##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:csaw.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings csaw_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/csaw.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘csaw/DESCRIPTION’ ... OK
* this is package ‘csaw’ version ‘1.41.1’
* 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 ‘csaw’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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:
  SEmethods.Rd: DGEList
  calculateCPM.Rd: scaleOffset, addPriorCount
  checkBimodality.Rd: BamFile-class, GenomicRanges-class,
    BiocParallelParam-class
  clusterWindows.Rd: GRanges-class, RangedSummarizedExperiment-class,
    GRanges, DataFrame-class
  clusterWindowsList.Rd: GRanges-class,
    RangedSummarizedExperiment-class
  combineTests.Rd: DataFrame-class, groupedSimes, glmQLFTest
  correlateReads.Rd: BamFile-class, BiocParallelParam-class
  detailRanges.Rd: GRanges-class
  empiricalFDR.Rd: DataFrame-class
  extractReads.Rd: BamFile-class, GRanges-class, GRangesList-class
  filterWindows.Rd: RangedSummarizedExperiment-class, rowRanges,
    resize, aveLogCPM
  findMaxima.Rd: aveLogCPM
  getBestTest.Rd: DataFrame-class, glmQLFTest
  mergeResults.Rd: GRanges-class, RangedSummarizedExperiment-class,
    findOverlaps, DataFrame-class, Hits-class
  mergeResultsList.Rd: GRanges-class, RangedSummarizedExperiment-class,
    mcols, findOverlaps, DataFrame-class, Hits-class
  mergeWindows.Rd: GRanges-class, RangedSummarizedExperiment-class
  mergeWindowsList.Rd: RangedSummarizedExperiment-class, GRanges-class,
    findOverlaps, Hits-class
  minimalTests.Rd: DataFrame-class, groupedHolmMin, glmQLFTest
  mixedTests.Rd: glmTreat, DataFrame-class
  normFactors.Rd: SummarizedExperiment-class, colData, DGEList,
    calcNormFactors
  normOffsets.Rd: SummarizedExperiment-class, colData, DGEList,
    loessFit, normalizeCyclicLoess
  overlapStats.Rd: Hits-class, findOverlaps,
    RangedSummarizedExperiment-class, DataFrame-class
  profileSites.Rd: BamFile-class, GenomicRanges-class,
    BiocParallelParam-class
  readParam.Rd: GRanges-class, BiocParallelParam
  regionCounts.Rd: BamFile-class, GenomicRanges-class,
    BiocParallelParam-class, countOverlaps,
    RangedSummarizedExperiment-class
  scaledAverage.Rd: SummarizedExperiment-class, aveLogCPM,
    addPriorCount, aveLogCPM.DGEList
  strandedCounts.Rd: BamFile-class
  windowCounts.Rd: BamFile-class, BiocParallelParam-class,
    RangedSummarizedExperiment-class
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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/csaw/libs/csaw.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)

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
detailRanges 13.467  0.559  14.163
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/csaw.Rcheck/00check.log’
for details.