Package: htSeqTools

Version: 1.4.0

Command: rm -rf htSeqTools.buildbin-libdir && mkdir htSeqTools.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=htSeqTools.buildbin-libdir htSeqTools_1.4.0.tar.gz >htSeqTools-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=htSeqTools.buildbin-libdir --install="check:htSeqTools-install.out" --force-multiarch --no-vignettes --timings htSeqTools_1.4.0.tar.gz && mv htSeqTools.buildbin-libdir/* htSeqTools.Rcheck/ && rmdir htSeqTools.buildbin-libdir

StartedAt: 2013-03-25 01:35:49 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:39:11 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 202.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: htSeqTools.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/htSeqTools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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
  'D:/biocbld/bbs-2.11-bioc/meat/htSeqTools.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'htSeqTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'htSeqTools' as htSeqTools_1.4.0.zip

* DONE (htSeqTools)