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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:contiBAIT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings contiBAIT_1.23.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'contiBAIT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'contiBAIT' version '1.23.1'
* 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 whether package 'contiBAIT' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
See 'D:/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
* 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 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
ideogramPlot.func: no visible binding for global variable 'w'
ideogramPlot.func: no visible binding for global variable 'w2'
makeChrTable: no visible global function definition for 'queryHits'
makeChrTable: no visible global function definition for 'subjectHits'
orderContigsGreedy: no visible global function definition for
  'makeCluster'
orderContigsGreedy: no visible global function definition for
  'clusterCall'
orderContigsGreedy: no visible global function definition for
  'stopCluster'
strandSeqFreqTable: no visible global function definition for
  'queryHits'
strandSeqFreqTable: no visible global function definition for
  'subjectHits'
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
  binding for global variable 'w'
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
  binding for global variable 'w2'
Undefined global functions or variables:
  clusterCall makeCluster queryHits stopCluster subjectHits w w2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plotLGDistances,LinkageGroupList,StrandStateMatrix-method':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/contiBAIT/libs/x64/contiBAIT.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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
* 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: 2 WARNINGs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL contiBAIT
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'contiBAIT' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c buildLinkageGroups.cpp -o buildLinkageGroups.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeSim.cpp -o computeSim.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
  converting help for package 'contiBAIT'
    finding HTML links ... done
    BAIT                                    html  
    ChrTable                                html  
    ContigOrdering                          html  
    LibraryGroupList                        html  
    LinkageGroupList                        html  
    StrandFreqMatrix                        html  
    StrandReadMatrix                        html  
    StrandStateList                         html  
    StrandStateMatrix                       html  
    barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
                                            html  
    clusterContigs-StrandStateMatrix-method
                                            html  
    contiBAIT                               html  
    exampleChrTable                         html  
    exampleContigOrder                      html  
    exampleCrickFreq                        html  
    exampleDividedChr                       html  
    exampleLGList                           html  
    exampleLibList                          html  
    exampleReadCounts                       html  
    exampleStrandFreq                       html  
    exampleWCMatrix                         html  
    exampleWatsonFreq                       html  
    findSexGroups-LinkageGroupList-StrandStateMatrix-method
                                            html  
    findSimilarLibraries                    html  
    fixLinkageGroups                        html  
    flipOrderedLinkageGroups                html  
    highlightAssemblyErrors                 html  
    ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
                                            html  
    locateMisorients                        html  
    makeBoxPlot                             html  
    makeChrTable                            html  
    mapGapFromOverlap                       html  
    mergeFlankedLGs                         html  
    orderAllLinkageGroups                   html  
    orderContigsGreedy                      html  
    orderContigsTSP                         html  
    plotContigOrder                         html  
    plotLGDistances-LinkageGroupList-StrandStateMatrix-method
                                            html  
    plotWCdistribution-StrandFreqMatrix-method
                                            html  
    preprocessStrandTable-StrandFreqMatrix-method
                                            html  
    reorientAndMergeLGs                     html  
    show-ContigOrdering-method              html  
    show-LibraryGroupList-method            html  
    show-LinkageGroupList-method            html  
    show-OrientationFrame-method            html  
    show-StrandFreqMatrix-method            html  
    show-StrandReadMatrix-method            html  
    show-StrandStateList-method             html  
    show-StrandStateMatrix-method           html  
    strandSeqFreqTable                      html  
    thoroughBed                             html  
    writeBed                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path
* DONE (contiBAIT)
Making 'packages.html' ... done