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This page was generated on 2021-10-15 15:06:56 -0400 (Fri, 15 Oct 2021).

CHECK results for tilingArray on machv2

To the developers/maintainers of the tilingArray package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tilingArray.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1917/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tilingArray 1.70.0  (landing page)
Zhenyu Xu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/tilingArray
git_branch: RELEASE_3_13
git_last_commit: 74c74b4
git_last_commit_date: 2021-05-19 11:35:27 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: tilingArray
Version: 1.70.0
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_1.70.0.tar.gz
StartedAt: 2021-10-15 00:43:55 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:46:59 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 183.5 seconds
RetCode: 0
Status:   OK  
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

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### Running 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_1.70.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/tilingArray.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.70.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/tilingArray.Rcheck/00check.log’
for details.



Installation output

tilingArray.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tilingArray
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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
PMindex000
class-segmentation0.0410.0030.043
comparisonPlot000
costMatrix0.0790.0040.084
findsegments0.0010.0000.001
gffSub0.1290.0130.142
normalizeByReference0.0000.0010.000
otherStrand0.0000.0000.001
plotAlongChrom0.2060.0200.227
plotAlongChromLegend000
plotSegmentationHeatmap0.0660.0090.075
plotpenLL0.1760.0050.183
posMin0.0010.0000.001
qcPlots000
readCel2eSet0.0010.0010.001
sampleStep0.0020.0000.002
segChrom0.0000.0000.001
segment0.0010.0000.002
segnf0.0770.0080.086