'min.cushion' object not found #163
Description
Hi All,
I updated gGnome to the latest version just now (af4ba04 commit), as well as gUtils (fc24db6 commit), and I am now getting an "Error: object 'min.cushion' not found" error when trying to run events(). This results in the events metadata not even being generated. This occurs not only with my jabba.rds files, but also when trying to use the gGnome tutorial code. Do you know why this is the case and if this could be fixed?
Testing Tutorial Code:
> hcc1954 = gG(jabba = system.file("extdata", "hcc1954", "jabba.rds", package = "gGnome"))
> hcc1954 = events(hcc1954, verbose = TRUE)
Finished simple
Finished amp (tyfonas, dm, cpxdm, bfb)
Finished chromothripsis
Finished del
Finished dup
Finished chromoplexy
Error: object 'min.cushion' not found
In addition: There were 40 warnings (use warnings() to see them)
Testing My Own Jabba.rds
> jabba <- readRDS("/path/to/jabba.rds")
> gg <- gG(jabba = jabba)
> gg <- events(gg, verbose = TRUE)
Finished simple
Finished amp (tyfonas, dm, cpxdm, bfb)
Finished chromothripsis
Finished del
Loading required package: MASS
Finished dup
Finished chromoplexy
Error: object 'min.cushion' not found
In addition: There were 21 warnings (use warnings() to see them)
Sys.info():
sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Indiana/Indianapolis
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] MASS_7.3-65 gGnome_0.1 reshape2_1.4.4 gTrack_0.1.0 gUtils_0.2.0
[6] GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0
[11] Matrix_1.7-2 igraph_2.1.4 data.table_1.17.0 remotes_2.5.0 testthat_3.2.3
[16] devtools_2.4.5 usethis_3.1.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 rlang_1.1.5 magrittr_2.0.3
[5] RSQLite_2.3.9 matrixStats_1.5.0 compiler_4.4.2 GenomicFeatures_1.58.0
[9] png_0.1-8 callr_3.7.6 vctrs_0.6.5 stringr_1.5.1
[13] profvis_0.4.0 pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[17] XVector_0.46.0 ellipsis_0.3.2 Rsamtools_2.22.0 promises_1.3.2
[21] sessioninfo_1.2.3 UCSC.utils_1.2.0 ps_1.9.0 bit_4.5.0.1
[25] purrr_1.0.4 zlibbioc_1.52.0 cachem_1.1.0 jsonlite_1.9.1
[29] blob_1.2.4 later_1.4.1 DelayedArray_0.32.0 BiocParallel_1.40.0
[33] parallel_4.4.2 R6_2.6.1 VariantAnnotation_1.52.0 stringi_1.8.4
[37] rtracklayer_1.66.0 pkgload_1.4.0 brio_1.1.5 Rcpp_1.0.14
[41] SummarizedExperiment_1.36.0 zoo_1.8-13 httpuv_1.6.15 tidyselect_1.2.1
[45] rstudioapi_0.17.1 abind_1.4-8 yaml_2.3.10 codetools_0.2-20
[49] miniUI_0.1.1.1 curl_6.2.1 processx_3.8.6 pkgbuild_1.4.6
[53] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9 KEGGREST_1.46.0
[57] Biobase_2.66.0 shiny_1.10.0 desc_1.4.3 urlchecker_1.0.1
[61] Biostrings_2.74.1 pillar_1.10.1 MatrixGenerics_1.18.1 plotly_4.10.4
[65] generics_0.1.3 RCurl_1.98-1.16 ggplot2_3.5.1 munsell_0.5.1
[69] scales_1.3.0 xtable_1.8-4 fishHook_0.1 glue_1.8.0
[73] lazyeval_0.2.2 tools_4.4.2 BiocIO_1.16.0 BSgenome_1.74.0
[77] GenomicAlignments_1.42.0 fs_1.6.5 XML_3.99-0.18 grid_4.4.2
[81] tidyr_1.3.1 AnnotationDbi_1.68.0 colorspace_2.1-1 GenomeInfoDbData_1.2.13
[85] restfulr_0.0.15 cli_3.6.4 S4Arrays_1.6.0 viridisLite_0.4.2
[89] dplyr_1.1.4 gtable_0.3.6 digest_0.6.37 SparseArray_1.6.2
[93] rjson_0.2.23 htmlwidgets_1.6.4 memoise_2.0.1 htmltools_0.5.8.1
[97] lifecycle_1.0.4 httr_1.4.7 mime_0.12 bit64_4.6.0-1
Thanks!
Sincerely,
Manoj