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

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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
###
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* 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.

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### Running command:
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###   /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)

name	user	system	elapsed
GenomeInfo-class	0.001	0.001	0.002
MapFilterProbe-class	12.012	0.215	12.303
WaveTilingFeatureSet-class	29.429	1.180	30.769
WfmFit-class	0.805	0.059	0.867
WfmFitCircadian-class	0.001	0.000	0.001
WfmFitCustom-class	0.001	0.000	0.002
WfmFitFactor-class	0.002	0.001	0.002
WfmFitTime-class	0.002	0.001	0.002
WfmInf-class	0.828	0.059	0.894
WfmInfCompare-class	0.001	0.000	0.001
WfmInfCustom-class	0.001	0.000	0.001
WfmInfEffects-class	0.001	0.000	0.001
WfmInfMeans-class	0.001	0.000	0.001
WfmInfOverallMean-class	0.000	0.000	0.001
addPheno	0.000	0.000	0.001
bgCorrQn	0.001	0.000	0.001
cel2TilingFeatureSet	0	0	0
filterOverlap	0	0	0
getNonAnnotatedRegions	5.332	0.601	6.188
getSigGenes	5.217	0.382	5.667
makeContrasts	0.001	0.000	0.001
makeDesign	0.010	0.001	0.011
plotWfm	3.439	0.155	3.612
selectProbesFromFilterOverlap	11.146	0.471	11.692
selectProbesFromTilingFeatureSet	0.001	0.000	0.001
wfm.fit	27.297	1.467	28.838
wfm.inference	1.250	0.125	1.375