BioC 2.12: CHECK report for htSeqTools on petty

Package: htSeqTools

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch htSeqTools_1.6.1.tar.gz

StartedAt: 2013-10-08 22:46:28 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:50:53 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 264.9 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '1.6.1'
* 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 'htSeqTools' can be installed ... [23s/27s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [30s/31s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
cmds 6.759  0.341    7.22
* 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 was 1 note.
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	0.673	0.024	0.699
cmds	6.759	0.341	7.220
cmdsFit-class	0.003	0.004	0.009
cmdsFit	0.003	0.004	0.007
countHitsWindow	0.141	0.009	0.150
coverageDiff	0.294	0.019	0.330
enrichedChrRegions	4.306	0.024	4.469
enrichedPeaks	1.650	0.024	1.690
enrichedRegions	0.619	0.012	0.639
extendRanges	0.343	0.009	0.358
fdrEnrichedCounts	0.226	0.012	0.239
filterDuplReads	0.721	0.018	0.742
giniCoverage	0.802	0.026	0.831
gridCover-class	0.002	0.002	0.005
htSample	0.507	0.019	0.529
islandCounts	0.713	0.010	0.725
listOverlap	0.036	0.006	0.042
mergeRegions	0.166	0.007	0.174
plot-methods	0.012	0.005	0.016
plotChrRegions	0.065	0.008	0.072
regionsCoverage	0.002	0.004	0.006
rowLogRegLRT	0.014	0.006	0.022
ssdCoverage	0.612	0.011	0.630
stdPeakLocation	0.227	0.010	0.237