##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chipseq.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings chipseq_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/chipseq.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'chipseq/DESCRIPTION' ... OK
* this is package 'chipseq' version '1.49.0'
* 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 'chipseq' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'IRanges' 'GenomicRanges' 'ShortRead'
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 R 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 ... NOTE
.genomicContext: no visible global function definition for
  'transcripts'
.genomicContext: no visible global function definition for 'cdsBy'
.genomicContext: no visible global function definition for
  'threeUTRsByTranscript'
.genomicContext: no visible global function definition for
  'fiveUTRsByTranscript'
.genomicContext: no visible global function definition for
  'intronsByTranscript'
.nearestTss: no visible global function definition for 'transcripts'
.nearestTss: no visible global function definition for 'seqlevels<-'
.nearestTss: no visible global function definition for 'seqlevels'
applyPosByChrAndStrand: no visible global function definition for
  'seqnames'
correlation.estimate: no visible binding for global variable 'mu'
correlation.estimate: no visible binding for global variable 'corr'
correlationProfile : <anonymous>: no visible global function definition
  for 'subseq'
coverage.estimate: no visible binding for global variable 'mu'
coverage.estimate: no visible binding for global variable 'covered'
islandDepthPlot: no visible binding for global variable 'depth'
islandDepthPlot : <anonymous>: no visible global function definition
  for 'panel.lines'
islandDepthPlot : <anonymous>: no visible global function definition
  for 'panel.xyplot'
laneSubsample: no visible global function definition for 'seqnames'
laneSubsample: no visible global function definition for 'GRangesList'
subsetSummary: no visible global function definition for 'seqlengths'
subsetSummary: no visible global function definition for 'GRanges'
subsetSummary: no visible global function definition for 'seqnames'
subsetSummary: no visible global function definition for 'seqlengths<-'
diffPeakSummary,RleViewsList-RleViewsList: no visible global function
  definition for 'GRanges'
estimate.mean.fraglen,GRanges: no visible global function definition
  for 'seqnames'
peakSummary,RleViewsList: no visible global function definition for
  'GRanges'
Undefined global functions or variables:
  GRanges GRangesList cdsBy corr covered depth fiveUTRsByTranscript
  intronsByTranscript mu panel.lines panel.xyplot seqlengths
  seqlengths<- seqlevels seqlevels<- seqnames subseq
  threeUTRsByTranscript transcripts
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'densityCorr' and siglist 'GenomicRanges'
  generic 'densityCorr' and siglist 'list'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estimate.mean.fraglen':
densityCorr
  Code: function(x, ...)
  Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width =
                 seqLen * 2L, seqLen = 100L, maxDist = 500L, ...)
  Argument names in docs not in code:
    shift center width seqLen maxDist
  Mismatches in argument names:
    Position: 2 Code: ... Docs: shift

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: 'BSgenome.Mmusculus.UCSC.mm9'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 'F:/biocbuild/bbs-3.17-bioc/R/library/chipseq/libs/x64/chipseq.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/chipseq.Rcheck/00check.log'
for details.