tanasa
commented
7 months ago I take the question back ; the events() function works in R 4.1.3 :
sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS
Matrix products: default BLAS/LAPACK: /home/tanasab/miniconda3/lib/libopenblasp-r0.3.21.so
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 stats graphics grDevices utils datasets methods [8] base
other attached packages: [1] MASS_7.3-58.3 gGnome_0.1 reshape2_1.4.4 [4] gTrack_0.1.0 gUtils_0.2.0 GenomicRanges_1.46.1 [7] GenomeInfoDb_1.35.16 IRanges_2.28.0 S4Vectors_0.32.4 [10] BiocGenerics_0.40.0 Matrix_1.5-3 igraph_1.4.2 [13] data.table_1.14.8
loaded via a namespace (and not attached): [1] MatrixGenerics_1.6.0 Biobase_2.54.0 [3] httr_1.4.5 tidyr_1.3.0 [5] bit64_4.0.5 jsonlite_1.8.4 [7] viridisLite_0.4.1 BiocFileCache_2.2.0 [9] blob_1.2.4 BSgenome_1.62.0 [11] GenomeInfoDbData_1.2.7 Rsamtools_2.10.0 [13] progress_1.2.2 yaml_2.3.7 [15] pillar_1.8.1 RSQLite_2.3.0 [17] lattice_0.20-45 glue_1.6.2 [19] digest_0.6.31 XVector_0.34.0 [21] colorspace_2.1-0 htmltools_0.5.4 [23] plyr_1.8.8 XML_3.99-0.14 [25] pkgconfig_2.0.3 biomaRt_2.50.0 [27] zlibbioc_1.40.0 purrr_1.0.1 [29] fishHook_0.1 scales_1.2.1 [31] BiocParallel_1.28.3 tibble_3.2.1 [33] KEGGREST_1.34.0 generics_0.1.3 [35] ggplot2_3.4.1 cachem_1.0.7 [37] SummarizedExperiment_1.24.0 GenomicFeatures_1.46.1 [39] lazyeval_0.2.2 cli_3.6.0 [41] magrittr_2.0.3 crayon_1.5.2 [43] memoise_2.0.1 fansi_1.0.4 [45] xml2_1.3.3 prettyunits_1.1.1 [47] tools_4.1.3 hms_1.1.3 [49] BiocIO_1.4.0 lifecycle_1.0.3 [51] matrixStats_0.63.0 stringr_1.5.0 [53] plotly_4.10.1 munsell_0.5.0 [55] DelayedArray_0.20.0 AnnotationDbi_1.56.2 [57] Biostrings_2.62.0 compiler_4.1.3 [59] rlang_1.1.0 grid_4.1.3 [61] RCurl_1.98-1.10 rappdirs_0.3.3 [63] VariantAnnotation_1.40.0 rjson_0.2.21 [65] htmlwidgets_1.6.2 bitops_1.0-7 [67] restfulr_0.0.15 gtable_0.3.3 [69] curl_4.3.3 DBI_1.1.3 [71] R6_2.5.1 GenomicAlignments_1.30.0 [73] zoo_1.8-12 dplyr_1.1.0 [75] rtracklayer_1.54.0 fastmap_1.1.1 [77] bit_4.0.5 utf8_1.2.3 [79] filelock_1.0.2 stringi_1.7.12 [81] parallel_4.1.3 Rcpp_1.0.10 [83] png_0.1-8 vctrs_0.6.0 [85] dbplyr_2.3.2 tidyselect_1.2.0
Dear all,
Please allow me to post this error on JaBaA github page, although it refers to gGnome package: I am following the manual, and I am getting the following error when I call the events() function :
hcc1954 = gG(jabba = system.file("extdata", "hcc1954", "jabba.rds", package = "gGnome")) hcc1954 = events(hcc1954) Finished simple Finished amp (tyfonas, dm, cpxdm, bfb) Finished chromothripsis Error in aggregate.formula(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin - : argument 'x' is missing -- it has been renamed from 'formula' In addition: There were 18 warnings (use warnings() to see them)
Any suggestions on how I could fix it ?
Session.Info() gives a long list of packages :
_sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur ... 10.16
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base
other attached packages: [1] MASS_7.3-58.1 gGnome_0.1 reshape2_1.4.4 [4] gTrack_0.1.0 gUtils_0.2.0 GenomicRanges_1.48.0 [7] GenomeInfoDb_1.35.16 IRanges_2.30.1 S4Vectors_0.34.0 [10] BiocGenerics_0.42.0 Matrix_1.5-3 igraph_1.3.5 [13] data.table_1.14.6
loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.63.0 [3] bit64_4.0.5 filelock_1.0.2 [5] progress_1.2.2 httr_1.4.4 [7] tools_4.2.2 utf8_1.2.2 [9] R6_2.5.1 DBI_1.1.3 [11] lazyeval_0.2.2 colorspace_2.1-0 [13] tidyselect_1.2.0 prettyunits_1.1.1 [15] bit_4.0.5 curl_5.0.0 [17] compiler_4.2.2 cli_3.6.0 [19] Biobase_2.56.0 xml2_1.3.3 [21] DelayedArray_0.22.0 plotly_4.10.1 [23] rtracklayer_1.56.1 scales_1.2.1 [25] rappdirs_0.3.3 stringr_1.5.0 [27] digest_0.6.31 Rsamtools_2.12.0 [29] XVector_0.36.0 pkgconfig_2.0.3 [31] htmltools_0.5.4 MatrixGenerics_1.8.1 [33] dbplyr_2.3.0 fastmap_1.1.0 [35] BSgenome_1.67.4 htmlwidgets_1.6.1 [37] rlang_1.1.2 RSQLite_2.2.20 [39] BiocIO_1.6.0 generics_0.1.3 [41] zoo_1.8-11 jsonlite_1.8.4 [43] BiocParallel_1.30.4 dplyr_1.1.0 [45] VariantAnnotation_1.42.1 RCurl_1.98-1.9 [47] magrittr_2.0.3 GenomeInfoDbData_1.2.8 [49] fishHook_0.1 Rcpp_1.0.10 [51] munsell_0.5.0 fansi_1.0.4 [53] lifecycle_1.0.3 stringi_1.7.12 [55] yaml_2.3.7 SummarizedExperiment_1.26.1 [57] zlibbioc_1.42.0 plyr_1.8.9 [59] BiocFileCache_2.4.0 grid_4.2.2 [61] blob_1.2.3 parallel_4.2.2 [63] crayon_1.5.2 lattice_0.20-45 [65] Biostrings_2.64.1 GenomicFeatures_1.48.4 [67] hms_1.1.2 KEGGREST_1.36.3 [69] pillar_1.8.1 rjson_0.2.21 [71] codetools_0.2-18 biomaRt_2.52.0 [73] XML_3.99-0.13 glue_1.6.2 [75] png_0.1-8 vctrs_0.6.5 [77] gtable_0.3.1 purrr_1.0.1 [79] tidyr_1.3.0 assertthat_0.2.1 [81] cachem_1.0.6 ggplot2_3.4.1 [83] restfulr_0.0.15 viridisLite_0.4.1 [85] tibble_3.2.1 GenomicAlignments_1.32.1 [87] AnnotationDbi_1.58.0 memoise2.0.1