Package: waveTiling

Version: 1.20.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings waveTiling_1.20.0.tar.gz

StartedAt: 2018-04-12 03:36:11 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:40:28 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 256.5 seconds

RetCode: 0

Status:  OK

CheckDir: waveTiling.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings waveTiling_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/waveTiling.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waveTiling/DESCRIPTION’ ... OK
* this is package ‘waveTiling’ version ‘1.20.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
WaveTilingFeatureSet-class    25.460  0.624  26.111
wfm.fit                       25.348  0.568  25.939
MapFilterProbe-class           8.868  0.096   9.012
selectProbesFromFilterOverlap  8.272  0.168   8.444
getNonAnnotatedRegions         5.636  0.252   6.302
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/waveTiling.Rcheck/00check.log’
for details.

* installing *source* package ‘waveTiling’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c waveTiling.c -o waveTiling.o
waveTiling.c: In function ‘MAPMARG’:
waveTiling.c:10:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function ‘MAPMARGEQSMOOTH’:
waveTiling.c:43:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function ‘MAPMARGIMP’:
waveTiling.c:81:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function ‘MAPMARGIMPEQSMOOTH’:
waveTiling.c:114:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o waveTiling.so waveTiling.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/waveTiling.Rcheck/waveTiling/libs
** R
** inst
** preparing 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	0.000	0.000	0.001
MapFilterProbe-class	8.868	0.096	9.012
WaveTilingFeatureSet-class	25.460	0.624	26.111
WfmFit-class	0.792	0.036	0.843
WfmFitCircadian-class	0.000	0.000	0.001
WfmFitCustom-class	0.000	0.000	0.001
WfmFitFactor-class	0.000	0.000	0.001
WfmFitTime-class	0.000	0.000	0.001
WfmInf-class	0.848	0.040	0.890
WfmInfCompare-class	0	0	0
WfmInfCustom-class	0.000	0.000	0.001
WfmInfEffects-class	0.004	0.000	0.001
WfmInfMeans-class	0.000	0.000	0.001
WfmInfOverallMean-class	0.000	0.000	0.001
addPheno	0.000	0.000	0.001
bgCorrQn	0	0	0
cel2TilingFeatureSet	0	0	0
filterOverlap	0.004	0.000	0.000
getNonAnnotatedRegions	5.636	0.252	6.302
getSigGenes	4.508	0.068	4.660
makeContrasts	0.004	0.000	0.001
makeDesign	0.008	0.000	0.008
plotWfm	3.120	0.080	3.201
selectProbesFromFilterOverlap	8.272	0.168	8.444
selectProbesFromTilingFeatureSet	0.004	0.000	0.000
wfm.fit	25.348	0.568	25.939
wfm.inference	1.424	0.004	1.429