BioC 2.13: CHECK report for waveTiling on zin1

Package: waveTiling

Version: 1.4.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings waveTiling_1.4.0.tar.gz

StartedAt: 2014-04-05 04:32:44 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:37:02 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 258.3 seconds

RetCode: 0

Status:  OK

CheckDir: waveTiling.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/waveTiling.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waveTiling/DESCRIPTION’ ... OK
* this is package ‘waveTiling’ version ‘1.4.0’
* 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 ... [15s/15s] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [116s/118s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
WaveTilingFeatureSet-class    36.411  0.844  37.379
wfm.fit                       32.938  0.584  33.610
selectProbesFromFilterOverlap 10.188  0.248  10.507
MapFilterProbe-class           9.092  0.100  10.234
getNonAnnotatedRegions         5.040  0.252   5.605
getSigGenes                    5.221  0.012   5.250
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/waveTiling.Rcheck/00check.log’
for details.

* installing *source* package ‘waveTiling’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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]
waveTiling.c: In function ‘MAPMARGEQSMOOTH’:
waveTiling.c:43:11: warning: unused variable ‘n’ [-Wunused-variable]
waveTiling.c: In function ‘MAPMARGIMP’:
waveTiling.c:81:11: warning: unused variable ‘n’ [-Wunused-variable]
waveTiling.c: In function ‘MAPMARGIMPEQSMOOTH’:
waveTiling.c:114:11: warning: unused variable ‘n’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o waveTiling.so waveTiling.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/waveTiling.Rcheck/waveTiling/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: subseq
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: subseq
* DONE (waveTiling)

name	user	system	elapsed
GenomeInfo-class	0.000	0.004	0.005
MapFilterProbe-class	9.092	0.100	10.234
WaveTilingFeatureSet-class	36.411	0.844	37.379
WfmFit-class	0.800	0.036	0.847
WfmFitCircadian-class	0.000	0.004	0.003
WfmFitCustom-class	0.000	0.000	0.003
WfmFitFactor-class	0.004	0.000	0.003
WfmFitTime-class	0.004	0.000	0.003
WfmInf-class	0.768	0.028	0.812
WfmInfCompare-class	0.000	0.000	0.001
WfmInfCustom-class	0.000	0.000	0.001
WfmInfEffects-class	0.004	0.000	0.002
WfmInfMeans-class	0.000	0.000	0.002
WfmInfOverallMean-class	0.000	0.004	0.003
addPheno	0.004	0.000	0.002
bgCorrQn	0.000	0.000	0.003
cel2TilingFeatureSet	0.004	0.000	0.002
filterOverlap	0.000	0.004	0.002
getNonAnnotatedRegions	5.040	0.252	5.605
getSigGenes	5.221	0.012	5.250
makeContrasts	0.000	0.000	0.002
makeDesign	0.008	0.000	0.009
plotWfm	4.008	0.180	4.192
selectProbesFromFilterOverlap	10.188	0.248	10.507
selectProbesFromTilingFeatureSet	0.000	0.000	0.003
wfm.fit	32.938	0.584	33.610
wfm.inference	1.689	0.040	1.730