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Error RangedData objects are deprecated #7

Closed step1xiao closed 5 years ago

step1xiao commented 5 years ago

Hi, My R version is 3.6 and bioconductor is the latest version, I run into this error:

command: Rscript --default-packages=methods,datasets,utils,grDevices,graphics,stats ReadInBams.R --bams bam --bed step1.bed.txt --fasta hg19.fa --out results

error: [1] "BEGIN ReadInBams.R" Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help. Registered S3 method overwritten by 'R.oo': method from
throw.default R.methodsS3 R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, gc, load, save

R.utils v2.9.0 successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

[1] "bam" Error: RangedData objects are deprecated and the rownames 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 Execution halted

Thanks in advance!