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BioC 3.5: CHECK report for tilingArray on tokay2

This page was generated on 2017-10-18 14:19:04 -0400 (Wed, 18 Oct 2017).

Package 1315/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tilingArray 1.54.0
Zhenyu Xu
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/tilingArray
Branch: RELEASE_3_5
Last Commit: dc85d24
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tilingArray
Version: 1.54.0
Command: rm -rf tilingArray.buildbin-libdir tilingArray.Rcheck && mkdir tilingArray.buildbin-libdir tilingArray.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tilingArray.buildbin-libdir tilingArray_1.54.0.tar.gz >tilingArray.Rcheck\00install.out 2>&1 && cp tilingArray.Rcheck\00install.out tilingArray-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=tilingArray.buildbin-libdir --install="check:tilingArray-install.out" --force-multiarch --no-vignettes --timings tilingArray_1.54.0.tar.gz
StartedAt: 2017-10-18 03:23:42 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:26:54 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 192.7 seconds
RetCode: 0
Status:  OK  
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf tilingArray.buildbin-libdir tilingArray.Rcheck && mkdir tilingArray.buildbin-libdir tilingArray.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=tilingArray.buildbin-libdir tilingArray_1.54.0.tar.gz >tilingArray.Rcheck\00install.out 2>&1 && cp tilingArray.Rcheck\00install.out tilingArray-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=tilingArray.buildbin-libdir --install="check:tilingArray-install.out" --force-multiarch --no-vignettes --timings tilingArray_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/tilingArray.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tilingArray/DESCRIPTION' ... OK
* this is package 'tilingArray' version '1.54.0'
* 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 '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
* 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
* 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 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 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/tilingArray.buildbin-libdir/tilingArray/libs/i386/tilingArray.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
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/tilingArray.Rcheck/00check.log'
for details.


tilingArray.Rcheck/00install.out:


install for i386

* installing *source* package 'tilingArray' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c findsegments.c -o findsegments.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sampleStep.c -o sampleStep.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o tilingArray.dll tmp.def findsegments.o sampleStep.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/tilingArray.buildbin-libdir/tilingArray/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 'tilingArray' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c findsegments.c -o findsegments.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sampleStep.c -o sampleStep.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o tilingArray.dll tmp.def findsegments.o sampleStep.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/tilingArray.buildbin-libdir/tilingArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tilingArray' as tilingArray_1.54.0.zip
* DONE (tilingArray)

tilingArray.Rcheck/examples_i386/tilingArray-Ex.timings:

nameusersystemelapsed
PMindex000
class-segmentation0.310.040.36
comparisonPlot000
costMatrix0.140.000.15
findsegments000
gffSub0.580.020.59
normalizeByReference000
otherStrand000
plotAlongChrom0.840.020.86
plotAlongChromLegend000
plotSegmentationHeatmap0.060.000.06
plotpenLL0.050.000.05
posMin0.020.000.01
qcPlots000
readCel2eSet000
sampleStep000
segChrom000
segment000
segnf0.040.010.07

tilingArray.Rcheck/examples_x64/tilingArray-Ex.timings:

nameusersystemelapsed
PMindex000
class-segmentation0.560.020.58
comparisonPlot000
costMatrix0.110.000.11
findsegments000
gffSub0.400.000.41
normalizeByReference000
otherStrand000
plotAlongChrom1.320.001.31
plotAlongChromLegend000
plotSegmentationHeatmap0.070.000.08
plotpenLL0.040.010.05
posMin000
qcPlots000
readCel2eSet000
sampleStep000
segChrom000
segment000
segnf0.080.000.08