beadarray 1.12.1
Mark Dunning
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/beadarray | | Last Changed Rev: 42135 / Revision: 42512 | | Last Changed Date: 2009-10-02 09:48:47 -0700 (Fri, 02 Oct 2009) |
| wilson1 | 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 (10.5.8) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/beadarray.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.12.1'
* 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 ... NOTE
bgCorrectSingleArray: no visible global function definition for
‘normexp.fit’
bgCorrectSingleArray: no visible global function definition for
‘normexp.signal’
getControlAnno: no visible binding for global variable
‘ExpressionControlData’
readIllumina: no visible binding for global variable
‘ExpressionControlData’
setAnnotation: no visible binding for global variable
‘ExpressionControlData’
backgroundCorrect,BeadLevelList: no visible global function definition
for ‘normexp.fit’
backgroundCorrect,BeadLevelList: no visible global function definition
for ‘normexp.signal’
* checking Rd files ... OK
* checking Rd files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package ‘beadarray’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -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-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
>>> Building/Updating help pages for package 'beadarray'
Formats: text html latex example
BASH text html latex example
BASHCompact text html latex example
BASHDiffuse text html latex example
BASHExtended text html latex example
BGFilter text html latex example
BGFilterWeighted text html latex example
BLData text html latex
BSData text html latex
ExpressionControlData text html latex example
HULK text html latex example
HULKResids text html latex example
addArrayMask text html latex example
arrayNames text html latex example
backgroundControlPlot text html latex
backgroundCorrect text html latex example
beadResids text html latex example
beadarrayUsersGuide text html latex example
boxplotBeads text html latex example
calculateBeadLevelScores text html latex
calculateDetection text html latex example
chooseClusters text html latex example
class-BeadLevelList text html latex
class.ExpressionSetIllumina text html latex
closeImage text html latex example
combineBeadLevelLists text html latex
copyBeadLevelLists text html latex example
createBeadSummaryData text html latex example
denseRegions text html latex example
findAllOutliers text html latex example
findBeadStatus text html latex example
generateE text html latex example
generateNeighbours text html latex example
getAnnotation text html latex example
getArrayData text html latex example
getVariance text html latex example
imageplot text html latex example
interactivePlots text html latex
lmhPlot text html latex
medianNormalise text html latex example
normaliseIllumina text html latex example
numBeads text html latex example
outlierplot text html latex
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
plotXY text html latex example
poscontPlot text html latex
probePairsPlot text html latex
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
setWeights text html latex example
viewBeads text html latex example
** building package indices ...
* DONE (beadarray)