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Package 297/609HostnameOS / ArchBUILDCHECKBUILD BIN
htSeqTools 1.4.0
Oscar Reina
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/htSeqTools
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: htSeqTools
Version: 1.4.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings htSeqTools_1.4.0.tar.gz
StartedAt: 2013-03-25 02:13:05 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:16:13 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 188.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: htSeqTools.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/htSeqTools.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.4.0’
* 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 whether package ‘htSeqTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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(s)
  (chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
  ‘chrLengths’
enrichedPeaks,RangedData-IRangesList-IRangesList: no visible global
  function definition for ‘pvec’
enrichedPeaks,RangedData-IRangesList-missing: no visible global
  function definition for ‘pvec’
extendRanges,GRanges: possible error in extendRanges(x, seqLen =
  seqLen, chrLength = chrLength, mc.cores = mc.cores): unused
  argument(s) (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(s) (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(s) ()
* 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 6.668   0.02   6.707
* 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-2.11-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
alignPeaks0.4880.0120.499
cmds6.6680.0206.707
cmdsFit-class0.0000.0000.001
cmdsFit000
countHitsWindow0.0880.0040.095
coverageDiff0.1960.0040.203
enrichedChrRegions2.5650.0002.564
enrichedPeaks1.0840.0001.084
enrichedRegions0.4120.0040.418
extendRanges0.2160.0000.215
fdrEnrichedCounts0.1360.0000.138
filterDuplReads0.4640.0000.464
giniCoverage0.5360.0000.536
gridCover-class000
htSample0.2880.0120.416
islandCounts0.4440.0000.442
listOverlap0.0080.0000.007
mergeRegions0.1040.0000.102
plot-methods000
plotChrRegions0.0400.0000.038
regionsCoverage000
rowLogRegLRT0.0040.0000.003
ssdCoverage0.440.000.44
stdPeakLocation0.1520.0000.154