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Package 50/514HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.4.2
Mark Dunning
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/beadarray
Last Changed Rev: 63576 / Revision: 64395
Last Changed Date: 2012-03-07 07:06:38 -0800 (Wed, 07 Mar 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: beadarray
Version: 2.4.2
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.4.2.tar.gz
StartedAt: 2012-03-23 23:33:48 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 23:49:54 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 966.8 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/beadarray.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.4.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'beadarray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    2.6Mb
* 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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
combinedControlPlot: no visible binding for global variable 'Control'
combinedControlPlot: no visible binding for global variable 'Negative'
combinedControlPlot: no visible binding for global variable 'ID'
combinedControlPlot: no visible binding for global variable
  'Log2Intensity'
combinedControlPlot: no visible binding for global variable
  'ControlType'
combinedControlPlot: no visible binding for global variable 'Masked'
getPlatformSigs: no visible global function definition for
  'lumiHumanIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiMouseIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiRatIDMapping_dbconn'
imageplot: no visible binding for global variable 'Var1'
imageplot: no visible binding for global variable 'Var2'
imageplot: no visible binding for global variable 'value'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'gridExtra'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

beadarray.Rcheck/00install.out:

* installing *source* package 'beadarray' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c BASH.c -o BASH.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c HULK.c -o HULK.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c determiningGridPositions.c -o determiningGridPositions.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:155: warning: 'ma' may be used uninitialized in this function
findAllOutliers.c:155: warning: 'm' may be used uninitialized in this function
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226: warning: 'status' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:238: warning: ignoring #pragma omp parallel
imageProcessing.c:245: warning: ignoring #pragma omp parallel
gcc -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 HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/beadarray.Rcheck/beadarray/libs/i386
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'boxplot' from package 'graphics' in package 'beadarray'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ImageProcessing.rnw' 
   'beadarray.rnw' 
   'beadlevel.rnw' 
   'beadsummary.rnw' 
** testing if installed package can be loaded

* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.0000.0010.000
BASHCompact0.0010.0000.001
BASHDiffuse0.0000.0010.001
BASHExtended000
HULK0.0000.0010.001
addFeatureData18.902 0.90120.535
annotationInterface21.043 1.44122.715
backgroundCorrectSingleSection0.0000.0000.001
beadarrayUsersGuide0.0060.0020.007
boxplot10.581 2.36113.084
calculateDetection20.173 1.16921.867
calculateOutlierStats35.147 5.73842.280
class-beadLevelData11.966 1.02113.696
class-illuminaChannel0.0030.0010.004
combine21.148 2.92726.503
controlProbeDetection25.793 2.68431.963
createTargetsFile0.0000.0000.001
expressionQCPipeline0.0720.0040.077
generateNeighbours0.0000.0000.001
getBeadData11.676 1.02415.254
identifyControlBeads23.003 1.33429.233
illuminaOutlierMethod13.310 1.57519.862
imageplot19.608 2.76924.614
insertBeadData12.516 1.59214.313
insertSectionData23.541 3.71627.650
makeControlProfile1.0470.0791.138
makeQCTable23.334 3.73327.319
medianNormalise4.8340.9945.909
metrics11.245 0.55312.105
noOutlierMethod11.291 0.59012.281
normaliseIllumina18.530 3.71822.899
numBeads11.665 0.57512.320
outlierplot45.437 3.31149.584
plotBeadIntensities13.506 1.69115.609
plotBeadLocations12.282 1.12213.584
plotChipLayout0.0000.0000.001
plotMAXY6.6821.2408.264
poscontPlot24.356 2.30827.028
quickSummary19.769 2.25823.116
readBeadSummaryData000
sectionNames11.582 0.59912.299
showArrayMask22.018 3.17625.630
squeezedVarOutlierMethod 98.017 2.120103.393
summarize67.026 9.02876.838
transformationFunctions13.086 1.61314.861
weightsOutlierMethod0.0000.0010.000