Package: maanova

Version: 1.7.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check maanova_1.7.0.tar.gz

RetCode: 0

Time: 32.5 seconds

Status: WARNINGS

CheckDir: maanova.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/maanova.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'maanova/DESCRIPTION' ... OK
* this is package 'maanova' version '1.7.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maanova' can be installed ... 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 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
exprSet2Rawdata: no visible global function definition for 'exprs'
exprSet2Rawdata: no visible global function definition for 'geneNames'
exprSet2Rawdata: no visible global function definition for 'pData'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'maanova-internal':
  plot.consensus.hc plot.consensus.kmean

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... WARNING
Found the following Makefiles with CR or CRLF line endings:
  src/Makefile
Some Unix makes require LF line endings.
* checking for portable use of $BLAS_LIBS ... OK
* creating maanova-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating maanova-manual.tex ... OK
* checking maanova-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.1-bioc/meat/maanova.Rcheck/00check.log
for details

* Installing *source* package 'maanova' ...
** libs
** arch - 
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c masvd.c -o masvd.o
masvd.c:114:2: warning: "/*" within comment
masvd.c:154:1: warning: "/*" within comment
masvd.c:161:5: warning: "/*" within comment
masvd.c:165:2: warning: "/*" within comment
masvd.c:189:2: warning: "/*" within comment
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c makeratio.c -o makeratio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c shift.c -o shift.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o maanova.so masvd.o makeratio.o util.o shift.o  -L/home/biocbuild/bbs-2.1-bioc/R/lib -lRlapack   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'maanova'
     Formats: text html latex example 
  Rmaanova.version                  text    html    latex   example
  abf1                              text    html    latex   example
  adjPval                           text    html    latex   example
  arrayview                         text    html    latex   example
  consensus                         text    html    latex   example
  createData                        text    html    latex   example
  dyeswapfilter                     text    html    latex   example
  exprSet2Rawdata                   text    html    latex
  fill.missing                      text    html    latex   example
  fitmaanova                        text    html    latex   example
  fom                               text    html    latex   example
  geneprofile                       text    html    latex   example
  gridcheck                         text    html    latex   example
  kidney                            text    html    latex   example
  maanova-internal                  text    html    latex   example
  macluster                         text    html    latex   example
  makeModel                         text    html    latex   example
  matest                            text    html    latex   example
  paigen                            text    html    latex   example
  read.madata                       text    html    latex   example
  resiplot                          text    html    latex   example
  riplot                            text    html    latex   example
  subset.madata                     text    html    latex   example
  transform.madata                  text    html    latex   example
  varplot                           text    html    latex   example
  volcano                           text    html    latex   example
  write.madata                      text    html    latex   example
** building package indices ...
* DONE (maanova)