Multiple platform build/check report for BioC 3.6 - CHECK report for contiBAIT on tokay1

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### Running command:
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###   rm -rf contiBAIT.buildbin-libdir contiBAIT.Rcheck && mkdir contiBAIT.buildbin-libdir contiBAIT.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=contiBAIT.buildbin-libdir contiBAIT_1.6.0.tar.gz >contiBAIT.Rcheck\00install.out 2>&1 && cp contiBAIT.Rcheck\00install.out contiBAIT-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=contiBAIT.buildbin-libdir --install="check:contiBAIT-install.out" --force-multiarch --no-vignettes --timings contiBAIT_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.0'
* 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 'contiBAIT' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.4Mb
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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
clusterContigs.func : runOnce: no visible global function definition
  for 'runif'
locateMisorients.func: no visible global function definition for
  'unstrand'
makeBoxPlot.func: no visible global function definition for 'boxplot'
makeChrTable: no visible global function definition for 'queryHits'
makeChrTable: no visible global function definition for 'subjectHits'
mergeFlankedLGs.func: no visible binding for global variable 'head'
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for 'head'
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for 'tail'
plotContigOrder.func: no visible global function definition for 'lm'
plotLGDistances.func: no visible global function definition for
  'legend'
plotWCdistribution.func : <anonymous>: no visible global function
  definition for 'hist'
plotWCdistribution.func: no visible global function definition for
  'rbinom'
plotWCdistribution.func: no visible global function definition for
  'boxplot'
plotWCdistribution.func: no visible global function definition for
  'lines'
plotWCdistribution.func: no visible global function definition for
  'text'
clusterContigs,StrandStateMatrix : runOnce: no visible global function
  definition for 'runif'
locateMisorients,GRanges: no visible global function definition for
  'unstrand'
makeBoxPlot,ChrTable-LinkageGroupList: no visible global function
  definition for 'boxplot'
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix: no visible binding
  for global variable 'head'
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for 'head'
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for 'tail'
plotContigOrder,ContigOrdering: no visible global function definition
  for 'lm'
plotLGDistances,LinkageGroupList-StrandStateMatrix: no visible global
  function definition for 'legend'
plotWCdistribution,StrandFreqMatrix : <anonymous>: no visible global
  function definition for 'hist'
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for 'rbinom'
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for 'boxplot'
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for 'lines'
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for 'text'
show,ContigOrdering: no visible global function definition for 'head'
show,ContigOrdering: no visible global function definition for 'tail'
show,LibraryGroupList: no visible global function definition for 'head'
show,LibraryGroupList: no visible global function definition for 'tail'
show,LinkageGroupList: no visible global function definition for 'head'
show,LinkageGroupList: no visible global function definition for 'tail'
show,StrandStateList: no visible global function definition for 'head'
show,StrandStateList: no visible global function definition for 'tail'
Undefined global functions or variables:
  boxplot head hist legend lines lm queryHits rbinom runif subjectHits
  tail text unstrand
Consider adding
  importFrom("graphics", "boxplot", "hist", "legend", "lines", "text")
  importFrom("stats", "lm", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
* 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 ... OK
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.buildbin-libdir/contiBAIT/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'switch' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
           user system elapsed
contiBAIT 10.53   0.12   10.66
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'switch' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
contiBAIT 8.16   0.09    8.25
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'contiBAIT' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c computeSim.cpp -o computeSim.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o contiBAIT.dll tmp.def computeSim.o orderContigsGreedy.o -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.buildbin-libdir/contiBAIT/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'contiBAIT'
    finding HTML links ... done
    BAIT                                    html  
    ChrTable                                html  
    ContigOrdering                          html  
    LibraryGroupList                        html  
    LinkageGroupList                        html  
    OrientationFrame                        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  
    findSimilarLibraries                    html  
    fixLinkageGroups                        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
In R CMD INSTALL

install for x64

* installing *source* package 'contiBAIT' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c computeSim.cpp -o computeSim.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o contiBAIT.dll tmp.def computeSim.o orderContigsGreedy.o -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/contiBAIT.buildbin-libdir/contiBAIT/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'contiBAIT' as contiBAIT_1.6.0.zip
* DONE (contiBAIT)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for contiBAIT on tokay1

Summary

Command output

Installation output

Tests output

Example timings