Package: simpleaffy

Version: 2.9.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check simpleaffy_2.9.1.tar.gz

RetCode: 0

Time: 70.1 seconds

Status: WARNINGS

CheckDir: simpleaffy.Rcheck

Warnings: 3

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/simpleaffy.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.9.1'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  cdfname methods
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'simpleaffy' can be installed ... WARNING
Found the following significant warnings:
  Warning: The exprSet class is deprecated, use ExpressionSet instead
See '/Users/biocbuild/2.0d/Rpacks/simpleaffy.Rcheck/00install.out' for details.
* 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 non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'plot' and siglist 'PairComp,ANY'
  generic 'plot' and siglist 'QCStats,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating simpleaffy-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating simpleaffy-manual.tex ... OK
* checking simpleaffy-manual.tex ... OK

WARNING: There were 3 warnings, see
  /Users/biocbuild/2.0d/Rpacks/simpleaffy.Rcheck/00check.log
for details

* Installing *source* package 'simpleaffy' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c simpleaffy.c -o simpleaffy.o
/var/tmp//ccgWZv8O.s:3394:indirect jmp without `*'
/var/tmp//ccgWZv8O.s:3409:indirect jmp without `*'
/var/tmp//ccgWZv8O.s:3424:indirect jmp without `*'
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/var/tmp//ccgWZv8O.s:3517:indirect jmp without `*'
/var/tmp//ccgWZv8O.s:3536:indirect jmp without `*'
gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o simpleaffy.so simpleaffy.o   -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c simpleaffy.c -o simpleaffy.o
gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o simpleaffy.so simpleaffy.o   -F/Library/Frameworks/R.framework/.. -framework R
** R
** data
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Warning: The exprSet class is deprecated, use ExpressionSet instead
** help
 >>> Building/Updating help pages for package 'simpleaffy'
     Formats: text html latex example 
  PairComp-class                    text    html    latex
  QCStats-accessor                  text    html    latex
  QCStats-class                     text    html    latex
  all.present                       text    html    latex   example
  all.present.in.group              text    html    latex   example
  alpha                             text    html    latex
  bg.correct.sa                     text    html    latex   example
  call.exprs                        text    html    latex   example
  detection.p.val                   text    html    latex   example
  get.annotation                    text    html    latex   example
  get.array.indices                 text    html    latex   example
  get.array.subset                  text    html    latex   example
  get.array.subset.affy             text    html    latex   example
  get.fold.change.and.t.test        text    html    latex   example
  getActin3                         text    html    latex   example
  getActin5                         text    html    latex   example
  getActinM                         text    html    latex   example
  getAllQCProbes                    text    html    latex   example
  getAllSpikeProbes                 text    html    latex   example
  getAlpha1                         text    html    latex   example
  getAlpha2                         text    html    latex   example
  getBioB                           text    html    latex   example
  getBioC                           text    html    latex   example
  getBioD                           text    html    latex   example
  getCreX                           text    html    latex   example
  getGapdh3                         text    html    latex   example
  getGapdh5                         text    html    latex   example
  getGapdhM                         text    html    latex   example
  getQCParams-methods               text    html    latex
  getTao                            text    html    latex   example
  haveQCParams                      text    html    latex   example
  hmap.colors                       text    html    latex   example
  hmap.eset                         text    html    latex   example
  hmap.pc                           text    html    latex   example
  journalpng                        text    html    latex   example
  justMAS                           text    html    latex   example
  pairwise.comparison               text    html    latex   example
  pairwise.filter                   text    html    latex   example
  plot.pairwise.comparison          text    html    latex   example
  plot.qc.stats                     text    html    latex   example
  qc                                text    html    latex   example
  qc.affy                           text    html    latex   example
  qc.probes                         text    html    latex
  read.affy                         text    html    latex   example
  read.affy.mixed                   text    html    latex   example
  spikes                            text    html    latex
  standard.pearson                  text    html    latex   example
  trad.scatter.plot                 text    html    latex   example
** building package indices ...
* DONE (simpleaffy)