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I'm getting an error repeatable error when I try to run code that worked with previous versions of DiffBind (3.4.11)
meta <- read_csv("../01b_ChIPQC/HCA_chipqc_meta_final.csv")[c(3:8),]
config <- data.frame(minQCth=30, fragmentSize=c(104,167,200,103,103,204), bCorPlot=T, th=0.05)
grey <- import.bed("../01c_greyLists/WT_greyList.bed")
trmB <- dba(sampleSheet = meta, peakFormat = "bed", minOverlap = 0.75, config = config)
returns the error r Error in if (res$config$bCorPlot) { : the condition has length > 1 This persists with R 4.2.1 on separate machines. Traceback returns the dba() function call. This issue is resolved when I revert to R 4.1.2 and DiffBind 3.4.11. Has anyone else encountered this error and found a work around in the current release?
sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DiffBind_3.6.3 SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.1 matrixStats_0.62.0
[6] rtracklayer_1.56.1 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0
[11] BiocGenerics_0.42.0 openxlsx_4.2.5 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9
[16] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6
[21] tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] amap_0.8-18 googledrive_2.0.0 colorspace_2.0-3 deldir_1.0-6 rjson_0.2.21 hwriter_1.3.2.1
[7] ellipsis_0.3.2 XVector_0.36.0 fs_1.5.2 rstudioapi_0.14 bit64_4.0.5 ggrepel_0.9.1
[13] mvtnorm_1.1-3 apeglm_1.18.0 fansi_1.0.3 lubridate_1.8.0 xml2_1.3.3 codetools_0.2-18
[19] knitr_1.40 jsonlite_1.8.0 Rsamtools_2.12.0 broom_1.0.1 ashr_2.2-54 dbplyr_2.2.1
[25] png_0.1-7 GreyListChIP_1.28.1 BiocManager_1.30.18 compiler_4.2.1 httr_1.4.4 backports_1.4.1
[31] assertthat_0.2.1 Matrix_1.4-1 fastmap_1.1.0 gargle_1.2.0 limma_3.52.2 cli_3.3.0
[37] htmltools_0.5.3 tools_4.2.1 coda_0.19-4 gtable_0.3.1 glue_1.6.2 GenomeInfoDbData_1.2.8
[43] systemPipeR_2.2.2 ShortRead_1.54.0 Rcpp_1.0.9 bbmle_1.0.25 cellranger_1.1.0 vctrs_0.4.1
[49] Biostrings_2.64.0 xfun_0.31 rvest_1.0.3 irlba_2.3.5 lifecycle_1.0.1 restfulr_0.0.15
[55] gtools_3.9.3 XML_3.99-0.10 googlesheets4_1.0.1 MASS_7.3-58 zlibbioc_1.42.0 scales_1.2.1
[61] vroom_1.5.7 BSgenome_1.64.0 hms_1.1.2 parallel_4.2.1 RColorBrewer_1.1-3 yaml_2.3.5
[67] emdbook_1.3.12 bdsmatrix_1.3-6 SQUAREM_2021.1 latticeExtra_0.6-30 stringi_1.7.8 BiocIO_1.6.0
[73] caTools_1.18.2 zip_2.2.0 BiocParallel_1.30.3 truncnorm_1.0-8 rlang_1.0.4 pkgconfig_2.0.3
[79] bitops_1.0-7 invgamma_1.1 evaluate_0.16 lattice_0.20-45 GenomicAlignments_1.32.1 htmlwidgets_1.5.4
[85] bit_4.0.4 tidyselect_1.1.2 plyr_1.8.7 magrittr_2.0.3 R6_2.5.1 gplots_3.1.3
[91] generics_0.1.3 DelayedArray_0.22.0 DBI_1.1.3 pillar_1.8.1 haven_2.5.0 withr_2.5.0
[97] mixsqp_0.3-43 RCurl_1.98-1.8 modelr_0.1.9 crayon_1.5.1 interp_1.1-3 KernSmooth_2.23-20
[103] utf8_1.2.2 tzdb_0.3.0 rmarkdown_2.16 jpeg_0.1-9 locfit_1.5-9.6 grid_4.2.1
[109] readxl_1.4.0 reprex_2.0.2 digest_0.6.29 numDeriv_2016.8-1.1 munsell_0.5.0
