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BioC 3.5: CHECK report for waveTiling on malbec2

This page was generated on 2017-10-18 14:14:45 -0400 (Wed, 18 Oct 2017).

Package 1366/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
waveTiling 1.18.0
Kristof De Beuf
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/waveTiling
Branch: RELEASE_3_5
Last Commit: a6e40b2
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: waveTiling
Version: 1.18.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings waveTiling_1.18.0.tar.gz
StartedAt: 2017-10-18 03:07:58 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:12:31 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 272.5 seconds
RetCode: 0
Status:  OK 
CheckDir: waveTiling.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings waveTiling_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/waveTiling.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.18.0’
* 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    25.328  0.752  26.379
wfm.fit                       24.684  0.880  25.583
MapFilterProbe-class           8.784  0.032   8.858
selectProbesFromFilterOverlap  8.192  0.092   8.288
getNonAnnotatedRegions         5.444  0.160   6.586
* 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-3.5-bioc/meat/waveTiling.Rcheck/00check.log’
for details.


waveTiling.Rcheck/00install.out:

* installing *source* package ‘waveTiling’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-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;
           ^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o waveTiling.so waveTiling.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/waveTiling.Rcheck/waveTiling/libs
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (waveTiling)

waveTiling.Rcheck/waveTiling-Ex.timings:

nameusersystemelapsed
GenomeInfo-class0.0040.0000.001
MapFilterProbe-class8.7840.0328.858
WaveTilingFeatureSet-class25.328 0.75226.379
WfmFit-class0.7640.0240.810
WfmFitCircadian-class000
WfmFitCustom-class0.0040.0000.001
WfmFitFactor-class0.0000.0000.001
WfmFitTime-class0.0000.0000.001
WfmInf-class0.7320.0280.777
WfmInfCompare-class0.0000.0000.001
WfmInfCustom-class0.0040.0000.001
WfmInfEffects-class0.0000.0000.001
WfmInfMeans-class0.0000.0000.001
WfmInfOverallMean-class0.0000.0000.001
addPheno0.0000.0000.001
bgCorrQn000
cel2TilingFeatureSet000
filterOverlap0.0000.0000.001
getNonAnnotatedRegions5.4440.1606.586
getSigGenes4.3640.0244.473
makeContrasts000
makeDesign0.0080.0000.008
plotWfm4.7760.0604.839
selectProbesFromFilterOverlap8.1920.0928.288
selectProbesFromTilingFeatureSet000
wfm.fit24.684 0.88025.583
wfm.inference2.1640.0122.176