Package: beadarray

Version: 1.2.2

Command: /loc/biocbuild/1.9d/R/bin/R CMD check beadarray_1.2.2.tar.gz

RetCode: 0

Time: 141.1 seconds

Status: WARNINGS

CheckDir: beadarray.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/beadarray.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.2.2'
* 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 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 whether the name space 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 ... WARNING
Codoc mismatches from documentation object 'backgroundCorrect':
backgroundCorrect
  Code: function(object, method = "subtract", offset = 0, verbose =
                 FALSE)
  Docs: function(object, method = "subtract", offset = 0)
  Argument names in code not in docs:
    verbose

* 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 beadarray-Ex.R ... OK
* checking examples ... OK
* creating beadarray-manual.tex ... OK
* checking beadarray-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/1.9d/Rpacks/beadarray.Rcheck/00check.log
for details

* Installing *source* package 'beadarray' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function `findAllOutliers':
createBeadSummaryData.c:243: warning: `status' might be used uninitialized in this function
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function `readBeadImage':
readBeadImages.c:554: warning: `BeginData' might be used uninitialized in this function
readBeadImages.c:554: warning: `ImageWidth' might be used uninitialized in this function
readBeadImages.c:554: warning: `ImageHeight' might be used uninitialized in this function
readBeadImages.c:554: warning: `StripOffset' might be used uninitialized in this function
readBeadImages.c:555: warning: `offset' might be used uninitialized in this function
readBeadImages.c:555: warning: `records' might be used uninitialized in this function
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c returnTIFF.c -o returnTIFF.o
returnTIFF.c: In function `readTIFF':
returnTIFF.c:101: warning: implicit declaration of function `getPixelIntensities'
returnTIFF.c:17: warning: `BeginData' might be used uninitialized in this function
returnTIFF.c:17: warning: `ImageWidth' might be used uninitialized in this function
returnTIFF.c:17: warning: `ImageHeight' might be used uninitialized in this function
returnTIFF.c:17: warning: `StripOffset' might be used uninitialized in this function
returnTIFF.c:18: warning: `offset' might be used uninitialized in this function
returnTIFF.c:18: warning: `records' might be used uninitialized in this function
gcc -shared -L/usr/local/lib64 -o beadarray.so BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o returnTIFF.o   
** R
** data
** inst
** preparing package 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()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affy
Loading required package: affyio
** help
 >>> Building/Updating help pages for package 'beadarray'
     Formats: text html latex example 
  BLData                            text    html    latex
  BSData                            text    html    latex
  BeadLevelNormalise                text    html    latex
  DiffScore                         text    html    latex
  LargeDataObject                   text    html    latex   example
  QC                                text    html    latex
  backgroundCorrect                 text    html    latex   example
  backgroundNormalise               text    html    latex   example
  cbind                             text    html    latex
  class-BeadLevelList               text    html    latex
  class.ExpressionSetIllumina       text    html    latex
  createBeadSummaryData             text    html    latex   example
  dim                               text    html    latex
  dimnames                          text    html    latex
  displayTIFFImage                  text    html    latex   example
  findAllOutliers                   text    html    latex   example
  findBeadStatus                    text    html    latex   example
  imageplot                         text    html    latex
  interactivePlots                  text    html    latex
  medianNormalise                   text    html    latex   example
  plotBeadIntensities               text    html    latex   example
  plotBeadLocations                 text    html    latex   example
  plotMA                            text    html    latex
  plotMAXY                          text    html    latex   example
  plotOnSAM                         text    html    latex
  plotXY                            text    html    latex
  rankInvariantNormalise            text    html    latex   example
  readBeadLevelData                 text    html    latex   example
  readBeadSummaryData               text    html    latex   example
  readBeadSummaryTargets            text    html    latex   example
  readBeadTargets                   text    html    latex   example
  readQC                            text    html    latex   example
** building package indices ...
* DONE (beadarray)