motifBreakR
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Simon-Coetzee
Too many stacks to draw of plotMB?
Hello, I caught error as follows: ####################### Error in .local(GdObject, ...) : Too many stacks to draw. Either increase the device size or limit the drawing to a smaller region. Calls: plotMB ... drawGD -> .local -> callNextMethod -> .nextMethod -> .local Execution halted #######################
How to fix this bug?
This is not a bug. MotifbreakR can't render the plot if there are too many results.
Sorry, I am just trying to reproduce the tutorial in step 3 https://www.bioconductor.org/packages/release/bioc/vignettes/motifbreakR/inst/doc/motifbreakR-vignette.html But instead of getting the plot that is where I get the error message from the first comment. I wonder what it could be? Thanks Diego
can you provide some info, what platform and version of R/Bioconductor etc
Hi, I am having this exact problem. I'm using an Rstudio server (version 3.6.0) and Bioconductor version 3.9
Getting similar error. Tried increasing the plot size and still have the same error
Error in .local(GdObject, ...): Too many stacks to draw. Either increase the device size or limit the drawing to a smaller region.
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 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=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.3
[2] SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5
[3] BSgenome_1.58.0
[4] rtracklayer_1.50.0
[5] motifbreakR_2.4.0
[6] MotifDb_1.32.0
[7] Biostrings_2.58.0
[8] XVector_0.30.0
[9] GenomicRanges_1.42.0
[10] GenomeInfoDb_1.26.2
[11] IRanges_2.24.1
[12] S4Vectors_0.28.1
[13] BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-0 grImport2_0.2-0
[3] ellipsis_0.3.1 biovizBase_1.38.0
[5] IRdisplay_0.7.0 htmlTable_2.1.0
[7] base64enc_0.1-3 dichromat_2.0-0
[9] rstudioapi_0.13 bit64_4.0.5
[11] AnnotationDbi_1.52.0 xml2_1.3.2
[13] splines_4.0.3 motifStack_1.34.0
[15] knitr_1.30 IRkernel_1.1.1.9000
[17] ade4_1.7-16 Formula_1.2-4
[19] jsonlite_1.7.2 splitstackshape_1.4.8
[21] Rsamtools_2.6.0 cluster_2.1.0
[23] dbplyr_2.0.0 png_0.1-7
[25] compiler_4.0.3 httr_1.4.2
[27] backports_1.2.1 assertthat_0.2.1
[29] Matrix_1.3-2 lazyeval_0.2.2
[31] htmltools_0.5.1 prettyunits_1.1.1
[33] tools_4.0.3 gtable_0.3.0
[35] glue_1.4.2 TFMPvalue_0.0.8
[37] GenomeInfoDbData_1.2.4 dplyr_1.0.2
[39] rappdirs_0.3.1 Rcpp_1.0.5
[41] Biobase_2.50.0 vctrs_0.3.6
[43] xfun_0.20 stringr_1.4.0
[45] lifecycle_0.2.0 ensembldb_2.14.0
[47] XML_3.99-0.5 zlibbioc_1.36.0
[49] MASS_7.3-53 scales_1.1.1
[51] VariantAnnotation_1.36.0 hms_1.0.0
[53] MatrixGenerics_1.2.0 ProtGenerics_1.22.0
[55] SummarizedExperiment_1.20.0 AnnotationFilter_1.14.0
[57] RColorBrewer_1.1-2 curl_4.3
[59] memoise_1.1.0 gridExtra_2.3
[61] ggplot2_3.3.3 biomaRt_2.46.0
[63] rpart_4.1-15 latticeExtra_0.6-29
[65] stringi_1.5.3 RSQLite_2.2.2
[67] checkmate_2.0.0 GenomicFeatures_1.42.1
[69] BiocParallel_1.24.1 repr_1.1.0
[71] rlang_0.4.10 pkgconfig_2.0.3
[73] matrixStats_0.57.0 bitops_1.0-6
[75] evaluate_0.14 lattice_0.20-41
[77] purrr_0.3.4 GenomicAlignments_1.26.0
[79] htmlwidgets_1.5.3 bit_4.0.4
[81] tidyselect_1.1.0 magrittr_2.0.1
[83] R6_2.5.0 generics_0.1.0
[85] Hmisc_4.4-2 pbdZMQ_0.3-4
[87] DelayedArray_0.16.0 DBI_1.1.0
[89] pillar_1.4.7 foreign_0.8-81
[91] survival_3.2-7 RCurl_1.98-1.2
[93] nnet_7.3-14 tibble_3.0.4
[95] crayon_1.3.4 uuid_0.1-4
[97] BiocFileCache_1.14.0 jpeg_0.1-8.1
[99] progress_1.2.2 data.table_1.13.6
[101] blob_1.2.1 digest_0.6.27
[103] openssl_1.4.3 munsell_0.5.0
[105] Gviz_1.34.0 askpass_1.1
