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CHECK report for tilingArray on malbec2

This page was generated on 2019-10-16 11:55:38 -0400 (Wed, 16 Oct 2019).

Package 1645/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tilingArray 1.62.0
Zhenyu Xu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/tilingArray
Branch: RELEASE_3_9
Last Commit: a4ba2bc
Last Changed Date: 2019-05-02 11:53:04 -0400 (Thu, 02 May 2019)
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

Summary

Package: tilingArray
Version: 1.62.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings tilingArray_1.62.0.tar.gz
StartedAt: 2019-10-16 05:26:25 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:28:31 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 126.5 seconds
RetCode: 0
Status:  OK 
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings tilingArray_1.62.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/tilingArray.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tilingArray/DESCRIPTION’ ... OK
* this is package ‘tilingArray’ version ‘1.62.0’
* 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 ‘tilingArray’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘pixmap’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
comparisonPlot : myColors: no visible global function definition for
  ‘quantile’
grid.image: no visible global function definition for ‘colorRamp’
grid.image: no visible global function definition for ‘rgb’
interpolateZ: no visible global function definition for ‘approx’
matDensities : densXY: no visible global function definition for
  ‘density’
myPixmap: no visible global function definition for ‘pixmapGrey’
myWrite: no visible global function definition for ‘write.pnm’
normalizeByReference: no visible global function definition for ‘exprs’
normalizeByReference: no visible global function definition for
  ‘quantile’
normalizeByReference: no visible global function definition for
  ‘approxfun’
normalizeByReference: no visible global function definition for ‘pdf’
normalizeByReference: no visible global function definition for
  ‘smoothScatter’
normalizeByReference: no visible global function definition for ‘lines’
normalizeByReference: no visible global function definition for
  ‘dev.off’
normalizeByReference: no visible global function definition for
  ‘exprs<-’
plotAlongChrom: no visible global function definition for ‘colorRamp’
plotAlongChrom: no visible global function definition for ‘quantile’
plotFeatures: no visible global function definition for ‘listLen’
plotPenLL: no visible binding for global variable ‘quantile’
plotPenLL: no visible global function definition for ‘matplot’
plotPenLL: no visible global function definition for ‘segments’
plotPenLL: no visible global function definition for ‘legend’
plotSegmentationDots: no visible global function definition for
  ‘quantile’
plotSegmentationHeatmap: no visible global function definition for
  ‘colorRamp’
plotSegmentationHeatmap: no visible global function definition for
  ‘quantile’
qcPlots: no visible global function definition for ‘pData’
qcPlots: no visible global function definition for ‘exprs’
qcPlots: no visible global function definition for ‘png’
qcPlots: no visible global function definition for ‘boxplot’
qcPlots: no visible global function definition for ‘dev.off’
qcPlots: no visible global function definition for ‘matplot’
qcPlots: no visible global function definition for ‘jpeg’
raster.image: no visible global function definition for ‘colorRamp’
raster.image: no visible global function definition for ‘rgb’
readCel2eSet: no visible global function definition for ‘varLabels’
segChrom: no visible global function definition for ‘exprs’
plot,segmentation-ANY: no visible global function definition for ‘note’
plot,segmentation-ANY: no visible global function definition for
  ‘plot.default’
plot,segmentation-ANY: no visible global function definition for
  ‘abline’
plot,segmentation-ANY: no visible global function definition for
  ‘mtext’
Undefined global functions or variables:
  abline addVigs2WinMenu approx approxfun boxplot colorRamp density
  dev.off exprs exprs<- jpeg legend lines listLen matplot mtext note
  pData pdf pixmapGrey plot.default png quantile rgb segments
  smoothScatter varLabels write.pnm
Consider adding
  importFrom("grDevices", "colorRamp", "dev.off", "jpeg", "pdf", "png",
             "rgb")
  importFrom("graphics", "abline", "boxplot", "legend", "lines",
             "matplot", "mtext", "plot.default", "segments",
             "smoothScatter")
  importFrom("stats", "approx", "approxfun", "density", "quantile")
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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/tilingArray.Rcheck/00check.log’
for details.



Installation output

tilingArray.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL tilingArray
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘tilingArray’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c findsegments.c -o findsegments.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c sampleStep.c -o sampleStep.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o tilingArray.so findsegments.o sampleStep.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-tilingArray/00new/tilingArray/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 (tilingArray)

Tests output


Example timings

tilingArray.Rcheck/tilingArray-Ex.timings

nameusersystemelapsed
PMindex000
class-segmentation0.0280.0040.031
comparisonPlot000
costMatrix0.0320.0080.040
findsegments0.0010.0000.000
gffSub0.0830.0160.099
normalizeByReference000
otherStrand000
plotAlongChrom0.1320.0000.131
plotAlongChromLegend000
plotSegmentationHeatmap0.0440.0040.048
plotpenLL0.0260.0000.026
posMin0.0000.0000.001
qcPlots000
readCel2eSet000
sampleStep0.0010.0000.001
segChrom000
segment0.0000.0000.001
segnf0.0550.0020.058