[Bioc-devel] RangedData objects deprecated

[Brent O'Carrigan]

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.OCarrigan using cruk.cam.ac.uk<mailto:Brent.OCarrigan using 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