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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:minfi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings minfi_1.53.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/minfi.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 ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.53.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘minfi’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/minfi.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::get_verbose_block_processing’
  ‘DelayedArray:::normarg_grid’ ‘bumphunter:::.getEstimate’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.guessArrayTypes’
* 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
Found the following possibly unsafe calls:
File ‘minfi/R/IlluminaMethylationManifest-class.R’:
  unlockBinding(name, env = object@data)

Warning: program compiled against libxml 212 using older 211
* checking Rd files ... NOTE
checkRd: (-1) gaphunter.Rd:19: Lost braces
    19 |     If one of the first two, code{\link{getBeta}} is used to calculate beta values. If a
       |                                  ^
checkRd: (-1) ratioConvert-methods.Rd:35: Lost braces
    35 |   \code{\link{RatioSet}} or code{\link{GenomicRatioSet}} for the output
       |                                 ^
checkRd: (-1) ratioConvert-methods.Rd:36: Lost braces
    36 |   object and \code{\link{MethylSet}} or code{\link{GenomicMethylSet}}
       |                                             ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MethylSet-class.Rd: eSet-class
  RGChannelSet-class.Rd: SummarizedExperiment-class
  RatioSet-class.Rd: eSet-class
  blockFinder.Rd: clusterMaker, bumphunter
  bumphunter.Rd: clusterMaker
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
combineArrays                     73.232  1.724  79.917
bumphunter                        34.265  0.546  36.335
read.metharray.exp                 9.656  0.033  10.555
read.metharray                     6.140  0.064   6.922
preprocessIllumina                 5.891  0.056   6.132
IlluminaMethylationManifest-class  5.341  0.207   5.660
densityPlot                        5.024  0.052   5.534
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/minfi.Rcheck/00check.log’
for details.