Open
Description
1. Bug description
Running MOTIFBREAKR_plot causes error in certain contexts. Documented here:
Simon-Coetzee/motifBreakR#31
Expected behaviour
Function should run in all contexts.
2. Reproducible example
Code
library(BSgenome) ## <-- IMPORTANT!
library(BSgenome.Hsapiens.UCSC.hg19) ## <-- IMPORTANT!
#### Example fine-mapping results ####
merged_DT <- echodata::get_Nalls2019_merged()
#### Run motif analyses ####
mb_res <- MOTIFBREAKR(rsid_list = c("rs11175620"),
# limit the number of datasets tested
# for demonstration purposes only
pwmList_max = 5,
calculate_pvals = FALSE)
plot_paths <- MOTIFBREAKR_plot(mb_res = mb_res)
Console output
When run via CRAN checks.
dat is already a GRanges object.
Plotting 1 unique RSID(s).
Plotting motif disruption results: rs11175620
Error in grid.Call.graphics(C_unsetviewport, as.integer(n)) :
cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
Calls: MOTIFBREAKR_plot ... drawGD -> .local -> popViewport -> grid.Call.graphics
Execution halted
When run in R console:
genome_build set to hg19 by default.
Loading required namespace: SNPlocs.Hsapiens.dbSNP144.GRCh37
Using genome_build hg19
+ MOTIFBREAKR:: Converting SNP list into motifbreakR input format.
3. Session info
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets
[7] methods base
other attached packages:
[1] echoannot_0.99.10
[2] BSgenome.Hsapiens.UCSC.hg19_1.4.3
[3] BSgenome_1.65.2
[4] rtracklayer_1.57.0
[5] Biostrings_2.65.6
[6] XVector_0.37.1
[7] GenomicRanges_1.49.1
[8] GenomeInfoDb_1.33.13
[9] IRanges_2.31.2
[10] S4Vectors_0.35.4
[11] BiocGenerics_0.43.4
loaded via a namespace (and not attached):
[1] utf8_1.2.2
[2] reticulate_1.26
[3] R.utils_2.12.0
[4] tidyselect_1.2.0
[5] poweRlaw_0.70.6
[6] RSQLite_2.2.18
[7] AnnotationDbi_1.59.1
[8] htmlwidgets_1.5.4
[9] grid_4.2.1
[10] BiocParallel_1.31.14
[11] XGR_1.1.8
[12] munsell_0.5.0
[13] codetools_0.2-18
[14] interp_1.1-3
[15] DT_0.26
[16] colorspace_2.0-3
[17] OrganismDbi_1.39.1
[18] Biobase_2.57.1
[19] filelock_1.0.2
[20] knitr_1.40
[21] supraHex_1.35.0
[22] rstudioapi_0.14
[23] DescTools_0.99.46
[24] motifStack_1.41.1
[25] MatrixGenerics_1.9.1
[26] GenomeInfoDbData_1.2.9
[27] bit64_4.0.5
[28] echoconda_0.99.7
[29] basilisk_1.9.11
[30] vctrs_0.4.2
[31] generics_0.1.3
[32] xfun_0.34
[33] biovizBase_1.45.0
[34] BiocFileCache_2.5.2
[35] R6_2.5.1
[36] splitstackshape_1.4.8
[37] grImport2_0.2-0
[38] AnnotationFilter_1.21.0
[39] bitops_1.0-7
[40] cachem_1.0.6
[41] reshape_0.8.9
[42] DelayedArray_0.23.2
[43] motifbreakR_2.11.2
[44] assertthat_0.2.1
[45] BiocIO_1.7.1
[46] scales_1.2.1
[47] nnet_7.3-18
[48] rootSolve_1.8.2.3
[49] gtable_0.3.1
[50] lmom_2.9
[51] ggbio_1.45.0
[52] ensembldb_2.21.5
[53] seqLogo_1.63.0
[54] rlang_1.0.6
[55] echodata_0.99.15
[56] splines_4.2.1
[57] lazyeval_0.2.2
[58] dichromat_2.0-0.1
[59] hexbin_1.28.2
[60] checkmate_2.1.0
[61] BiocManager_1.30.18
[62] yaml_2.3.6
[63] reshape2_1.4.4
[64] GenomicFeatures_1.49.7
[65] ggnetwork_0.5.10
[66] backports_1.4.1
[67] Hmisc_4.7-1
[68] RBGL_1.73.0
[69] tools_4.2.1
[70] ggplot2_3.3.6
[71] ellipsis_0.3.2
[72] RColorBrewer_1.1-3
[73] proxy_0.4-27
[74] Rcpp_1.0.9
[75] plyr_1.8.7
[76] base64enc_0.1-3
[77] progress_1.2.2
[78] zlibbioc_1.43.0
[79] purrr_0.3.5
[80] RCurl_1.98-1.9
[81] basilisk.utils_1.9.4
[82] prettyunits_1.1.1
[83] rpart_4.1.16
[84] deldir_1.0-6
[85] SummarizedExperiment_1.27.3
[86] ggrepel_0.9.1
[87] cluster_2.1.4
[88] fs_1.5.2
[89] crul_1.3
[90] magrittr_2.0.3
[91] data.table_1.14.4
[92] echotabix_0.99.8
[93] dnet_1.1.7
[94] openxlsx_4.2.5
[95] MotifDb_1.39.0
[96] mvtnorm_1.1-3
[97] ProtGenerics_1.29.1
[98] matrixStats_0.62.0
[99] pkgload_1.3.0
[100] xtable_1.8-4
[101] patchwork_1.1.2
[102] hms_1.1.2
[103] XML_3.99-0.11
[104] jpeg_0.1-9
[105] readxl_1.4.1
[106] gridExtra_2.3
[107] compiler_4.2.1
[108] biomaRt_2.53.3
[109] tibble_3.1.8
[110] crayon_1.5.2
[111] R.oo_1.25.0
[112] htmltools_0.5.3
[113] tzdb_0.3.0
[114] TFBSTools_1.35.0
[115] Formula_1.2-4
[116] tidyr_1.2.1
[117] expm_0.999-6
[118] Exact_3.2
[119] DBI_1.1.3
[120] dbplyr_2.2.1
[121] MASS_7.3-58.1
[122] rappdirs_0.3.3
[123] boot_1.3-28
[124] ade4_1.7-19
[125] Matrix_1.5-1
[126] readr_2.1.3
[127] piggyback_0.1.4
[128] cli_3.4.1
[129] R.methodsS3_1.8.2
[130] Gviz_1.41.1
[131] parallel_4.2.1
[132] igraph_1.3.5
[133] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20
[134] pkgconfig_2.0.3
[135] TFMPvalue_0.0.9
[136] GenomicAlignments_1.33.1
[137] dir.expiry_1.5.1
[138] RCircos_1.2.2
[139] foreign_0.8-83
[140] osfr_0.2.9
[141] xml2_1.3.3
[142] annotate_1.75.0
[143] DirichletMultinomial_1.39.0
[144] stringr_1.4.1
[145] VariantAnnotation_1.43.3
[146] digest_0.6.30
[147] pracma_2.4.2
[148] CNEr_1.33.0
[149] graph_1.75.0
[150] httpcode_0.3.0
[151] cellranger_1.1.0
[152] htmlTable_2.4.1
[153] gld_2.6.5
[154] restfulr_0.0.15
[155] curl_4.3.3
[156] gtools_3.9.3
[157] Rsamtools_2.13.4
[158] rjson_0.2.21
[159] lifecycle_1.0.3
[160] nlme_3.1-160
[161] jsonlite_1.8.3
[162] fansi_1.0.3
[163] downloadR_0.99.4
[164] pillar_1.8.1
[165] lattice_0.20-45
[166] GGally_2.1.2
[167] GO.db_3.16.0
[168] KEGGREST_1.37.3
[169] fastmap_1.1.0
[170] httr_1.4.4
[171] survival_3.4-0
[172] glue_1.6.2
[173] zip_2.2.1
[174] png_0.1-7
[175] bit_4.0.4
[176] Rgraphviz_2.41.1
[177] class_7.3-20
[178] stringi_1.7.8
[179] blob_1.2.3
[180] caTools_1.18.2
[181] latticeExtra_0.6-30
[182] memoise_2.0.1
[183] dplyr_1.0.10
[184] e1071_1.7-11
[185] ape_5.6-2
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