Package: beadarray

Version: 1.1.6

Command: /loc/biocbuild/1.9d/R/bin/R CMD check beadarray_1.1.6.tar.gz

RetCode: 0

Time: 406.8 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 alpha (2006-09-10 r39242)
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.1.6'
* checking package dependencies ... WARNING
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 '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 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 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
  BLImagePlot                       text    html    latex
  BSData                            text    html    latex
  BeadLevelList                     text    html    latex
  BeadLevelNormalise                text    html    latex
  BeadSummaryList                   text    html    latex
  DiffScore                         text    html    latex
  LargeDataObject                   text    html    latex   example
  QC                                text    html    latex
  backgroundCorrectBeads            text    html    latex   example
  backgroundNormalise               text    html    latex   example
  cbind                             text    html    latex
  checkRandomness                   text    html    latex   example
  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
  findHighestChis                   text    html    latex   example
  findHighestSD                     text    html    latex   example
  findLowestCounts                  text    html    latex   example
  findMostOutliers                  text    html    latex   example
  getDimensions                     text    html    latex   example
  getProbeCoords                    text    html    latex   example
  getProbeIntensities               text    html    latex   example
  histBeadCounts                    text    html    latex   example
  interactivePlots                  text    html    latex
  medianNormalise                   text    html    latex   example
  plotArray                         text    html    latex
  plotBeadIntensities               text    html    latex   example
  plotBeadLocations                 text    html    latex   example
  plotMA.beads                      text    html    latex
  plotMAXY                          text    html    latex   example
  plotOnSAM                         text    html    latex
  plotXY.beads                      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
  removeArrays                      text    html    latex   example
  subsetting                        text    html    latex
** building package indices ...
* DONE (beadarray)