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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings srnadiff_1.27.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/srnadiff.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘srnadiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘srnadiff’ version ‘1.27.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘srnadiff’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
  Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
  Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
  Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
  Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
  Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
  Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
  Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
  Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
  Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
  Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
  Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
See ‘/home/biocbuild/bbs-3.21-bioc/meat/srnadiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocManager’ ‘BiocStyle’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotRegions.Rd: GenomeAxisTrack, GeneRegionTrack, AnnotationTrack,
    DataTrack
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
parameters                12.236  3.157  13.799
plotRegions               12.892  2.268  14.339
countMatrix               11.327  1.533  11.977
regions                    7.422  1.440   8.066
srnadiff                   6.273  2.236   7.679
srnadiffDefaultParameters  6.248  1.647   7.140
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’