BioC 2.12: CHECK report for waveTiling on pelham

Package: waveTiling

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch waveTiling_1.1.1.tar.gz

StartedAt: 2013-03-24 11:05:04 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 11:13:29 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 504.6 seconds

RetCode: 0

Status: OK

CheckDir: waveTiling.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/waveTiling.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'waveTiling/DESCRIPTION' ... OK
* this is package 'waveTiling' version '1.1.1'
* 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 ... [28s/28s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
  .C("dwt", ..., PACKAGE = "waveslim")
  .C("idwt", ..., PACKAGE = "waveslim")
See the chapter 'System and foreign language interfaces' of 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 gdPlot(trackInfo, minBase = minBase,
  maxBase = maxBase, overlay = overlayInfoCorr[hlpIndex]): partial
  argument match of 'overlay' to 'overlays'
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'
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [226s/239s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
WaveTilingFeatureSet-class    71.177  2.809  75.053
wfm.fit                       63.836  4.910  75.141
selectProbesFromFilterOverlap 17.593  1.480  21.394
MapFilterProbe-class          15.440  0.412  16.133
getNonAnnotatedRegions         9.083  1.418  11.600
getSigGenes                    8.661  0.504   9.493
plotWfm                        6.962  1.094   8.155
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/waveTiling.Rcheck/00check.log'
for details.

* installing *source* package 'waveTiling' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c waveTiling.c -o waveTiling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o waveTiling.so waveTiling.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/waveTiling.Rcheck/waveTiling/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'waveTiling-vignette.Rnw' 
** testing if installed package can be loaded
* DONE (waveTiling)

name	user	system	elapsed
GenomeInfo-class	0.360	0.005	0.370
MapFilterProbe-class	15.440	0.412	16.133
WaveTilingFeatureSet-class	71.177	2.809	75.053
WfmFit-class	1.226	0.141	1.408
WfmFitCircadian-class	0.003	0.008	0.011
WfmFitCustom-class	0.004	0.008	0.011
WfmFitFactor-class	0.403	0.206	0.616
WfmFitTime-class	0.003	0.005	0.009
WfmInf-class	1.142	0.154	1.430
WfmInfCompare-class	0.003	0.006	0.009
WfmInfCustom-class	0.003	0.007	0.010
WfmInfEffects-class	0.004	0.006	0.009
WfmInfMeans-class	0.003	0.007	0.011
WfmInfOverallMean-class	0.004	0.006	0.011
addPheno	0.003	0.008	0.011
bgCorrQn	0.003	0.009	0.011
cel2TilingFeatureSet	0.003	0.006	0.009
filterOverlap	0.003	0.007	0.009
getNonAnnotatedRegions	9.083	1.418	11.600
getSigGenes	8.661	0.504	9.493
makeContrasts	0.005	0.006	0.011
makeDesign	0.016	0.007	0.023
plotWfm	6.962	1.094	8.155
selectProbesFromFilterOverlap	17.593	1.480	21.394
selectProbesFromTilingFeatureSet	0.004	0.007	0.011
wfm.fit	63.836	4.910	75.141
wfm.inference	3.269	0.676	4.333

Summary

Command output