Entering edit mode
Performing dba.count() seems to mess up options('mc.cores') in the global environment
options('mc.cores' = 6L)
peaks <- dba(sampleSheet = samples_df)
peaks <- dba.count(peaks)
class(peaks)
# [1] "DBA"
options('mc.cores')
# $mc.cores
# $mc.cores$mc.cores
# $mc.cores$mc.cores$mc.cores
# [1] 6
This then leads to downstream issues with dba.blacklist() and I end up with the message
dba.blacklist(peaks)
...[filenames]...
Computing summits...
Re-centering peaks...
Genome detected: Hsapiens.UCSC.hg19
Applying blacklist...
Removed: 1 of 16215 intervals.
Error: number of cores must be a non-negative integer. Did you mis-specify R_PARALLELLY_AVAILABLECORES_FALLBACK,
BIOCPARALLEL_WORKER_NUMBER, or options('mc.cores')?
I can fix by resetting the mc.cores setting in the global enrivonment but clearly this is not how the package should behave
options('mc.cores' = 6L)
peaks <- dba(sampleSheet = samples_df)
peaks <- dba.count(peaks)
options('mc.cores' = 6L)
peaks <- dba.blacklist(peaks)
sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8
[6] LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] htmltools_0.5.3 plyranges_1.18.0 glue_1.6.2 edgeR_3.40.0
[5] limma_3.54.0 scales_1.2.1 rtracklayer_1.58.0 extraChIPs_1.2.0
[9] BiocParallel_1.32.1 reactable_0.3.0 pander_0.6.5 forcats_0.5.2
[13] stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5 readr_2.1.3
[17] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2
[21] DiffBind_3.8.0 SummarizedExperiment_1.28.0 Biobase_2.58.0 MatrixGenerics_1.10.0
[25] matrixStats_0.62.0 GenomicRanges_1.50.1 GenomeInfoDb_1.34.3 IRanges_2.32.0
[29] S4Vectors_0.36.0 BiocGenerics_0.44.0 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 coda_0.19-4 csaw_1.32.0 bit64_4.0.5 knitr_1.40
[6] irlba_2.3.5.1 DelayedArray_0.24.0 data.table_1.14.4 rpart_4.1.19 hwriter_1.3.2.1
[11] KEGGREST_1.38.0 RCurl_1.98-1.9 AnnotationFilter_1.22.0 doParallel_1.0.17 generics_0.1.3
[16] GenomicFeatures_1.50.2 callr_3.7.3 EnrichedHeatmap_1.27.2 lambda.r_1.2.4 RSQLite_2.2.18
[21] bit_4.0.4 tzdb_0.3.0 xml2_1.3.3 lubridate_1.9.0 httpuv_1.6.6
[26] assertthat_0.2.1 gargle_1.2.1 amap_0.8-19 apeglm_1.20.0 xfun_0.34
[31] hms_1.1.2 evaluate_0.18 promises_1.2.0.1 fansi_1.0.3 restfulr_0.0.15
[36] progress_1.2.2 caTools_1.18.2 dbplyr_2.2.1 readxl_1.4.1 geneplotter_1.76.0
[41] igraph_1.3.5 DBI_1.1.3 htmlwidgets_1.5.4 futile.logger_1.4.3 googledrive_2.0.0
[46] ellipsis_0.3.2 backports_1.4.1 annotate_1.76.0 biomaRt_2.54.0 deldir_1.0-6
[51] vctrs_0.5.0 here_1.0.1 ensembldb_2.22.0 cachem_1.0.6 withr_2.5.0
[56] ggforce_0.4.1 Gviz_1.42.0 BSgenome_1.66.1 bdsmatrix_1.3-6 checkmate_2.1.0
[61] GenomicAlignments_1.34.0 prettyunits_1.1.1 cluster_2.1.4 lazyeval_0.2.2 crayon_1.5.2
[66] genefilter_1.80.0 pkgconfig_2.0.3 tweenr_2.0.2 ProtGenerics_1.30.0 nnet_7.3-18
[71] rlang_1.0.6 lifecycle_1.0.3 filelock_1.0.2 BiocFileCache_2.6.0 modelr_0.1.10
[76] dichromat_2.0-0.1 VennDiagram_1.7.3 invgamma_1.1 cellranger_1.1.0 rprojroot_2.0.3
[81] polyclip_1.10-4 Matrix_1.5-3 ashr_2.2-54 reprex_2.0.2 base64enc_0.1-3
[86] whisker_0.4 GlobalOptions_0.1.2 processx_3.8.0 googlesheets4_1.0.1 png_0.1-7
[91] rjson_0.2.21 GenomicInteractions_1.32.0 bitops_1.0-7 getPass_0.2-2 KernSmooth_2.23-20
[96] Biostrings_2.66.0 blob_1.2.3 shape_1.4.6 mixsqp_0.3-43 SQUAREM_2021.1
[101] ShortRead_1.56.0 jpeg_0.1-9 memoise_2.0.1 magrittr_2.0.3 plyr_1.8.8
[106] gplots_3.1.3 zlibbioc_1.44.0 compiler_4.2.1 BiocIO_1.8.0 bbmle_1.0.25
[111] RColorBrewer_1.1-3 clue_0.3-62 DESeq2_1.38.0 Rsamtools_2.14.0 cli_3.4.1
[116] systemPipeR_2.4.0 XVector_0.38.0 patchwork_1.1.2 ps_1.7.2 htmlTable_2.4.1
[121] formatR_1.12 Formula_1.2-4 ggside_0.2.1 MASS_7.3-58.1 tidyselect_1.2.0
[126] stringi_1.7.8 emdbook_1.3.12 yaml_2.3.6 locfit_1.5-9.6 latticeExtra_0.6-30
[131] ggrepel_0.9.2 grid_4.2.1 VariantAnnotation_1.44.0 tools_4.2.1 timechange_0.1.1
[136] parallel_4.2.1 circlize_0.4.15 rstudioapi_0.14 foreach_1.5.2 foreign_0.8-83
[141] git2r_0.30.1 metapod_1.6.0 gridExtra_2.3 farver_2.1.1 ComplexUpset_1.3.3
[146] digest_0.6.30 Rcpp_1.0.9 broom_1.0.1 later_1.3.0 httr_1.4.4
[151] AnnotationDbi_1.60.0 biovizBase_1.46.0 ComplexHeatmap_2.14.0 colorspace_2.0-3 rvest_1.0.3
[156] XML_3.99-0.12 fs_1.5.2 truncnorm_1.0-8 splines_4.2.1 xtable_1.8-4
[161] jsonlite_1.8.3 futile.options_1.0.1 R6_2.5.1 Hmisc_4.7-1 pillar_1.8.1
[166] fastmap_1.1.0 codetools_0.2-18 GreyListChIP_1.30.0 mvtnorm_1.1-3 utf8_1.2.2
[171] lattice_0.20-45 numDeriv_2016.8-1.1 curl_4.3.3 gtools_3.9.3 interp_1.1-3
[176] survival_3.4-0 rmarkdown_2.18 InteractionSet_1.26.0 munsell_0.5.0 GetoptLong_1.0.5
[181] GenomeInfoDbData_1.2.9 iterators_1.0.14 haven_2.5.1 gtable_0.3.1
