Package: Biobase

Version: 1.10.1

Command: /loc/biocbuild/1.8d/R/bin/R CMD check Biobase_1.10.1.tar.gz

RetCode: 0

Time: 133.0 seconds

Status: WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/Rpacks/Biobase.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '1.10.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Biobase' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'eset' is deprecated.
* 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 syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating Biobase-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Biobase-manual.tex ... OK
* checking Biobase-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/1.8d/Rpacks/Biobase.Rcheck/00check.log
for details

* Installing *source* package 'Biobase' ...
** libs
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -c Rinit.c -o Rinit.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -c envir.c -o envir.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fPIC  -g -O2 -std=gnu99 -c matchpt.c -o matchpt.o
gcc -G -L/usr/local/lib -o Biobase.so Rinit.o envir.o matchpt.o   
** R
** data
** inst
** save image
Loading required package: tools
Creating a new generic function for 'nrow' in 'Biobase'
Creating a new generic function for 'ncol' in 'Biobase'
** help
 >>> Building/Updating help pages for package 'Biobase'
     Formats: text html latex example 
  Aggregate                         text    html    latex   example
  Biobase-package                   text    html    latex
  abstract                          text    html    latex
  addVig2Menu                       text    html    latex   example
  annotation                        text    html    latex
  assayData                         text    html    latex
  biocReposList                     text    html    latex   example
  cache                             text    html    latex   example
  class.AnnotatedDataFrame          text    html    latex
  class.AssayData                   text    html    latex
  class.ExpressionSet               text    html    latex   example
  class.MIAME                       text    html    latex
  class.MultiSet                    text    html    latex   example
  class.SnpSet                      text    html    latex
  class.aggregator                  text    html    latex
  class.annotatedDataset            text    html    latex
  class.characterORmiame            text    html    latex
  class.container                   text    html    latex   example
  class.eSet                        text    html    latex   example
  class.exprList                    text    html    latex   example
  class.exprMatrix                  text    html    latex
  class.exprSet                     text    html    latex   example
  class.phenoData                   text    html    latex   example
  combine                           text    html    latex
  contents                          text    html    latex   example
  copyEnv                           text    html    latex   example
  copySubstitute                    text    html    latex   example
  createPackage                     text    html    latex   example
  data.aaMap                        text    html    latex   example
  data.eset                         text    html    latex   example
  data.geneData                     text    html    latex   example
  data.reporter                     text    html    latex   example
  data.sample.ExpressionSet         text    html    latex   example
  data.sample.eSet                  text    html    latex   example
  data.sample.exprSet.1             text    html    latex   example
  data.sample.exprSet               text    html    latex   example
  defunct                           text    html    latex
  description                       text    html    latex
  dims                              text    html    latex
  dumpPackTxt                       text    html    latex   example
  esApply                           text    html    latex   example
  exprs                             text    html    latex
  featureNames                      text    html    latex
  getPkgVigs                        text    html    latex   example
  internals                         text    html    latex
  isUnique                          text    html    latex   example
  matchpt                           text    html    latex   example
  multiassign                       text    html    latex   example
  note                              text    html    latex   example
  notes                             text    html    latex
  openPDF                           text    html    latex   example
  openVignette                      text    html    latex   example
  package.version                   text    html    latex   example
  phenoData                         text    html    latex
  read.MIAME                        text    html    latex   example
  read.exprSet                      text    html    latex   example
  read.phenoData                    text    html    latex   example
  reporterInfo                      text    html    latex
  reverseSplit                      text    html    latex   example
  rowQ                              text    html    latex   example
  storageMode                       text    html    latex
  strbreak                          text    html    latex   example
  testBioCConnection                text    html    latex   example
  updateOldESet                     text    html    latex   example
** building package indices ...
Warning: 'eset' is deprecated.
Use 'sample.exprSet.1' instead.
See help("Deprecated")
* DONE (Biobase)