beadarray 1.7.9
Mark Dunning
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray | | Last Changed Rev: 30925 / Revision: 30951 | | Last Changed Date: 2008-04-08 11:19:33 -0700 (Tue, 08 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/beadarray.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.7.9'
* 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 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 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 using pdflatex ... OK
* Installing *source* package 'beadarray' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function 'findAllOutliers':
createBeadSummaryData.c:223: warning: 'status' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -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
gcc -std=gnu99 -shared -L/usr/local/lib -o beadarray.so BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** 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()'. 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
** help
>>> Building/Updating help pages for package 'beadarray'
Formats: text html latex example
BLData text html latex
BSData text html latex
LargeDataObject text html latex example
QC text html latex example
arrayNames text html latex example
backgroundCorrect text html latex example
beadResids text html latex example
boxplotBeads text html latex example
class-BeadLevelList text html latex
class.ExpressionSetIllumina text html latex
combineBeadLevelLists text html latex
copyBeadLevelLists text html latex example
createBeadSummaryData text html latex example
findAllOutliers text html latex example
findBeadStatus text html latex example
getArrayData text html latex example
getVariance text html latex example
imageplot text html latex example
interactivePlots text html latex
medianNormalise text html latex example
normaliseIllumina text html latex example
numBeads text html latex example
plotBeadDensities text html latex example
plotBeadIntensities text html latex example
plotBeadLocations text html latex example
plotMA text html latex example
plotMAXY text html latex example
plotOnSAM text html latex
plotRG text html latex example
plotXY text html latex example
qcBeadLevel text html latex example
rankInvariantNormalise text html latex example
readBGX text html latex example
readBeadSummaryData text html latex example
readIllumina text html latex example
readQC text html latex example
** building package indices ...
Loading required package: methods
* DONE (beadarray)