##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:batchelor.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings batchelor_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/batchelor.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'batchelor/DESCRIPTION' ... OK
* this is package 'batchelor' version '1.23.0'
* 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 whether package 'batchelor' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 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 ... 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 ... OK
* checking whether the namespace can be unloaded cleanly ... 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:
  BatchelorParam.Rd: SimpleList-class
  applyMultiSCE.Rd: applySCE, SingleCellExperiment,
    SingleCellExperiment-class, altExps, simplifyToSCE
  batchCorrect.Rd: SingleCellExperiment-class
  checkInputs.Rd: SingleCellExperiment-class
  clusterMNN.Rd: SingleCellExperiment-class, BiocSingularParam-class,
    BiocNeighborParam-class, BiocParallelParam-class, colData, metadata
  convertPCsToSCE.Rd: SingleCellExperiment-class, DataFrame-class,
    metadata, reducedDims, LowRankMatrix-class, colData, rowData
  correctExperiments.Rd: SingleCellExperiment-class, rowRanges,
    colData, mcols, assays, reducedDims, rowData, metadata
  cosineNorm.Rd: BiocParallelParam-class, DelayedArray-class,
    DelayedMatrix-class
  diagnostics-cluster.Rd: normalizeCounts
  fastMNN.Rd: SingleCellExperiment-class, BiocSingularParam-class,
    BiocNeighborParam-class, BiocParallelParam-class, DataFrame-class,
    List-class, altExps
  intersectRows.Rd: SingleCellExperiment-class
  mnnCorrect.Rd: SingleCellExperiment-class, BiocSingularParam-class,
    BiocNeighborParam-class, BiocParallelParam-class, List-class
  mnnDeltaVariance.Rd: SingleCellExperiment-class, DataFrame-class,
    BiocParallelParam-class, metadata
  multiBatchNorm.Rd: SingleCellExperiment-class,
    BiocParallelParam-class, logNormCounts, altExps
  multiBatchPCA.Rd: SingleCellExperiment-class,
    BiocSingularParam-class, runSVD, BiocParallelParam-class,
    List-class, IrlbaParam, RandomParam, bsdeferred
  noCorrect.Rd: SingleCellExperiment-class, colData
  quickCorrect.Rd: SingleCellExperiment-class, DataFrame,
    DataFrame-class
  reducedMNN.Rd: BiocNeighborParam-class, BiocParallelParam-class,
    DataFrame-class
  regressBatches.Rd: SingleCellExperiment-class, ResidualMatrix,
    BiocSingularParam-class, BiocParallelParam-class,
    ResidualMatrix-class, reducedDims, altExps
  rescaleBatches.Rd: SingleCellExperiment-class, altExps
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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/batchelor/libs/x64/batchelor.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
correctExperiments 8.03   0.12    8.16
applyMultiSCE      5.78   0.23    6.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/batchelor.Rcheck/00check.log'
for details.