BioC 3.5: CHECK report for CNAnorm on tokay2

Package: CNAnorm

Version: 1.22.1

Command: rm -rf CNAnorm.buildbin-libdir CNAnorm.Rcheck && mkdir CNAnorm.buildbin-libdir CNAnorm.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNAnorm.buildbin-libdir CNAnorm_1.22.1.tar.gz >CNAnorm.Rcheck\00install.out 2>&1 && cp CNAnorm.Rcheck\00install.out CNAnorm-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CNAnorm.buildbin-libdir --install="check:CNAnorm-install.out" --force-multiarch --no-vignettes --timings CNAnorm_1.22.1.tar.gz

StartedAt: 2017-08-15 22:48:28 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:50:07 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 98.9 seconds

RetCode: 0

Status:  OK

CheckDir: CNAnorm.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CNAnorm.buildbin-libdir CNAnorm.Rcheck && mkdir CNAnorm.buildbin-libdir CNAnorm.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNAnorm.buildbin-libdir CNAnorm_1.22.1.tar.gz >CNAnorm.Rcheck\00install.out 2>&1 && cp CNAnorm.Rcheck\00install.out CNAnorm-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CNAnorm.buildbin-libdir --install="check:CNAnorm-install.out" --force-multiarch --no-vignettes --timings CNAnorm_1.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNAnorm.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNAnorm/DESCRIPTION' ... OK
* this is package 'CNAnorm' version '1.22.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CNAnorm' 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
.OTquantileWeights: no visible global function definition for 'median'
.OTquantileWeights: no visible global function definition for
  'quantile'
.TTquantileWeights: no visible global function definition for 'median'
.TTquantileWeights: no visible global function definition for
  'quantile'
.exportTable: no visible global function definition for 'write.table'
.gaussianWeights: no visible global function definition for 'median'
.gaussianWeights: no visible global function definition for 'sd'
.guessPeaksAndPloidy: no visible global function definition for
  'density'
.guessPeaksAndPloidy: no visible global function definition for
  'median'
.peakPloidy: no visible global function definition for 'median'
.plotGenome: no visible global function definition for 'plot'
.plotGenome: no visible global function definition for 'text'
.plotGenome: no visible global function definition for 'par'
.plotGenome: no visible global function definition for 'points'
.plotGenome: no visible global function definition for 'axis'
.plotGenome: no visible global function definition for 'axTicks'
.plotGenome: no visible global function definition for 'title'
.plotGenome: no visible global function definition for 'mtext'
.plotGenome: no visible global function definition for 'abline'
.plotGenome: no visible global function definition for 'data'
.plotGenome: no visible global function definition for 'lines'
.plotPeaks: no visible global function definition for 'density'
.plotPeaks: no visible global function definition for 'median'
.plotPeaks: no visible global function definition for 'plot'
.plotPeaks: no visible global function definition for 'lines'
.plotPeaks: no visible global function definition for 'abline'
.plotPeaks: no visible global function definition for 'text'
.plotPeaks: no visible global function definition for 'legend'
.plotPeaks_old: no visible global function definition for 'median'
.plotPeaks_old: no visible global function definition for 'plot'
.plotPeaks_old: no visible global function definition for 'lines'
.plotPeaks_old: no visible global function definition for 'abline'
.plotPeaks_old: no visible global function definition for 'text'
.plotPeaks_old: no visible global function definition for 'legend'
Rcheck: no visible global function definition for 'lm'
bandseg: no visible global function definition for 'filter'
brute.seg: no visible global function definition for 'median'
findOutliers: no visible global function definition for 'median'
findOutliers: no visible global function definition for 'density'
gcNormalize: no visible global function definition for 'loess'
gcNormalize: no visible global function definition for 'predict'
gcNormalize: no visible global function definition for 'median'
get.initial.values: no visible global function definition for 'var'
get.initial.values: no visible global function definition for
  'quantile'
getMQR: no visible global function definition for 'lm'
global.norm: no visible global function definition for 'lm'
global.norm: no visible global function definition for 'predict'
medianWinSize: no visible global function definition for 'median'
myDensity: no visible global function definition for 'median'
myDensity: no visible global function definition for 'sd'
myDensity: no visible global function definition for 'density'
myPeaks: no visible global function definition for 'embed'
pdetect: no visible global function definition for 'rnorm'
pdetect: no visible global function definition for 'density'
pdetect: no visible global function definition for 'var'
pdetect: no visible global function definition for 'quantile'
pdetect: no visible global function definition for 'dnorm'
pdetect: no visible global function definition for 'median'
pdetect.iter: no visible global function definition for 'var'
pdetect.iter: no visible global function definition for 'dnorm'
pdetect.iter: no visible global function definition for 'median'
plotPeaksMixture: no visible global function definition for 'median'
plotPeaksMixture: no visible global function definition for 'hist'
plotPeaksMixture: no visible global function definition for 'abline'
rseg: no visible global function definition for 'median'
smoothseg: no visible global function definition for 'plot'
smoothseg: no visible global function definition for 'lines'
suggest.k: no visible global function definition for 'plot'
exportTable,CNAnorm: no visible global function definition for
  'write.table'
peakPloidy,CNAnorm: no visible global function definition for 'median'
plotGenome,CNAnorm: no visible global function definition for 'plot'
plotGenome,CNAnorm: no visible global function definition for 'text'
plotGenome,CNAnorm: no visible global function definition for 'par'
plotGenome,CNAnorm: no visible global function definition for 'points'
plotGenome,CNAnorm: no visible global function definition for 'axis'
plotGenome,CNAnorm: no visible global function definition for 'axTicks'
plotGenome,CNAnorm: no visible global function definition for 'title'
plotGenome,CNAnorm: no visible global function definition for 'mtext'
plotGenome,CNAnorm: no visible global function definition for 'abline'
plotGenome,CNAnorm: no visible global function definition for 'data'
plotGenome,CNAnorm: no visible global function definition for 'lines'
plotPeaks,CNAnorm: no visible global function definition for 'density'
plotPeaks,CNAnorm: no visible global function definition for 'median'
plotPeaks,CNAnorm: no visible global function definition for 'plot'
plotPeaks,CNAnorm: no visible global function definition for 'lines'
plotPeaks,CNAnorm: no visible global function definition for 'abline'
plotPeaks,CNAnorm: no visible global function definition for 'text'
plotPeaks,CNAnorm: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline axTicks axis data density dnorm embed filter hist legend lines
  lm loess median mtext par plot points predict quantile rnorm sd text
  title var write.table
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "hist", "legend",
             "lines", "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "density", "dnorm", "embed", "filter", "lm",
             "loess", "median", "predict", "quantile", "rnorm", "sd",
             "var")
  importFrom("utils", "data", "write.table")
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 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-3.5-bioc/meat/CNAnorm.buildbin-libdir/CNAnorm/libs/i386/CNAnorm.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
peakPloidy 16.77   0.27   17.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
peakPloidy 19.41   0.11   19.52
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/CNAnorm.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CNAnorm' ...
** libs
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c daxpy.f -o daxpy.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c ddot.f -o ddot.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c dgbfa.f -o dgbfa.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c dgbsl.f -o dgbsl.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c dscal.f -o dscal.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c dsmooth.f -o dsmooth.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c idamax.f -o idamax.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CNAnorm.dll tmp.def daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -LC:/local323/lib/i386 -LC:/local323/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNAnorm.buildbin-libdir/CNAnorm/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'CNAnorm' ...
** libs
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c daxpy.f -o daxpy.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c ddot.f -o ddot.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c dgbfa.f -o dgbfa.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c dgbsl.f -o dgbsl.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c dscal.f -o dscal.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c dsmooth.f -o dsmooth.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c idamax.f -o idamax.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CNAnorm.dll tmp.def daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -LC:/local323/lib/x64 -LC:/local323/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CNAnorm.buildbin-libdir/CNAnorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNAnorm' as CNAnorm_1.22.1.zip
* DONE (CNAnorm)

name	user	system	elapsed
CNAnorm-class	0.06	0.00	0.06
DerivData-class	0.07	0.00	0.06
InData-class	0	0	0
Params-class	0.00	0.01	0.01
addDNACopy-methods	1.35	0.00	1.35
addSmooth-methods	0.57	0.00	0.57
chrsAndpos-methods	0.03	0.00	0.04
dataFrame2object	0.02	0.00	0.01
discreteNorm-methods	0.02	0.00	0.02
exportTable-method	0.14	0.00	0.14
gcNorm-methods	0.45	0.00	0.45
peakPloidy	16.77	0.27	17.03
plotGenome-methods	1.37	0.00	1.38
plotPeaks-methods	0.06	0.00	0.06
ratio-methods	0.41	0.00	0.41
suggValid-methods	0.01	0.00	0.01
validation-methods	0.02	0.00	0.02
workflowWrapper	1.38	0.00	1.37

name	user	system	elapsed
CNAnorm-class	0.05	0.02	0.06
DerivData-class	0.06	0.00	0.07
InData-class	0	0	0
Params-class	0.01	0.00	0.02
addDNACopy-methods	0.88	0.00	0.87
addSmooth-methods	0.79	0.00	0.80
chrsAndpos-methods	0.01	0.00	0.01
dataFrame2object	0.00	0.01	0.02
discreteNorm-methods	0.02	0.00	0.01
exportTable-method	0.12	0.00	0.13
gcNorm-methods	0.44	0.00	0.43
peakPloidy	19.41	0.11	19.52
plotGenome-methods	1.31	0.00	1.31
plotPeaks-methods	0.08	0.00	0.08
ratio-methods	0.41	0.00	0.41
suggValid-methods	0.02	0.00	0.02
validation-methods	0	0	0
workflowWrapper	0.9	0.0	0.9