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affy

1.12.2

Rafael A. Irizarry
Last Changed Date: 2006-11-30 10:56:59 -0800
Last Changed Rev: 21322
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
churchill Solaris 2.9 sparc  OK  OK 
lemming Windows Server 2003 x86_64  OK [ OK ] OK 
Package: affy
Version: 1.12.2
Command: D:\biocbld\bbs-1.9\R\bin\R.exe CMD check affy_1.12.2.tar.gz
RetCode: 0
Time: 225.9 seconds
Status: OK
CheckDir: affy.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-1.9/meat/affy.Rcheck'
* using R version 2.4.1 (2006-12-18)
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.12.2'
* 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 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 ... OK
* 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 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 `/cygdrive/d/biocbld/bbs-1.9/meat/affy.Rcheck/tests'
  Running 'affybatch.R'
  Running 'bg.correct.R'
  Running 'expression.values.R'
  Running 'normalize.methods.R'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-1.9/meat/affy.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating affy-manual.tex ... OK
* checking affy-manual.tex ... OK

affy.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-1.9/meat/affy.Rcheck


---------- Making package affy ------------

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************

  adding build stamp to DESCRIPTION
  making DLL ...
making chipbackground.d from chipbackground.c
making getall_locations.d from getall_locations.c
making mas5calls.d from mas5calls.c
making qnorm.d from qnorm.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c chipbackground.c -o chipbackground.o
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c getall_locations.c -o getall_locations.o
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c mas5calls.c -o mas5calls.o
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1521: warning: unused variable `ind'
qnorm.c:1522: warning: unused variable `dimat'
qnorm.c:1526: warning: unused variable `ranks'
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1604: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1596: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:116: warning: 'min' defined but not used
qnorm.c:389: warning: 'qnorm_c_old' defined but not used
qnorm.c:463: warning: 'qnorm_robust_c_old' defined but not used
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c rma2.c -o rma2.o
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c rma_background2.c -o rma_background2.o
gcc  -Id:/biocbld/bbs-1.9/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-1.9/R/include  -Wall -O2 -std=gnu99   -c rma_common.c -o rma_common.o
windres --include-dir d:/biocbld/bbs-1.9/R/include  -i affy_res.rc -o affy_res.o
gcc  -shared -s  -o affy.dll affy.def chipbackground.o getall_locations.o mas5calls.o qnorm.o rma2.o rma_background2.o rma_common.o affy_res.o  -Ld:/biocbld/bbs-1.9/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  save image
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
[1] "ProgressBarText"
[1] "initialize"
[1] "open"
[1] "open"
[1] "update"
[1] "update"
[1] "close"
[1] "close"
[1] "AffyBatch"
[1] "cdfName"
[1] "cdfName"
[1] "intensity"
[1] "intensity"
[1] "intensity<-"
[1] "intensity<-"
[1] "length"
[1] "ncol"
[1] "nrow"
[1] "nrow"
[1] "geneNames"
[1] "geneNames<-"
[1] "show"
[1] "indexProbes"
[1] "indexProbes"
[1] "indexProbes"
[1] "pmindex"
[1] "pmindex"
[1] "mmindex"
[1] "mmindex"
[1] "probeNames"
[1] "probeNames"
[1] "probes"
[1] "probes"
[1] "pm"
[1] "pm"
[1] "pm<-"
[1] "pm<-"
[1] "mm"
[1] "mm"
[1] "mm<-"
[1] "mm<-"
[1] "probeset"
[1] "probeset"
[1] "["
[1] "[<-"
[1] "bg.correct"
[1] "bg.correct"
[1] "normalize.methods"
[1] "normalize.methods"
[1] "normalize"
[1] "normalize"
[1] "computeExprSet"
[1] "computeExprSet"
[1] "image"
[1] "image"
[1] "boxplot"
[1] "boxplot"
[1] "hist"
[1] "hist"
[1] "mas5calls"
[1] "mas5calls"
[1] "Mbox"
[1] "Mbox"
[1] "MAplot"
[1] "MAplot"
[1] "ProbeSet"
[1] "show"
[1] "colnames"
[1] "sampleNames"
[1] "colnames"
[1] "pm"
[1] "pm<-"
[1] "mm"
[1] "mm<-"
[1] "express.summary.stat"
[1] "express.summary.stat"
[1] "barplot"
[1] "barplot"
[1] "mas5calls"
  installing demos
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'affy'
     Formats: text html latex example chm 
  AffyBatch-class                   text    html    latex   example chm
  AffyRNAdeg                        text    html    latex   example chm
  MAplot                            text    html    latex   example chm
  ProbeSet-class                    text    html    latex   example chm
  ProgressBarText-class             text    html    latex   example chm
  SpikeIn                           text    html    latex           chm
  affy-options                      text    html    latex   example chm
  affy.scalevalue.exprSet           text    html    latex           chm
  affybatch.example                 text    html    latex           chm
  barplot.ProbeSet                  text    html    latex   example chm
  bg.adjust                         text    html    latex           chm
  bgc                               text    html    latex   example chm
  cdfFromBioC                       text    html    latex   example chm
  cdfenv.example                    text    html    latex           chm
  cleancdfname                      text    html    latex   example chm
  debug.affy123                     text    html    latex           chm
  expresso                          text    html    latex   example chm
  expressoWidget                    text    html    latex   example chm
  fit.li.wong                       text    html    latex   example chm
  generateExprSet-methods           text    html    latex   example chm
  generateExprVal-methods           text    html    latex   example chm
  generateExprVal.method.avgdiff    text    html    latex   example chm
  generateExprVal.method.playerout  text    html    latex           chm
  hlog                              text    html    latex           chm
  justrma                           text    html    latex   example chm
  list.celfiles                     text    html    latex   example chm
  loess.normalize                   text    html    latex           chm
  maffy.normalise                   text    html    latex   example chm
  maffy.subset                      text    html    latex   example chm
  mas5                              text    html    latex   example chm
  mas5calls                         text    html    latex   example chm
  merge.AffyBatch                   text    html    latex   example chm
  multiloess                        text    html    latex           chm
  mva.pairs                         text    html    latex   example chm
  normalize-methods                 text    html    latex   example chm
  normalize                         text    html    latex           chm
  normalize.constant                text    html    latex           chm
  normalize.contrast                text    html    latex   example chm
  normalize.invariantset            text    html    latex           chm
  normalize.loess                   text    html    latex   example chm
  normalize.qspline                 text    html    latex           chm
  normalize.quantiles               text    html    latex           chm
  normalize.quantiles.robust        text    html    latex           chm
  pairs.AffyBatch                   text    html    latex   example chm
  plot.ProbeSet                     text    html    latex   example chm
  plot.density                      text    html    latex   example chm
  plotLocation                      text    html    latex   example chm
  pmcorrect                         text    html    latex   example chm
  ppsetApply                        text    html    latex   example chm
  probeMatch-methods                text    html    latex           chm
  probeNames-methods                text    html    latex           chm
  read.affybatch                    text    html    latex   example chm
  read.probematrix                  text    html    latex   example chm
  rma                               text    html    latex   example chm
  setAffyOptions                    text    html    latex   example chm
  simplemultiLoess                  text    html    latex           chm
  summary                           text    html    latex           chm
  tukey.biweight                    text    html    latex           chm
  whatcdf                           text    html    latex           chm
  xy2indices                        text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-1.9\meat\affy.Rcheck\00_pkg_src\affy\chm\affy.chm


Compile time: 0 minutes, 0 seconds
61	Topics
293	Local links
9	Internet links
1	Graphic


Created d:\biocbld\bbs-1.9\meat\affy.Rcheck\00_pkg_src\affy\chm\affy.chm, 97,843 bytes
Compression decreased file by 152,373 bytes.
  adding MD5 sums

* DONE (affy)