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CHECK report for tilingArray on machv2

This page was generated on 2020-10-17 11:59:47 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE tilingArray PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1799/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tilingArray 1.66.0
Zhenyu Xu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/tilingArray
Branch: RELEASE_3_11
Last Commit: b21b72c
Last Changed Date: 2020-04-27 14:11:01 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: tilingArray
Version: 1.66.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tilingArray_1.66.0.tar.gz
StartedAt: 2020-10-17 05:54:13 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:57:14 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 180.3 seconds
RetCode: 0
Status:  OK 
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tilingArray_1.66.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/tilingArray.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tilingArray/DESCRIPTION’ ... OK
* this is package ‘tilingArray’ version ‘1.66.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/tilingArray.Rcheck/00check.log’
for details.



Installation output

tilingArray.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tilingArray
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘tilingArray’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c findsegments.c -o findsegments.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sampleStep.c -o sampleStep.o
clang -mmacosx-version-min=10.13 -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 tilingArray.so findsegments.o sampleStep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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
PMindex0.0000.0010.001
class-segmentation0.0460.0030.048
comparisonPlot0.0010.0000.001
costMatrix0.0630.0030.067
findsegments0.0000.0000.001
gffSub0.5240.0150.540
normalizeByReference0.0010.0010.000
otherStrand0.0000.0000.001
plotAlongChrom0.2150.0210.236
plotAlongChromLegend0.0000.0000.001
plotSegmentationHeatmap0.0450.0060.053
plotpenLL0.1980.0050.204
posMin0.0010.0000.000
qcPlots000
readCel2eSet0.0000.0000.001
sampleStep0.0010.0010.002
segChrom0.0000.0010.001
segment0.0020.0000.002
segnf0.0520.0050.056