Package: aCGH

Version: 1.23.0

Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes aCGH_1.23.0.tar.gz

StartedAt: 2009-12-07 15:28:35 -0800 (Mon, 07 Dec 2009)

EndedAt: 2009-12-07 15:30:06 -0800 (Mon, 07 Dec 2009)

EllapsedTime: 91.6 seconds

RetCode: 0

Status: OK

CheckDir: aCGH.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/aCGH.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.23.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[.aCGH: no visible binding for global variable 'joan'
changeProp.func: no visible binding for global variable
  'data.screen.norm.thres'
computeSD.func: no visible binding for global variable 'states.bic'
findAber.func: no visible binding for global variable 'states.bic'
findAmplif.func: no visible binding for global variable 'res3'
findAmplif.func: no visible binding for global variable 'res2'
findAmplif.func: no visible binding for global variable 'res1'
findAmplif.func: no visible binding for global variable 'states.bic'
findOutliers.func: no visible binding for global variable 'madGenome'
findOutliers.func: no visible binding for global variable 'states.bic'
findTrans.func: no visible binding for global variable 'res1'
findTrans.func: no visible binding for global variable 'res2'
findTrans.func: no visible binding for global variable 'states.bic'
mergeFunc: no visible binding for global variable 'states.bic'
plotCGH.func: no visible binding for global variable 'data.cgh'
plotCGH.func: no visible binding for global variable 'map.cgh'
plotCGH.hmm.func: no visible binding for global variable 'dat'
plotCGH.hmm.func: no visible binding for global variable 'states.bic'
plotCGH.hmm.func: no visible binding for global variable 'res4'
plotCGH.hmm.func: no visible binding for global variable 'res2'
plotCGH.hmm.func: no visible binding for global variable 'res1'
plotCGH.hmm.func: no visible binding for global variable 'res3'
plotChrom.grey.samples.func: no visible binding for global variable
  'states.bic'
plotChrom.grey.samples.func: no visible binding for global variable
  'res4'
plotChrom.grey.samples.func: no visible binding for global variable
  'res2'
plotChrom.grey.samples.func: no visible binding for global variable
  'res1'
plotChrom.grey.samples.func: no visible binding for global variable
  'res3'
plotChrom.hmm.func: no visible binding for global variable 'states.bic'
plotChrom.hmm.func: no visible binding for global variable 'res4'
plotChrom.hmm.func: no visible binding for global variable 'res2'
plotChrom.hmm.func: no visible binding for global variable 'res1'
plotChrom.hmm.func: no visible binding for global variable 'res3'
plotChrom.samples.func: no visible binding for global variable
  'states.bic'
plotChrom.samples.func: no visible binding for global variable 'res4'
plotChrom.samples.func: no visible binding for global variable 'res2'
plotChrom.samples.func: no visible binding for global variable 'res1'
plotChrom.samples.func: no visible binding for global variable 'res3'
plotfreq.givenstat.final.colors.func: no visible binding for global
  variable 'stats'
plotfreq.givenstat.final.colors.func: no visible binding for global
  variable 'statsPerm'
plotfreq.givenstat.final.colors.func: possible error in gainLoss(dat =
  data, cols = cols, thres = thres, quant = quant.col): unused
  argument(s) (quant = quant.col)
plotfreq.stat.chrom.final.func: no visible binding for global variable
  '.mt.naNUM'
plotfreq.stat.chrom.final.func: no visible global function definition
  for 'exit'
plotfreq.stat.final.func: no visible binding for global variable
  '.mt.naNUM'
plotFreqStatColors: no visible global function definition for
  'plotfreq.stat'
plotFreqStatGrey: no visible global function definition for
  'plotfreq.stat'
plotGeneSign: no visible binding for global variable '.mt.naNUM'
plotSummaryProfile: no visible binding for global variable
  'numchromgain'
plotSummaryProfile: no visible binding for global variable
  'numchromloss'
plotSummaryProfile: no visible binding for global variable 'numtrans'
plotSummaryProfile: no visible binding for global variable
  'numtrans.binary'
plotSummaryProfile: no visible binding for global variable 'numaber'
plotSummaryProfile: no visible binding for global variable 'numamplif'
plotSummaryProfile: no visible binding for global variable
  'numamplif.binary'
plotSummaryProfile: no visible binding for global variable
  'numamplicon'
plotSummaryProfile: no visible binding for global variable
  'sizeamplicon'
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'aCGH' ...
** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include" -g3       -O2 -Wall  -c hmm.cpp -o hmm.o
g++ -shared -s -o aCGH.dll tmp.def hmm.o -lm -Le:/biocbld/bbs-2.6-bioc/R/bin -lR
  ... done
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (aCGH)