat_2.0-0.1
[101] assertthat_0.2.1 rjson_0.2.21 withr_2.5.0 GenomeInfoDbData_1.2.8 hms_1.1.1
[106] grid_4.2.0 rpart_4.1.16 biovizBase_1.44.0 base64enc_0.1-3 restfulr_0.0.13

[xiaohe0404]

Hi, have you solved this error? I also encountered the same error.