beadarray 1.10.0
Mark Dunning
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/beadarray | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/beadarray.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.10.0'
* 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 ... NOTE
getControlAnno: no visible binding for global variable
'ExpressionControlData'
readIllumina: no visible binding for global variable
'ExpressionControlData'
setAnnotation: no visible binding for global variable
'ExpressionControlData'
* 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 R.css in E:/biocbld/bbs-2.3-bioc/meat/beadarray.Rcheck
---------- Making package beadarray ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making BASH.d from BASH.c
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 -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c BASH.c -o BASH.o
BASH.c: In function 'BGFilter':
BASH.c:201: warning: unused variable 'mean'
BASH.c: In function 'BGFilterWeighted':
BASH.c:308: warning: unused variable 'mad'
BASH.c:308: warning: unused variable 'median'
BASH.c:308: warning: unused variable 'mean'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i beadarray_res.rc -o beadarray_res.o
gcc -std=gnu99 -shared -s -o beadarray.dll beadarray.def BASH.o BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o beadarray_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
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: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Attaching package: 'geneplotter'
The following object(s) are masked from package:lattice :
panel.smoothScatter
Loading required package: hwriter
Loading required package: sma
installing man source files
installing indices
Loading required package: methods
Loading required package: Biobase
Loading required package: tools
Loading required package: utils
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
not zipping data
installing help
>>> Building/Updating help pages for package 'beadarray'
Formats: text html latex example chm
BASH text html latex example chm
BASHCompact text html latex example chm
BASHDiffuse text html latex example chm
BASHExtended text html latex example chm
BGFilter text html latex example chm
BGFilterWeighted text html latex example chm
BLData text html latex chm
BSData text html latex chm
ExpressionControlData text html latex example chm
addArrayMask text html latex example chm
arrayNames text html latex example chm
backgroundControlPlot text html latex chm
backgroundCorrect text html latex example chm
beadResids text html latex example chm
beadarrayUsersGuide text html latex example chm
boxplotBeads text html latex example chm
calculateBeadLevelScores text html latex chm
calculateDetection text html latex chm
chooseClusters text html latex example chm
class-BeadLevelList text html latex chm
class.ExpressionSetIllumina text html latex chm
closeImage text html latex example chm
combineBeadLevelLists text html latex chm
copyBeadLevelLists text html latex example chm
createBeadSummaryData text html latex example chm
denseRegions text html latex example chm
findAllOutliers text html latex example chm
findBeadStatus text html latex example chm
generateE text html latex example chm
generateNeighbours text html latex example chm
getAnnotation 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
lmhPlot text html latex chm
medianNormalise text html latex example chm
normaliseIllumina text html latex example chm
numBeads text html latex example chm
Note: removing empty section \value in file 'outlierplot.Rd'
Note: removing empty section \value in file 'outlierplot.Rd'
outlierplot text html latex 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 chm
plotXY text html latex example chm
poscontPlot text html latex chm
probePairsPlot text html latex 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
setWeights text html latex example chm
viewBeads text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\beadarray.Rcheck\00_pkg_src\beadarray\chm\beadarray.chm
Compile time: 0 minutes, 0 seconds
59 Topics
235 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\beadarray.Rcheck\00_pkg_src\beadarray\chm\beadarray.chm, 104,394 bytes
Compression decreased file by 145,733 bytes.
adding MD5 sums
* DONE (beadarray)