BioC 2.12: CHECK report for waveTiling on petty

Package: waveTiling

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch waveTiling_1.2.0.tar.gz

StartedAt: 2013-10-09 00:09:05 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:16:03 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 418.8 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 3.0.1 (2013-05-16)
* 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 '1.2.0'
* 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 ... [31s/32s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [152s/154s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
WaveTilingFeatureSet-class    47.552  1.653  49.240
wfm.fit                       40.698  2.392  43.115
MapFilterProbe-class          12.064  0.284  12.390
selectProbesFromFilterOverlap 11.652  0.657  12.309
getNonAnnotatedRegions         6.613  0.876   8.341
getSigGenes                    6.355  0.288   6.669
plotWfm                        5.292  0.606   6.063
* 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 -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
** testing if installed package can be loaded
* DONE (waveTiling)

name	user	system	elapsed
GenomeInfo-class	0.005	0.002	0.007
MapFilterProbe-class	12.064	0.284	12.390
WaveTilingFeatureSet-class	47.552	1.653	49.240
WfmFit-class	1.029	0.091	1.309
WfmFitCircadian-class	0.003	0.004	0.175
WfmFitCustom-class	0.003	0.004	0.007
WfmFitFactor-class	0.003	0.003	0.087
WfmFitTime-class	0.002	0.003	0.005
WfmInf-class	0.986	0.088	1.088
WfmInfCompare-class	0.003	0.004	0.006
WfmInfCustom-class	0.002	0.003	0.006
WfmInfEffects-class	0.002	0.004	0.007
WfmInfMeans-class	0.003	0.004	0.007
WfmInfOverallMean-class	0.002	0.004	0.006
addPheno	0.002	0.005	0.007
bgCorrQn	0.003	0.004	0.007
cel2TilingFeatureSet	0.001	0.004	0.005
filterOverlap	0.003	0.004	0.007
getNonAnnotatedRegions	6.613	0.876	8.341
getSigGenes	6.355	0.288	6.669
makeContrasts	0.003	0.003	0.007
makeDesign	0.012	0.004	0.015
plotWfm	5.292	0.606	6.063
selectProbesFromFilterOverlap	11.652	0.657	12.309
selectProbesFromTilingFeatureSet	0.002	0.003	0.005
wfm.fit	40.698	2.392	43.115
wfm.inference	2.072	0.320	2.392