Package: aCGH

Version: 1.12.0

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check aCGH_1.12.0.tar.gz

RetCode: 0

Time: 165.7 seconds

Status: WARNINGS

CheckDir: aCGH.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/aCGH.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.12.0'
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
floor:
  function(x)
floor.func:
  function(x, floor, x.na)

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* 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'
Found possibly global 'T' or 'F' in the following functions:
  combine.func plotfreq.givenstat.final.colors.func
  plotfreq.stat.chrom.final.func plotfreq.stat.final.func
* checking Rd files ... 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
* creating aCGH-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating aCGH-manual.tex ... OK
* checking aCGH-manual.tex ... OK

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.1-bioc/meat/aCGH.Rcheck/00check.log
for details

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/aCGH.Rcheck


---------- Making package aCGH ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making hmm.d from hmm.cpp
g++-sjlj  -g3 -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O2  -c hmm.cpp -o hmm.o
hmm.cpp: In function 'double calc_observed_likelihood_iter(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, double*, bool, double*, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, bool)':
hmm.cpp:32: warning: deprecated conversion from string constant to 'char*'
hmm.cpp:42: warning: deprecated conversion from string constant to 'char*'
hmm.cpp:82: warning: deprecated conversion from string constant to 'char*'
hmm.cpp:87: warning: deprecated conversion from string constant to 'char*'
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.1-bioc/R/include  -i aCGH_res.rc -o aCGH_res.o
g++-sjlj   -shared -s  -o aCGH.dll aCGH.def hmm.o aCGH_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin -lm   -lR
  ... DLL made
  installing DLL
  installing R files
  installing demos
  installing inst files
  installing data files
  preparing package aCGH for lazy loading
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: multtest
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: sma
  installing man source files
  installing indices
  not zipping data
  installing help
Note: unmatched right brace in 'aCGH.process' on or after line 28
Note: unmatched right brace in 'aCGH.process.Rd' on or after line 28
 >>> Building/Updating help pages for package 'aCGH'
     Formats: text html latex example chm 
  aCGH                              text    html    latex   example chm
  aCGH.process                      text    html    latex   example chm
  aCGH.read.Sprocs                  text    html    latex   example chm
  aCGH.test                         text    html    latex   example chm
  clusterGenome                     text    html    latex   example chm
  colorectal                        text    html    latex   example chm
  computeSD.func                    text    html    latex           chm
  fga.func                          text    html    latex   example chm
  find.genomic.events               text    html    latex           chm
  find.hmm.states                   text    html    latex   example chm
  findAber.func                     text    html    latex           chm
  findAmplif.func                   text    html    latex           chm
  findOutliers.func                 text    html    latex           chm
  findTrans.func                    text    html    latex           chm
  gainLoss                          text    html    latex   example chm
  heatmap                           text    html    latex   example chm
  human.chrom.info.Jul03            text    html    latex           chm
  human.chrom.info.May04            text    html    latex           chm
  impute.HMM                        text    html    latex   example chm
  impute.lowess                     text    html    latex   example chm
  mergeFunc                         text    html    latex           chm
  mergeLevels                       text    html    latex   example chm
  plotFreqStat                      text    html    latex   example chm
  plotGenome                        text    html    latex   example chm
  plotHmmStates                     text    html    latex   example chm
  plotSummaryProfile                text    html    latex   example chm
  states.hmm.func                   text    html    latex           chm
  summarize.clones                  text    html    latex   example chm
  threshold.func                    text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\aCGH.Rcheck\00_pkg_src\aCGH\chm\aCGH.chm


Compile time: 0 minutes, 0 seconds
30	Topics
248	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\aCGH.Rcheck\00_pkg_src\aCGH\chm\aCGH.chm, 73,625 bytes
Compression decreased file by 87,772 bytes.
  adding MD5 sums

* DONE (aCGH)