Entering edit mode
I am running Diffbind for a chipseq dataset for the last 2 years or so. I did'nt had any problem before, though i am not very expert. Now when i am running Diffind, it gives me error during ploting profiles. when i run
profiles <- dba.plotProfile(DiffPeaks)
dba.plotProfile(profiles)
it gives me this error
Error in value[[3L]](cond) :
profileplyr error: Error: BiocParallel errors
1 remote errors, element index: 1
5 unevaluated and other errors
first remote error:
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in DataFrame(..., check.names = FALSE): different row counts implied by arguments
the bam and peak files seems OK, hrere is the session info. I have tried to uninstall R and re-install it updating packages but no luck
R version 4.5.0 (2025-04-11 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocParallel_1.42.0 here_1.0.1 profileplyr_1.24.1 DiffBind_3.18.0
[5] SummarizedExperiment_1.38.1 Biobase_2.68.0 MatrixGenerics_1.20.0 matrixStats_1.5.0
[9] GenomicRanges_1.60.0 GenomeInfoDb_1.44.0 IRanges_2.42.0 S4Vectors_0.46.0
[13] BiocGenerics_0.54.0 generics_0.1.4 BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] later_1.4.2 splines_4.5.0
[3] BiocIO_1.18.0 bitops_1.0-9
[5] ggplotify_0.1.2 tibble_3.2.1
[7] R.oo_1.27.1 preprocessCore_1.70.0
[9] XML_3.99-0.18 lifecycle_1.0.4
[11] pwalign_1.4.0 mixsqp_0.3-54
[13] rprojroot_2.0.4 doParallel_1.0.17
[15] lattice_0.22-7 MASS_7.3-65
[17] systemPipeR_2.14.0 magrittr_2.0.3
[19] limma_3.64.0 yaml_2.3.10
[21] plotrix_3.8-4 httpuv_1.6.16
[23] ggtangle_0.0.6 cowplot_1.1.3
[25] DBI_1.2.3 RColorBrewer_1.1-3
[27] abind_1.4-8 ShortRead_1.66.0
[29] purrr_1.0.4 R.utils_2.13.0
[31] RCurl_1.98-1.17 yulab.utils_0.2.0
[33] circlize_0.4.16 GenomeInfoDbData_1.2.14
[35] enrichplot_1.28.2 ggrepel_0.9.6
[37] irlba_2.3.5.1 tidytree_0.4.6
[39] pheatmap_1.0.12 ChIPseeker_1.44.0
[41] codetools_0.2-20 DelayedArray_0.34.1
[43] DOSE_4.2.0 DT_0.33
[45] tidyselect_1.2.1 shape_1.4.6.1
[47] aplot_0.2.5 UCSC.utils_1.4.0
[49] farver_2.1.2 GenomicAlignments_1.44.0
[51] jsonlite_2.0.0 GetoptLong_1.0.5
[53] iterators_1.0.14 foreach_1.5.2
[55] bbmle_1.0.25.1 progress_1.2.3
[57] tools_4.5.0 treeio_1.32.0
[59] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 snow_0.4-4
[61] Rcpp_1.0.14 glue_1.8.0
[63] SparseArray_1.8.0 DESeq2_1.48.1
[65] qvalue_2.40.0 amap_0.8-20
[67] dplyr_1.1.4 withr_3.0.2
[69] numDeriv_2016.8-1.1 fastmap_1.2.0
[71] latticeExtra_0.6-30 boot_1.3-31
[73] caTools_1.18.3 digest_0.6.37
[75] truncnorm_1.0-9 mime_0.13
[77] R6_2.6.1 gridGraphics_0.5-1
[79] colorspace_2.1-1 GO.db_3.21.0
[81] GreyListChIP_1.40.0 gtools_3.9.5
[83] jpeg_0.1-11 RSQLite_2.3.11
[85] R.methodsS3_1.8.2 tidyr_1.3.1
[87] data.table_1.17.0 rtracklayer_1.68.0
[89] prettyunits_1.2.0 httr_1.4.7
[91] htmlwidgets_1.6.4 S4Arrays_1.8.0
[93] org.Mm.eg.db_3.21.0 pkgconfig_2.0.3
[95] gtable_0.3.6 blob_1.2.4
[97] ComplexHeatmap_2.24.0 hwriter_1.3.2.1
[99] XVector_0.48.0 chipseq_1.58.0
[101] htmltools_0.5.8.1 fgsea_1.34.0
[103] clue_0.3-66 scales_1.4.0
[105] TxDb.Hsapiens.UCSC.hg38.knownGene_3.21.0 png_0.1-8
[107] ashr_2.2-63 ggfun_0.1.8
[109] reshape2_1.4.4 rjson_0.2.23
[111] coda_0.19-4.1 nlme_3.1-168
[113] curl_6.2.2 bdsmatrix_1.3-7
[115] org.Hs.eg.db_3.21.0 cachem_1.1.0
[117] GlobalOptions_0.1.2 stringr_1.5.1
[119] KernSmooth_2.23-26 parallel_4.5.0
[121] AnnotationDbi_1.70.0 restfulr_0.0.15
[123] apeglm_1.30.0 pillar_1.10.2
[125] grid_4.5.0 vctrs_0.6.5
[127] gplots_3.2.0 promises_1.3.2
[129] cluster_2.1.8.1 xtable_1.8-4
[131] rGREAT_2.10.0 EnrichedHeatmap_1.38.0
[133] invgamma_1.1 GenomicFeatures_1.60.0
[135] mvtnorm_1.3-3 cli_3.6.5
[137] locfit_1.5-9.12 compiler_4.5.0
[139] Rsamtools_2.24.0 rlang_1.1.6
[141] crayon_1.5.3 SQUAREM_2021.1
[143] labeling_0.4.3 interp_1.1-6
[145] emdbook_1.3.13 plyr_1.8.9
[147] fs_1.6.6 stringi_1.8.7
[149] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 deldir_2.0-4
[151] Biostrings_2.76.0 tiff_0.1-12
[153] lazyeval_0.2.2 GOSemSim_2.34.0
[155] Matrix_1.7-3 BSgenome_1.76.0
[157] hms_1.1.3 patchwork_1.3.0
[159] bit64_4.6.0-1 ggplot2_3.5.2
[161] shiny_1.10.0 KEGGREST_1.48.0
[163] statmod_1.5.0 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
[165] igraph_2.1.4 memoise_2.0.1
[167] ggtree_3.16.0 fastmatch_1.1-6
[169] soGGi_1.40.1 bit_4.6.0
Any help will be appreciated Thanks
