Package: beadarray

Version: 1.3.0

Command: /loc/biocbuild/2.0d/R/bin/R CMD check beadarray_1.3.0.tar.gz

RetCode: 1

Time: 55.9 seconds

Status: ERROR

CheckDir: beadarray.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/beadarray.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.3.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarray' can be installed ... WARNING
Found the following significant warnings:
  Warning: '\.' is an unrecognized escape in a character string
  Warning: unrecognized escape removed from "AVG_Signal.(\.+)"
See '/loc/biocbuild/2.0d/Rpacks/beadarray.Rcheck/00install.out' for details.
* 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 ... WARNING
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "AVG_Signal.(\.+)"
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... ERROR
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
Error in dyn.load(x, as.logical(local), as.logical(now)) : 
	unable to load shared library '/loc/biocbuild/2.0d/Rpacks/beadarray.Rcheck/beadarray/libs/beadarray.so':
  ld.so.1: R: fatal: relocation error: file /loc/biocbuild/2.0d/Rpacks/beadarray.Rcheck/beadarray/libs/beadarray.so: symbol log2: referenced symbol not found
Error: package/namespace load failed for 'beadarray'
Execution halted

It looks like this package has a loading problem: see the messages for
details.

* Installing *source* package 'beadarray' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
BLImagePlot.c: In function 'BLImagePlot':
BLImagePlot.c:17: warning: implicit declaration of function 'log2'
BLImagePlot.c:17: warning: incompatible implicit declaration of built-in function 'log2'
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function 'findAllOutliers':
createBeadSummaryData.c:243: warning: 'status' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function 'readBeadImage':
readBeadImages.c:555: warning: 'offset' may be used uninitialized in this function
readBeadImages.c:555: warning: 'records' may be used uninitialized in this function
readBeadImages.c:554: warning: 'StripOffset' may be used uninitialized in this function
readBeadImages.c:554: warning: 'ImageHeight' may be used uninitialized in this function
readBeadImages.c:554: warning: 'ImageWidth' may be used uninitialized in this function
readBeadImages.c:554: warning: 'BeginData' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c returnTIFF.c -o returnTIFF.o
returnTIFF.c: In function 'readTIFF':
returnTIFF.c:101: warning: implicit declaration of function 'getPixelIntensities'
returnTIFF.c:18: warning: 'offset' may be used uninitialized in this function
returnTIFF.c:18: warning: 'records' may be used uninitialized in this function
returnTIFF.c:17: warning: 'StripOffset' may be used uninitialized in this function
returnTIFF.c:17: warning: 'ImageHeight' may be used uninitialized in this function
returnTIFF.c:17: warning: 'ImageWidth' may be used uninitialized in this function
returnTIFF.c:17: warning: 'BeginData' may be used uninitialized in this function
gcc -std=gnu99 -G -L/usr/local/lib -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
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "AVG_Signal.(\.+)"
** 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)