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CHECK report for waveTiling on merida2

This page was generated on 2019-04-09 13:27:20 -0400 (Tue, 09 Apr 2019).

Package 1683/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
waveTiling 1.25.0
Kristof De Beuf
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/waveTiling
Branch: master
Last Commit: 691ec72
Last Changed Date: 2018-10-30 11:54:30 -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: waveTiling
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:waveTiling.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings waveTiling_1.25.0.tar.gz
StartedAt: 2019-04-09 04:22:56 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:28:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 324.5 seconds
RetCode: 0
Status:  OK 
CheckDir: waveTiling.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:waveTiling.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings waveTiling_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/waveTiling.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waveTiling/DESCRIPTION’ ... OK
* this is package ‘waveTiling’ version ‘1.25.0’
* 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 ‘waveTiling’ 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
Package in Depends field not imported from: ‘GenomeGraphs’
  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 ... NOTE
Foreign function calls to a different package:
  .C("dwt", ..., PACKAGE = "waveslim")
  .C("idwt", ..., PACKAGE = "waveslim")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[1]]), end(regions[[1]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[2]]), end(regions[[2]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[effectId[effectNo] + 1]]),
  end(regions[[effectId[effectNo] + 1]]))), location = Gloc, start =
  sta, end = end, region = c(trackCount, trackCount), dp =
  DisplayPars(color = "darkgrey", alpha = 0.1)): partial argument match
  of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[effectId[length(effectsToPlot) -
  2] + 2]]), end(regions[[effectId[length(effectsToPlot) - 2] + 2]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[i + 1]]), end(regions[[i +
  1]]))), location = Gloc, start = sta, end = end, region =
  c(trackCount, trackCount), dp = DisplayPars(color = "darkgrey", alpha
  = 0.1)): partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[i]]), end(regions[[i]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘DisplayPars’
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘transcripts’
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘elementMetadata’
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘makeTextOverlay’
makeNewAnnotationTrack: no visible global function definition for
  ‘DisplayPars’
makeNewAnnotationTrack: no visible global function definition for
  ‘exons’
makeNewAnnotationTrack: no visible global function definition for
  ‘elementMetadata’
makeNewAnnotationTrack: no visible global function definition for
  ‘makeAnnotationTrack’
makeNewTranscriptRectangleOverlay: no visible global function
  definition for ‘DisplayPars’
makeNewTranscriptRectangleOverlay: no visible global function
  definition for ‘makeRectangleOverlay’
pm2mm: no visible global function definition for ‘subseq’
filterOverlap,WaveTilingFeatureSet: no visible global function
  definition for ‘ac.character’
filterOverlap,WaveTilingFeatureSet: no visible binding for global
  variable ‘dataMMSegRevComp’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
  definition for ‘exons’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
  definition for ‘Rle’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
  ‘transcripts’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
  ‘queryHits’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
  ‘subjectHits’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘makeGenericArray’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘DisplayPars’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘makeGenomeAxis’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘gdPlot’
Undefined global functions or variables:
  DisplayPars Rle ac.character dataMMSegRevComp elementMetadata exons
  gdPlot makeAnnotationTrack makeGenericArray makeGenomeAxis
  makeRectangleOverlay makeTextOverlay queryHits subjectHits subseq
  transcripts
* 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 line endings in C/C++/Fortran sources/headers ... 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
Examples with CPU or elapsed time > 5s
                                user system elapsed
WaveTilingFeatureSet-class    29.429  1.180  30.769
wfm.fit                       27.297  1.467  28.838
MapFilterProbe-class          12.012  0.215  12.303
selectProbesFromFilterOverlap 11.146  0.471  11.692
getNonAnnotatedRegions         5.332  0.601   6.188
getSigGenes                    5.217  0.382   5.667
* 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-3.9-bioc/meat/waveTiling.Rcheck/00check.log’
for details.



Installation output

waveTiling.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL waveTiling
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘waveTiling’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c waveTiling.c -o waveTiling.o
waveTiling.c:10:11: warning: unused variable 'n' [-Wunused-variable]
int i,j,m,n,Jcount=0;
          ^
waveTiling.c:43:11: warning: unused variable 'n' [-Wunused-variable]
int i,j,m,n,Jcount=0;
          ^
waveTiling.c:81:11: warning: unused variable 'n' [-Wunused-variable]
int i,j,m,n,Jcount=0;
          ^
waveTiling.c:114:11: warning: unused variable 'n' [-Wunused-variable]
int i,j,m,n,Jcount=0;
          ^
4 warnings generated.
clang -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 waveTiling.so waveTiling.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/waveTiling/libs
** R
** 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
* DONE (waveTiling)

Tests output


Example timings

waveTiling.Rcheck/waveTiling-Ex.timings

nameusersystemelapsed
GenomeInfo-class0.0010.0010.002
MapFilterProbe-class12.012 0.21512.303
WaveTilingFeatureSet-class29.429 1.18030.769
WfmFit-class0.8050.0590.867
WfmFitCircadian-class0.0010.0000.001
WfmFitCustom-class0.0010.0000.002
WfmFitFactor-class0.0020.0010.002
WfmFitTime-class0.0020.0010.002
WfmInf-class0.8280.0590.894
WfmInfCompare-class0.0010.0000.001
WfmInfCustom-class0.0010.0000.001
WfmInfEffects-class0.0010.0000.001
WfmInfMeans-class0.0010.0000.001
WfmInfOverallMean-class0.0000.0000.001
addPheno0.0000.0000.001
bgCorrQn0.0010.0000.001
cel2TilingFeatureSet000
filterOverlap000
getNonAnnotatedRegions5.3320.6016.188
getSigGenes5.2170.3825.667
makeContrasts0.0010.0000.001
makeDesign0.0100.0010.011
plotWfm3.4390.1553.612
selectProbesFromFilterOverlap11.146 0.47111.692
selectProbesFromTilingFeatureSet0.0010.0000.001
wfm.fit27.297 1.46728.838
wfm.inference1.2500.1251.375