BioC 3.4: CHECK report for CNAnorm on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNAnorm_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CNAnorm.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.19.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 13.218  0.098   13.32
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/CNAnorm.Rcheck/00check.log’
for details.

* installing *source* package ‘CNAnorm’ ...
** libs
gfortran-4.8   -fPIC  -g -O2 -Wall  -c daxpy.f -o daxpy.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c ddot.f -o ddot.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dgbfa.f -o dgbfa.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dgbsl.f -o dgbsl.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dscal.f -o dscal.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c dsmooth.f -o dsmooth.o
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dsmooth.f:62.20:

      do 10 i=1,n-1                                                     
                    1
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dsmooth.f:70.7:

     &       diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1                   
       1
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dsmooth.f: In function ‘amed3’:
dsmooth.f:50:0: warning: ‘__result_amed3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  function amed3(a,b,c)
 ^
gfortran-4.8   -fPIC  -g -O2 -Wall  -c idamax.f -o idamax.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/CNAnorm.Rcheck/CNAnorm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNAnorm)

name	user	system	elapsed
CNAnorm-class	0.048	0.003	0.051
DerivData-class	0.004	0.001	0.005
InData-class	0.005	0.001	0.005
Params-class	0.004	0.002	0.005
addDNACopy-methods	0.938	0.005	0.960
addSmooth-methods	0.367	0.002	0.370
chrsAndpos-methods	0.025	0.001	0.026
dataFrame2object	0.002	0.000	0.003
discreteNorm-methods	0.011	0.001	0.012
exportTable-method	0.045	0.002	0.046
gcNorm-methods	0.350	0.001	0.351
peakPloidy	13.218	0.098	13.320
plotGenome-methods	1.068	0.004	1.074
plotPeaks-methods	0.024	0.002	0.027
ratio-methods	0.384	0.001	0.386
suggValid-methods	0.049	0.002	0.051
validation-methods	0.010	0.001	0.012
workflowWrapper	0.844	0.009	0.853

BioC 3.4: CHECK report for CNAnorm on morelia

Summary

Command output