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Package 6/233HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.16.0
Rafael A. Irizarry
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK [ OK ]
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: affy
Version: 1.16.0
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check affy_1.16.0.tar.gz
StartedAt: 2008-04-09 14:47:47 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 14:49:48 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 121.8 seconds
RetCode: 0
Status: OK
CheckDir: affy.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.1-bioc/meat/affy.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.16.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affy' 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
AllButCelsForReadAffy: no visible binding for global variable 'tksn'
cleancdfname: no visible binding for global variable 'mapCdfName'
normalize.AffyBatch.invariantset : do.normalize.Affybatch.invariantset:
  no visible global function definition for 'chipNames'
* 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 'barplot.ProbeSet':

S3 methods shown with full name in documentation object 'merge.AffyBatch':

S3 methods shown with full name in documentation object 'pairs.AffyBatch':

S3 methods shown with full name in documentation object 'plot.ProbeSet':

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
* 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 affy-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.1-bioc/meat/affy.Rcheck/tests'
  Running 'affybatch.R'
  Running 'bg.correct.R'
  Running 'expression.values.R'
  Running 'normalize.methods.R'
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.1-bioc/meat/affy.Rcheck/tests'
* checking package vignettes in 'inst/doc' ... OK
* creating affy-manual.tex ... OK
* checking affy-manual.tex ... OK


* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o chipbackground.o getall_locations.o mas5calls.o rma2.o rma_background2.o rma_common.o -lz   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** demo
** inst
** preparing package for lazy loading
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: affyio
Loading required package: preprocessCore
Creating a new generic function for "open" in "affy"
Creating a new generic function for "update" in "affy"
Creating a new generic function for "close" in "affy"
** help
 >>> Building/Updating help pages for package 'affy'
     Formats: text html latex example 
  AffyBatch-class                   text    html    latex   example
  AffyRNAdeg                        text    html    latex   example
  MAplot                            text    html    latex   example
  ProbeSet-class                    text    html    latex   example
  ProgressBarText-class             text    html    latex   example
  SpikeIn                           text    html    latex
  affy-options                      text    html    latex   example
  affy.scalevalue.exprSet           text    html    latex
  affybatch.example                 text    html    latex
  barplot.ProbeSet                  text    html    latex   example
  bg.adjust                         text    html    latex
  bgc                               text    html    latex   example
  cdfFromBioC                       text    html    latex   example
  cdfenv.example                    text    html    latex
  cleancdfname                      text    html    latex   example
  debug.affy123                     text    html    latex
  expresso                          text    html    latex   example
  expressoWidget                    text    html    latex   example                       text    html    latex   example
  generateExprSet-methods           text    html    latex   example
  generateExprVal-methods           text    html    latex   example
  generateExprVal.method.avgdiff    text    html    latex   example
  generateExprVal.method.playerout  text    html    latex
  hlog                              text    html    latex
  justrma                           text    html    latex   example
  list.celfiles                     text    html    latex   example
  loess.normalize                   text    html    latex
  maffy.normalise                   text    html    latex   example
  maffy.subset                      text    html    latex   example
  mas5                              text    html    latex   example
  mas5calls                         text    html    latex   example
  merge.AffyBatch                   text    html    latex   example
  multiloess                        text    html    latex
  mva.pairs                         text    html    latex   example
  normalize-methods                 text    html    latex   example
  normalize                         text    html    latex
  normalize.constant                text    html    latex
  normalize.contrast                text    html    latex   example
  normalize.invariantset            text    html    latex
  normalize.loess                   text    html    latex   example
  normalize.qspline                 text    html    latex
  normalize.quantiles               text    html    latex
  normalize.quantiles.robust        text    html    latex
  pairs.AffyBatch                   text    html    latex   example
  plot.ProbeSet                     text    html    latex   example
  plot.density                      text    html    latex   example
  plotLocation                      text    html    latex   example
  pmcorrect                         text    html    latex   example
  ppsetApply                        text    html    latex   example
  probeMatch-methods                text    html    latex
  probeNames-methods                text    html    latex
  read.affybatch                    text    html    latex   example
  read.probematrix                  text    html    latex   example
  rma                               text    html    latex   example
  setAffyOptions                    text    html    latex   example
  simplemultiLoess                  text    html    latex
  summary                           text    html    latex
  tukey.biweight                    text    html    latex
  whatcdf                           text    html    latex
  xy2indices                        text    html    latex   example
** building package indices ...
* DONE (affy)