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Package 304/631HostnameOS / ArchBUILDCHECKBUILD BIN
htSeqTools 1.5.1
Oscar Reina
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/htSeqTools
Last Changed Rev: 72366 / Revision: 72575
Last Changed Date: 2013-01-08 08:09:00 -0800 (Tue, 08 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: htSeqTools
Version: 1.5.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.5.1.tar.gz
StartedAt: 2013-01-16 03:33:53 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 03:36:59 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 186.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: htSeqTools.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/htSeqTools.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* this is package ‘htSeqTools’ version ‘1.5.1’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
      user system elapsed
cmds 6.584  0.048   6.631
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.

htSeqTools.Rcheck/00install.out:

* 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
   ‘htSeqTools.Rnw’ 
** testing if installed package can be loaded

* DONE (htSeqTools)

htSeqTools.Rcheck/htSeqTools-Ex.timings:

nameusersystemelapsed
alignPeaks0.2440.0160.260
cmds6.5840.0486.631
cmdsFit-class0.0080.0000.009
cmdsFit0.0000.0040.004
countHitsWindow0.0960.0040.098
coverageDiff0.1760.0160.191
enrichedChrRegions2.7090.0002.711
enrichedPeaks1.0720.0201.094
enrichedRegions0.4160.0000.415
extendRanges0.2360.0000.238
fdrEnrichedCounts0.1480.0000.148
filterDuplReads0.4640.0000.467
giniCoverage0.5640.0000.562
gridCover-class0.0160.0000.015
htSample0.2960.0000.303
islandCounts0.4920.0000.491
listOverlap0.0400.0000.041
mergeRegions0.1040.0000.106
plot-methods0.0160.0000.016
plotChrRegions0.060.000.06
regionsCoverage0.0040.0000.004
rowLogRegLRT0.0040.0040.009
ssdCoverage0.4560.0000.458
stdPeakLocation0.1840.0000.182