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CHECK report for CNAnorm on malbec2

This page was generated on 2019-04-09 11:31:27 -0400 (Tue, 09 Apr 2019).

Package 296/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNAnorm 1.29.0
Stefano Berri
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CNAnorm
Branch: master
Last Commit: ef18867
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: CNAnorm
Version: 1.29.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CNAnorm_1.29.0.tar.gz
StartedAt: 2019-04-08 23:33:03 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:34:02 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 59.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CNAnorm.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CNAnorm_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CNAnorm.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.29.0’
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 15.948   0.02  16.074
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CNAnorm.Rcheck/00check.log’
for details.



Installation output

CNAnorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CNAnorm
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CNAnorm’ ...
** using staged installation
** libs
gfortran  -fpic  -g -O2  -Wall -c daxpy.f -o daxpy.o
gfortran  -fpic  -g -O2  -Wall -c ddot.f -o ddot.o
gfortran  -fpic  -g -O2  -Wall -c dgbfa.f -o dgbfa.o
gfortran  -fpic  -g -O2  -Wall -c dgbsl.f -o dgbsl.o
gfortran  -fpic  -g -O2  -Wall -c dscal.f -o dscal.o
gfortran  -fpic  -g -O2  -Wall -c dsmooth.f -o dsmooth.o
f951: Warning: Nonconforming tab character in column 1 of line 14 [-Wtabs]
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f951: Warning: Nonconforming tab character in column 1 of line 96 [-Wtabs]
dsmooth.f:62:20:

  do 10 i=1,n-1
                    1
Warning: Nonconforming tab character at (1) [-Wtabs]
dsmooth.f:70:7:

      &       diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1
       1
Warning: Nonconforming tab character at (1) [-Wtabs]
dsmooth.f:50:0:

  function amed3(a,b,c)
 
Warning: ‘__result_amed3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fpic  -g -O2  -Wall -c idamax.f -o idamax.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CNAnorm/00new/CNAnorm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CNAnorm)

Tests output


Example timings

CNAnorm.Rcheck/CNAnorm-Ex.timings

nameusersystemelapsed
CNAnorm-class0.0230.0000.023
DerivData-class0.0040.0000.004
InData-class0.0010.0040.005
Params-class0.0040.0000.004
addDNACopy-methods0.8680.0120.980
addSmooth-methods0.5760.0040.579
chrsAndpos-methods0.0310.0010.032
dataFrame2object0.0010.0020.004
discreteNorm-methods0.0180.0000.017
exportTable-method0.150.000.15
gcNorm-methods0.4990.0000.499
peakPloidy15.948 0.02016.074
plotGenome-methods1.0490.0001.052
plotPeaks-methods0.0560.0000.059
ratio-methods0.5270.0000.528
suggValid-methods0.0110.0040.015
validation-methods0.0080.0040.012
workflowWrapper1.0410.0001.043