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CHECK report for CNAnorm on tokay1

This page was generated on 2018-04-12 13:21:14 -0400 (Thu, 12 Apr 2018).

Package 257/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNAnorm 1.24.0
Stefano Berri
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CNAnorm
Branch: RELEASE_3_6
Last Commit: 8405e2a
Last Changed Date: 2017-10-30 12:39:36 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CNAnorm
Version: 1.24.0
Command: rm -rf CNAnorm.buildbin-libdir CNAnorm.Rcheck && mkdir CNAnorm.buildbin-libdir CNAnorm.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNAnorm.buildbin-libdir CNAnorm_1.24.0.tar.gz >CNAnorm.Rcheck\00install.out 2>&1 && cp CNAnorm.Rcheck\00install.out CNAnorm-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CNAnorm.buildbin-libdir --install="check:CNAnorm-install.out" --force-multiarch --no-vignettes --timings CNAnorm_1.24.0.tar.gz
StartedAt: 2018-04-11 23:01:50 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:03:23 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 92.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CNAnorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNAnorm.buildbin-libdir CNAnorm.Rcheck && mkdir CNAnorm.buildbin-libdir CNAnorm.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNAnorm.buildbin-libdir CNAnorm_1.24.0.tar.gz >CNAnorm.Rcheck\00install.out 2>&1 && cp CNAnorm.Rcheck\00install.out CNAnorm-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CNAnorm.buildbin-libdir --install="check:CNAnorm-install.out" --force-multiarch --no-vignettes --timings CNAnorm_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CNAnorm.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 'CNAnorm/DESCRIPTION' ... OK
* this is package 'CNAnorm' 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 '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-3.6-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 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
peakPloidy 14.36   0.16   14.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
peakPloidy 19.99   0.79   20.78
* 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-3.6-bioc/meat/CNAnorm.Rcheck/00check.log'
for details.



Installation output

CNAnorm.Rcheck/00install.out


install for i386

* installing *source* package 'CNAnorm' ...
** libs
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c daxpy.f -o daxpy.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c ddot.f -o ddot.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c dgbfa.f -o dgbfa.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c dgbsl.f -o dgbsl.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c dscal.f -o dscal.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c dsmooth.f -o dsmooth.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=generic -c idamax.f -o idamax.o
C:/Rtools/mingw_32/bin/g++ -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˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CNAnorm.buildbin-libdir/CNAnorm/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CNAnorm'
    finding HTML links ... done
    CN                                      html  
    CNAnorm-class                           html  
    DerivData-class                         html  
    InData-class                            html  
    LS041                                   html  
    Params-class                            html  
    addDNACopy-methods                      html  
    addSmooth-methods                       html  
    chrsAndpos-methods                      html  
    data-hg19_hs_ideogr                     html  
    dataFrame2object                        html  
    discreteNorm-methods                    html  
    exportTable-method                      html  
    gPar                                    html  
    gcNorm-methods                          html  
    peakPloidy                              html  
    plotGenome-methods                      html  
    plotPeaks-methods                       html  
    ratio-methods                           html  
    suggValid-methods                       html  
    validation-methods                      html  
    workflowWrapper                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CNAnorm' ...
** libs
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c daxpy.f -o daxpy.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c ddot.f -o ddot.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dgbfa.f -o dgbfa.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dgbsl.f -o dgbsl.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dscal.f -o dscal.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dsmooth.f -o dsmooth.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c idamax.f -o idamax.o
C:/Rtools/mingw_64/bin/g++ -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˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CNAnorm.buildbin-libdir/CNAnorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNAnorm' as CNAnorm_1.24.0.zip
* DONE (CNAnorm)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

CNAnorm.Rcheck/examples_i386/CNAnorm-Ex.timings

nameusersystemelapsed
CNAnorm-class0.050.000.05
DerivData-class0.040.020.06
InData-class000
Params-class000
addDNACopy-methods1.200.011.21
addSmooth-methods0.570.000.57
chrsAndpos-methods0.030.000.03
dataFrame2object000
discreteNorm-methods0.000.020.01
exportTable-method0.110.030.14
gcNorm-methods0.450.010.47
peakPloidy14.36 0.1614.51
plotGenome-methods1.380.001.38
plotPeaks-methods0.050.000.05
ratio-methods0.40.00.4
suggValid-methods0.020.000.02
validation-methods0.010.000.01
workflowWrapper1.250.001.25

CNAnorm.Rcheck/examples_x64/CNAnorm-Ex.timings

nameusersystemelapsed
CNAnorm-class0.030.000.03
DerivData-class0.140.000.14
InData-class0.000.010.01
Params-class000
addDNACopy-methods101
addSmooth-methods0.600.000.59
chrsAndpos-methods0.090.000.10
dataFrame2object000
discreteNorm-methods0.020.000.01
exportTable-method0.120.000.13
gcNorm-methods0.390.020.41
peakPloidy19.99 0.7920.78
plotGenome-methods1.100.031.13
plotPeaks-methods0.060.000.07
ratio-methods0.370.000.37
suggValid-methods0.020.000.02
validation-methods0.020.000.01
workflowWrapper0.920.000.92