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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: program compiled against libxml 212 using older 211
  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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.2Mb
    libs      3.6Mb
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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                18.064  2.040  20.505
plotRegions               17.997  1.466  19.593
countMatrix               15.571  1.168  18.673
regions                   10.347  1.029  12.440
srnadiff                   9.010  1.009  10.819
srnadiffDefaultParameters  9.089  0.866  10.487
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’