Package: htSeqTools

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch htSeqTools_1.6.0.tar.gz

StartedAt: 2013-05-01 06:53:47 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:57:44 -0700 (Wed, 01 May 2013)

EllapsedTime: 237.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: htSeqTools.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/htSeqTools.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'htSeqTools' can be installed ... [21s/21s] 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 ... WARNING
'library' or 'require' call not declared from: 'species'
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 ... OK
* checking R code for possible problems ... NOTE
countHitsWindow,GRanges: possible error in countHitsWindow(x,
  chrLengths = chrLengths, windowSize = windowSize): unused argument
  (chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
  'chrLengths'
extendRanges,GRanges: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
  (chrLength = chrLength)
extendRanges,GRanges: no visible binding for global variable
  'chrLength'
extendRanges,GRangesList: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
  (chrLength = chrLength)
extendRanges,GRangesList: no visible binding for global variable
  'chrLength'
tabDuplReads,GRangesList: possible error in tabDuplReads(x, ,
  minRepeats = minRepeats, mc.cores = mc.cores): unused argument ()
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
cmds 7.512  0.511   8.179
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/htSeqTools.Rcheck/00check.log'
for details.

* installing *source* package 'htSeqTools' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'htSeqTools'
Creating a generic function for 'lines' from package 'graphics' in package 'htSeqTools'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (htSeqTools)

name	user	system	elapsed
alignPeaks	0.582	0.026	0.607
cmds	7.512	0.511	8.179
cmdsFit-class	0.003	0.006	0.010
cmdsFit	0.002	0.005	0.007
countHitsWindow	0.114	0.011	0.140
coverageDiff	0.221	0.020	0.244
enrichedChrRegions	3.252	0.041	3.332
enrichedPeaks	1.258	0.028	1.346
enrichedRegions	0.466	0.012	0.488
extendRanges	0.274	0.011	0.288
fdrEnrichedCounts	0.202	0.016	0.240
filterDuplReads	0.528	0.020	0.559
giniCoverage	0.612	0.029	0.642
gridCover-class	0.002	0.003	0.005
htSample	0.349	0.021	0.371
islandCounts	0.510	0.012	0.523
listOverlap	0.042	0.007	0.049
mergeRegions	0.143	0.008	0.153
plot-methods	0.013	0.003	0.017
plotChrRegions	0.062	0.009	0.072
regionsCoverage	0.013	0.004	0.017
rowLogRegLRT	0.007	0.004	0.010
ssdCoverage	0.504	0.011	0.523
stdPeakLocation	0.169	0.012	0.185