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

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### Running command:
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###   rm -rf Repitools.buildbin-libdir Repitools.Rcheck && mkdir Repitools.buildbin-libdir Repitools.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.24.0.tar.gz >Repitools.Rcheck\00install.out 2>&1 && cp Repitools.Rcheck\00install.out Repitools-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.24.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Repitools.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 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.24.0'
* 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 'Repitools' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwTwbGy/R.INSTALL398c42026767/Repitools/man/BAM2GRanges.Rd:27: missing file link 'ScanBamParam'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Repitools.Rcheck/00install.out' for details.
* 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 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
.cpgBoxplots: no visible global function definition for 'pdf'
.cpgBoxplots: no visible global function definition for 'par'
.cpgBoxplots: no visible global function definition for 'dev.off'
.diracBetaDirac: no visible global function definition for 'dbeta'
.doBiasPlot: no visible global function definition for 'plot'
.doBiasPlot: no visible global function definition for 'lines'
.doBiasPlot: no visible global function definition for 'lowess'
.doChrPlot: no visible global function definition for 'plot'
.doChrPlot: no visible global function definition for 'points'
.doChrPlot: no visible global function definition for 'abline'
.drawSegs : <anonymous>: no visible global function definition for
  'lines'
.makeClusters : clusterScores: no visible global function definition
  for 'embed'
.makeClusters : clusterScores: no visible global function definition
  for 'filter'
.methylEstbeta: no visible global function definition for 'qnorm'
.mydmarginal: no visible global function definition for 'dbeta'
.mydmarginalDBD: no visible global function definition for 'dbeta'
.plotFreqs: no visible global function definition for 'layout'
.plotFreqs : <anonymous>: no visible global function definition for
  'matplot'
.plotFreqs : <anonymous>: no visible global function definition for
  'abline'
.plotFreqs : <anonymous>: no visible global function definition for
  'legend'
determineOffset: no visible global function definition for 'par'
determineOffset: no visible global function definition for 'grid'
determineOffset: no visible global function definition for 'abline'
determineOffset: no visible global function definition for 'text'
getSampleOffsets: no visible global function definition for 'grid'
getSampleOffsets: no visible global function definition for 'abline'
loadPairFile: no visible global function definition for 'read.table'
plotQdnaByCN: no visible global function definition for 'layout'
plotQdnaByCN: no visible global function definition for 'grid'
plotQdnaByCN: no visible global function definition for 'abline'
plotQdnaByCN: no visible global function definition for 'plot'
processNDF: no visible global function definition for 'read.table'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for 'nbrOfArrays'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for 'extract'
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
  variable 'verbose'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for 'getCdf'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for 'extractMatrix'
.blocksStats,GRangesList-GRanges: no visible global function definition
  for 'p.adjust'
.blocksStats,matrix-GRanges: no visible global function definition for
  't.test'
.blocksStats,matrix-GRanges: no visible global function definition for
  'pt'
.blocksStats,matrix-GRanges: no visible global function definition for
  'p.adjust'
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for 'getCdf'
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
  variable 'verbose'
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for 'extractMatrix'
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
  global function definition for 'lm'
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
  global function definition for 'predict'
GCbiasPlots,AdjustedCopyEstimate: no visible global function definition
  for 'par'
GCbiasPlots,AdjustedCopyEstimate : <anonymous>: no visible global
  function definition for 'abline'
binPlots,ScoresList: no visible global function definition for 'par'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'layout'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'par'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'matplot'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'plot.new'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'legend'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'mtext'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'axis'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'plot'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'plot.window'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'text'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'title'
binPlots,ScoresList : <anonymous>: no visible global function
  definition for 'persp'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'par'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'matplot'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'axis'
checkProbes,GRanges-GRanges : <anonymous> : <anonymous>: no visible
  global function definition for 'matlines'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'plot'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'text'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'mtext'
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for 'abline'
chromosomeCNplots,AdjustedCopyEstimate: no visible global function
  definition for 'par'
chromosomeCNplots,CopyEstimate : <anonymous>: no visible global
  function definition for 'str'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'layout'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'par'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'plot.new'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'legend'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'matplot'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'axis'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'mtext'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'par'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'layout'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'matplot'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'axis'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'mtext'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'title'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'plot.new'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'plot.window'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'text'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'bxp'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'rect'
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for 'abline'
clusterPlots,ClusteredScoresList: no visible global function definition
  for 'plot'
clusterPlots,ScoresList: no visible global function definition for
  'kmeans'
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  'Arguments'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'pushState'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'popState'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'nbrOfArrays'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'getCdf'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'getMainCdf'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'nbrOfUnits'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'indexOf'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'enter'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'getCellIndices'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'exit'
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  'AromaCellSequenceFile'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'getChipType'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'countBases'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'extract'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'getNames'
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  'extractMatrix'
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  'AromaCellCpgFile'
cpgBoxplots,matrix: no visible binding for global variable 'Arguments'
cpgBoxplots,matrix: no visible global function definition for
  'pushState'
cpgBoxplots,matrix: no visible global function definition for
  'popState'
cpgBoxplots,matrix: no visible global function definition for 'enter'
cpgBoxplots,matrix: no visible global function definition for 'exit'
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
  for 'DNAString'
cpgDensityPlot,GRangesList: no visible global function definition for
  'rainbow'
cpgDensityPlot,GRangesList: no visible global function definition for
  'plot'
cpgDensityPlot,GRangesList: no visible global function definition for
  'lines'
cpgDensityPlot,GRangesList: no visible global function definition for
  'legend'
enrichmentPlot,GRangesList: no visible global function definition for
  'rainbow'
enrichmentPlot,GRangesList: no visible global function definition for
  'plot'
enrichmentPlot,GRangesList: no visible global function definition for
  'lines'
enrichmentPlot,GRangesList: no visible global function definition for
  'legend'
genQC,SequenceQCSet: no visible global function definition for
  'matplot'
genQC,SequenceQCSet: no visible global function definition for 'legend'
genQC,SequenceQCSet: no visible global function definition for 'par'
genQC,SequenceQCSet: no visible global function definition for 'layout'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'par'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'matplot'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'abline'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'plot.new'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'legend'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'barplot'
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for 'axis'
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for 'getCellIndices'
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
  variable 'AromaCellPositionFile'
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for 'getChipType'
plotClusters,GRanges : <anonymous>: no visible global function
  definition for 'par'
plotClusters,GRanges : <anonymous>: no visible global function
  definition for 'plot'
plotClusters,GRanges : <anonymous>: no visible global function
  definition for 'title'
plotClusters,GRanges : <anonymous>: no visible global function
  definition for 'mtext'
plotClusters,GRanges : <anonymous>: no visible global function
  definition for 'axis'
profilePlots,ScoresList: no visible global function definition for
  'rainbow'
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for 'matplot'
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for 'polygon'
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for 'legend'
regionStats,AffymetrixCelSet: no visible global function definition for
  'getCdf'
regionStats,AffymetrixCelSet: no visible global function definition for
  'getCellIndices'
regionStats,AffymetrixCelSet: no visible global function definition for
  'nbrOfArrays'
regionStats,AffymetrixCelSet: no visible binding for global variable
  'AromaCellPositionFile'
regionStats,AffymetrixCelSet: no visible global function definition for
  'getChipType'
regionStats,AffymetrixCelSet: no visible global function definition for
  'extract'
regionStats,AffymetrixCelSet: no visible global function definition for
  'extractMatrix'
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
  definition for 'matchPattern'
writeWig,AffymetrixCelSet: no visible global function definition for
  'getNames'
writeWig,AffymetrixCelSet: no visible global function definition for
  'extract'
writeWig,AffymetrixCelSet: no visible global function definition for
  'getCdf'
writeWig,AffymetrixCelSet: no visible global function definition for
  'extractMatrix'
Undefined global functions or variables:
  Arguments AromaCellCpgFile AromaCellPositionFile
  AromaCellSequenceFile DNAString abline axis barplot bxp countBases
  dbeta dev.off embed enter exit extract extractMatrix filter getCdf
  getCellIndices getChipType getMainCdf getNames grid indexOf kmeans
  layout legend lines lm lowess matchPattern matlines matplot mtext
  nbrOfArrays nbrOfUnits p.adjust par pdf persp plot plot.new
  plot.window points polygon popState predict pt pushState qnorm
  rainbow read.table rect str t.test text title verbose
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "bxp", "grid",
             "layout", "legend", "lines", "matlines", "matplot", "mtext",
             "par", "persp", "plot", "plot.new", "plot.window", "points",
             "polygon", "rect", "text", "title")
  importFrom("stats", "dbeta", "embed", "filter", "kmeans", "lm",
             "lowess", "p.adjust", "predict", "pt", "qnorm", "t.test")
  importFrom("utils", "read.table", "str")
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/Repitools.buildbin-libdir/Repitools/libs/i386/Repitools.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. 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' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
methylEst         96.77   0.02   96.79
empBayes          38.52   2.23   40.75
cpgDensityCalc     9.01   0.53   19.47
sequenceCalc       8.91   0.53    9.44
BayMethList-class  8.52   0.56   10.46
determineOffset    6.10   0.41    6.50
maskOut            6.36   0.08    6.43
gcContentCalc      4.83   0.53    5.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
methylEst         73.03   0.33   73.38
empBayes          38.38   1.97   40.36
BayMethList-class 13.82   0.40   14.22
sequenceCalc      11.22   0.68   11.92
cpgDensityCalc     9.86   0.75   10.60
determineOffset    9.41   0.72   10.13
maskOut            7.33   0.13    7.45
gcContentCalc      5.82   0.40    6.22
cpgDensityPlot     4.81   0.53    5.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'tests.R'
 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Repitools.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'Repitools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=generic -c const.c -o const.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:101:0: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
 #define SING  _SING
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:104:0: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:105:0: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 ^
In file included from mtherr.c:58:0:
./mconf.h:101:0: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
 #define SING  _SING
 ^
In file included from mtherr.c:58:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 ^
In file included from mtherr.c:58:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 ^
In file included from mtherr.c:58:0:
./mconf.h:104:0: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 ^
In file included from mtherr.c:58:0:
./mconf.h:105:0: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -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/Repitools.buildbin-libdir/Repitools/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'windows' in package 'Repitools'
** help
*** installing help indices
  converting help for package 'Repitools'
    finding HTML links ... done
    AdjustedCopyEstimate-class              html  
    finding level-2 HTML links ... done

    AffymetrixCdfFile-class                 html  
    AffymetrixCelSet-class                  html  
    BAM2GRanges                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwTwbGy/R.INSTALL398c42026767/Repitools/man/BAM2GRanges.Rd:27: missing file link 'ScanBamParam'
    BayMethList-class                       html  
    ChromaBlocks                            html  
    ChromaResults-class                     html  
    ClusteredScoresList-class               html  
    CopyEstimate-class                      html  
    FastQC-class                            html  
    GCAdjustParams-class                    html  
    GCadjustCopy                            html  
    GCbiasPlots                             html  
    MappabilitySource-class                 html  
    QdnaData                                html  
    ScoresList-class                        html  
    abcdDNA                                 html  
    absoluteCN                              html  
    annoDF2GR                               html  
    annoGR2DF                               html  
    annotationBlocksCounts                  html  
    annotationBlocksLookup                  html  
    annotationCounts                        html  
    annotationLookup                        html  
    binPlots                                html  
    blocksStats                             html  
    checkProbes                             html  
    chr21genes                              html  
    chromosomeCNplots                       html  
    clusterPlots                            html  
    cpgBoxPlots                             html  
    cpgDensityCalc                          html  
    cpgDensityPlot                          html  
    determineOffset                         html  
    empBayes                                html  
    enrichmentCalc                          html  
    enrichmentPlot                          html  
    expr                                    html  
    featureBlocks                           html  
    featureScores                           html  
    findClusters                            html  
    gcContentCalc                           html  
    genQC                                   html  
    genomeBlocks                            html  
    getProbePositionsDf                     html  
    getSampleOffsets                        html  
    hcRegions                               html  
    hyper                                   html  
    loadPairFile                            html  
    loadSampleDirectory                     html  
    makeWindowLookupTable                   html  
    mappabilityCalc                         html  
    maskOut                                 html  
    mergeReplicates                         html  
    methylEst                               html  
    multiHeatmap                            html  
    plotClusters                            html  
    plotQdnaByCN                            html  
    processNDF                              html  
    profilePlots                            html  
    regionStats                             html  
    relativeCN                              html  
    samplesList                             html  
    sequenceCalc                            html  
    setCNVOffsets                           html  
    summarizeScores                         html  
    writeWig                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Repitools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=generic -c const.c -o const.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:101:0: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
 #define SING  _SING
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:104:0: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 ^
In file included from hyp2f1.c:81:0:
./mconf.h:105:0: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rmath.h:45:0,
                 from hyp2f1.c:80:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 ^
In file included from mtherr.c:58:0:
./mconf.h:101:0: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
 #define SING  _SING
 ^
In file included from mtherr.c:58:0:
./mconf.h:102:0: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 ^
In file included from mtherr.c:58:0:
./mconf.h:103:0: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 ^
In file included from mtherr.c:58:0:
./mconf.h:104:0: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 ^
In file included from mtherr.c:58:0:
./mconf.h:105:0: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:58:0,
                 from mtherr.c:56:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -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/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.24.0.zip
* DONE (Repitools)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("Repitools")
Loading required package: Repitools
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'Repitools'

The following object is masked from 'package:grDevices':

    windows

> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:Repitools':

    blocks

> options(warn = -1)
> 
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
> 
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
> 
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch))) 
+ 	stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
> 
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
> 
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+     stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
> 
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+     stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+     stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+     stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+     stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
> 
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+     stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
> 
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+     stop("Error in sequenceCalc function counting task")
> 
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+     stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
> 
> proc.time()
   user  system elapsed 
 105.98    7.84  118.15

CHECK report for Repitools on tokay1

Summary

Command output

Installation output

Tests output

Example timings