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beadarray 1.6.0
Mark Dunning
Last Changed Date: 2007-10-02 17:41:09 -0700
Last Changed Rev: 27709
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) x64  OK [ OK ] OK 
pitt Mac OS X (10.4.10) i386  OK  OK  OK 
Package: beadarray
Version: 1.6.0
Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check beadarray_1.6.0.tar.gz
RetCode: 0
Time: 122.8 seconds
Status: OK
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/beadarray.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarray' 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 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 whether the name space 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 ... 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 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 use of $BLAS_LIBS ... OK
* creating beadarray-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating beadarray-manual.tex ... OK
* checking beadarray-manual.tex ... OK

beadarray.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/beadarray.Rcheck


---------- Making package beadarray ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making BLImagePlot.d from BLImagePlot.c
making createBeadSummaryData.d from createBeadSummaryData.c
making findProbeIndices.d from findProbeIndices.c
making readBeadImages.d from readBeadImages.c
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c BLImagePlot.c -o BLImagePlot.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function 'findAllOutliers':
createBeadSummaryData.c:223: warning: 'status' may be used uninitialized in this function
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c findProbeIndices.c -o findProbeIndices.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function 'readBeadImage':
readBeadImages.c:571: warning: 'offset' may be used uninitialized in this function
readBeadImages.c:571: warning: 'records' may be used uninitialized in this function
readBeadImages.c:570: warning: 'StripOffset' may be used uninitialized in this function
readBeadImages.c:570: warning: 'ImageHeight' may be used uninitialized in this function
readBeadImages.c:570: warning: 'ImageWidth' may be used uninitialized in this function
readBeadImages.c:570: warning: 'BeginData' may be used uninitialized in this function
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.1-bioc/R/include  -i beadarray_res.rc -o beadarray_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o beadarray.dll beadarray.def BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o beadarray_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
Loading required package: methods
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'beadarray'
     Formats: text html latex example chm 
  BLData                            text    html    latex           chm
  BSData                            text    html    latex           chm
  LargeDataObject                   text    html    latex   example chm
  QC                                text    html    latex   example chm
  arrayNames                        text    html    latex   example chm
  backgroundCorrect                 text    html    latex   example chm
  beadResids                        text    html    latex   example chm
  boxplotBeads                      text    html    latex   example chm
  class-BeadLevelList               text    html    latex           chm
  class.ExpressionSetIllumina       text    html    latex           chm
  combineBeadLevelLists             text    html    latex           chm
  copyBeadLevelLists                text    html    latex   example chm
  createBeadSummaryData             text    html    latex   example chm
  findAllOutliers                   text    html    latex   example chm
  findBeadStatus                    text    html    latex   example chm
  getArrayData                      text    html    latex   example chm
  getVariance                       text    html    latex   example chm
  imageplot                         text    html    latex   example chm
  interactivePlots                  text    html    latex           chm
  medianNormalise                   text    html    latex   example chm
  normaliseIllumina                 text    html    latex   example chm
  numBeads                          text    html    latex   example chm
  plotBeadDensities                 text    html    latex   example chm
  plotBeadIntensities               text    html    latex   example chm
  plotBeadLocations                 text    html    latex   example chm
  plotMA                            text    html    latex   example chm
  plotMAXY                          text    html    latex   example chm
  plotOnSAM                         text    html    latex           chm
  plotRG                            text    html    latex   example chm
  plotXY                            text    html    latex   example chm
  qcBeadLevel                       text    html    latex   example chm
  rankInvariantNormalise            text    html    latex   example chm
  readBGX                           text    html    latex   example chm
  readBeadSummaryData               text    html    latex   example chm
  readIllumina                      text    html    latex   example chm
  readQC                            text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\beadarray.Rcheck\00_pkg_src\beadarray\chm\beadarray.chm


Compile time: 0 minutes, 0 seconds
37	Topics
128	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\beadarray.Rcheck\00_pkg_src\beadarray\chm\beadarray.chm, 67,216 bytes
Compression decreased file by 88,207 bytes.
  preparing package beadarray for lazy loading
Loading required package: limma
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: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
  adding MD5 sums

* DONE (beadarray)