Dear Bioc devel team, Can you advise how to amend the following code to update references to RangedData objects?
I’m running the Broad ichorCNA, which had a similar issue described in the package internal code, which I gather has been addressed https://github.com/broadinstitute/ichorCNA/issues/50 A colleague has written a wrapper script in part of our shared pipeline, which I think was under R 3.5.3, and I think the RangedData references in this script may need updating - which I have not been able to do. Kind regards, Dr Brent O'Carrigan Clinical Research Training Fellow | PhD candidate CRUK Cambridge Institute | Caldas Group Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE E: brent.ocarri...@cruk.cam.ac.uk<mailto:brent.ocarri...@cruk.cam.ac.uk> | T: (+44) 01223 769500 > source('make.ichor.summary.R') data.table 1.12.6 using 10 threads (see ?getDTthreads). Latest news: r-datatable.com Loading required package: HMMcopy Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:base’: expand.grid Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Loading required package: geneplotter Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: lattice Loading required package: annotate Loading required package: AnnotationDbi Loading required package: XML Loading required package: ichorCNA Attaching package: ‘ichorCNA’ The following object is masked from ‘package:HMMcopy’: HMMsegment Loading required package: GenomicRanges Loading required package: GenomeInfoDb [1] "./ichor/ichor.default/raw/041V10.sorted.dedupped.RDS" [1] "Running ichorCNA" Error: RangedData objects are deprecated and the colnames setter for RangedData objects is now defunct. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData In addition: Warning messages: 1: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 2: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 3: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 4: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 5: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 6: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 7: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData 8: RangedData objects are deprecated. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /home/bioinformatics/software/R/R-3.6.1/lib64/R/lib/libRblas.so LAPACK: /home/bioinformatics/software/R/R-3.6.1/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 ichorCNA_0.3.2 [4] HMMcopy_1.26.0 geneplotter_1.64.0 annotate_1.64.0 [7] XML_3.98-1.20 AnnotationDbi_1.48.0 lattice_0.20-38 [10] Biobase_2.46.0 IRanges_2.20.0 S4Vectors_0.24.0 [13] BiocGenerics_0.32.0 data.table_1.12.6 loaded via a namespace (and not attached): [1] Rcpp_1.0.3 pillar_1.4.2 compiler_3.6.1 [4] RColorBrewer_1.1-2 plyr_1.8.4 XVector_0.26.0 [7] zlibbioc_1.32.0 bitops_1.0-6 zeallot_0.1.0 [10] digest_0.6.23 bit_1.1-14 RSQLite_2.1.3 [13] memoise_1.1.0 tibble_2.1.3 pkgconfig_2.0.3 [16] rlang_0.4.2 DBI_1.0.0 GenomeInfoDbData_1.2.2 [19] vctrs_0.2.0 bit64_0.9-7 grid_3.6.1 [22] blob_1.2.0 backports_1.1.5 xtable_1.8-4 [25] RCurl_1.95-4.12 crayon_1.3.4 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel