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BioC 3.4: CHECK report for Repitools on moscato1

This page was generated on 2016-09-21 03:43:30 -0700 (Wed, 21 Sep 2016).

Package 1006/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Repitools 1.19.2
Mark Robinson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools
Last Changed Rev: 120561 / Revision: 121152
Last Changed Date: 2016-08-29 18:00:07 -0700 (Mon, 29 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Repitools
Version: 1.19.2
Command: rm -rf Repitools.buildbin-libdir Repitools.Rcheck && mkdir Repitools.buildbin-libdir Repitools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.19.2.tar.gz >Repitools.Rcheck\00install.out 2>&1 && cp Repitools.Rcheck\00install.out Repitools-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.19.2.tar.gz
StartedAt: 2016-09-20 15:13:37 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:31:25 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1067.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Repitools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Repitools.buildbin-libdir Repitools.Rcheck && mkdir Repitools.buildbin-libdir Repitools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Repitools.buildbin-libdir Repitools_1.19.2.tar.gz >Repitools.Rcheck\00install.out 2>&1 && cp Repitools.Rcheck\00install.out Repitools-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Repitools.buildbin-libdir --install="check:Repitools-install.out" --force-multiarch --no-vignettes --timings Repitools_1.19.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Repitools.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.19.2'
* 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 ... OK
* 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 'D:/biocbld/bbs-3.4-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 the system RNG.
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         107.67   0.10  107.79
empBayes           51.34   1.14   52.48
cpgDensityCalc      9.89   0.55   28.74
BayMethList-class   9.81   0.36   11.37
sequenceCalc        9.50   0.26    9.76
determineOffset     6.42   0.31    6.72
maskOut             5.35   0.03    5.39
cpgDensityPlot      4.85   0.17    5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
methylEst         98.58   0.02   98.62
empBayes          44.31   1.03   45.34
BayMethList-class 10.19   0.33   10.51
cpgDensityCalc     9.08   0.51    9.59
sequenceCalc       9.25   0.34    9.59
determineOffset    6.72   0.30    7.02
maskOut            5.54   0.08    5.61
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/Repitools.Rcheck/00check.log'
for details.


Repitools.Rcheck/00install.out:


install for i386

* installing *source* package 'Repitools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -c const.c -o const.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -D R_NO_REMAP -I.    -O3 -Wall  -std=gnu99 -mtune=core2 -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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Repitools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -c const.c -o const.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/Rmath.h:48:0,
                 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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mtune=core2 -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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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 D:/biocbld/BBS-3˜1.4-B/R/include/R.h:48:0,
                 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/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.19.2.zip
* DONE (Repitools)

Repitools.Rcheck/examples_i386/Repitools-Ex.timings:

nameusersystemelapsed
BAM2GRanges0.440.000.53
BayMethList-class 9.81 0.3611.37
GCadjustCopy000
GCbiasPlots000
QdnaData0.130.000.12
abcdDNA000
absoluteCN0.000.010.02
annoDF2GR0.010.000.01
annoGR2DF0.080.030.11
annotationBlocksCounts0.140.020.15
annotationBlocksLookup0.040.000.03
annotationCounts0.150.000.15
annotationLookup0.080.000.08
binPlots1.890.222.11
blocksStats0.20.00.2
checkProbes0.170.000.19
chromosomeCNplots000
clusterPlots1.330.041.37
cpgDensityCalc 9.89 0.5528.74
cpgDensityPlot4.850.175.03
determineOffset6.420.316.72
empBayes51.34 1.1452.48
enrichmentCalc2.040.032.07
enrichmentPlot1.840.001.84
featureBlocks0.010.000.02
featureScores1.060.001.06
findClusters1.840.021.86
gcContentCalc3.630.193.82
genQC000
genomeBlocks0.040.000.03
getProbePositionsDf000
getSampleOffsets000
hyper000
loadPairFile000
loadSampleDirectory000
makeWindowLookupTable0.060.000.06
mappabilityCalc000
maskOut5.350.035.39
mergeReplicates0.620.010.64
methylEst107.67 0.10107.79
multiHeatmap0.050.000.05
plotClusters0.140.000.14
plotQdnaByCN000
processNDF000
profilePlots000
regionStats000
relativeCN0.050.000.05
sequenceCalc9.500.269.76
setCNVOffsets000
summarizeScores0.980.061.05
writeWig000

Repitools.Rcheck/examples_x64/Repitools-Ex.timings:

nameusersystemelapsed
BAM2GRanges0.140.000.14
BayMethList-class10.19 0.3310.51
GCadjustCopy000
GCbiasPlots000
QdnaData0.090.000.09
abcdDNA000
absoluteCN000
annoDF2GR0.020.000.01
annoGR2DF0.040.050.10
annotationBlocksCounts0.160.010.17
annotationBlocksLookup0.050.000.05
annotationCounts0.150.000.15
annotationLookup0.050.020.07
binPlots1.930.202.16
blocksStats0.170.020.19
checkProbes0.170.010.21
chromosomeCNplots000
clusterPlots1.690.051.80
cpgDensityCalc9.080.519.59
cpgDensityPlot4.240.194.43
determineOffset6.720.307.02
empBayes44.31 1.0345.34
enrichmentCalc1.590.001.59
enrichmentPlot1.660.001.65
featureBlocks0.010.000.02
featureScores0.970.000.97
findClusters2.270.002.28
gcContentCalc3.330.253.57
genQC000
genomeBlocks0.040.000.05
getProbePositionsDf000
getSampleOffsets000
hyper000
loadPairFile000
loadSampleDirectory000
makeWindowLookupTable0.060.000.06
mappabilityCalc000
maskOut5.540.085.61
mergeReplicates0.730.000.74
methylEst98.58 0.0298.62
multiHeatmap0.060.000.06
plotClusters0.160.000.16
plotQdnaByCN000
processNDF000
profilePlots000
regionStats000
relativeCN0.050.000.05
sequenceCalc9.250.349.59
setCNVOffsets000
summarizeScores1.140.021.15
writeWig000