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Package 49/462HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.3.1
Mark Dunning
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray
Last Changed Rev: 55216 / Revision: 55359
Last Changed Date: 2011-05-03 07:49:30 -0700 (Tue, 03 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: beadarray
Version: 2.3.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.3.1.tar.gz
StartedAt: 2011-05-09 13:19:39 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 13:24:54 -0700 (Mon, 09 May 2011)
EllapsedTime: 314.8 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 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.3.1’
* 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 installed package size ... NOTE
  installed size is 14.5Mb
  sub-directories of 1Mb or more:
    data      7.0Mb
    doc       3.1Mb
    extdata   4.0Mb
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
checkPlatform: no visible binding for global variable ‘platformSigs’
makeControlProfile: no visible binding for global variable
  ‘ExpressionControlData’
poscontPlot: no visible binding for global variable
  ‘ExpressionControlData’
quickSummary: no visible binding for global variable
  ‘ExpressionControlData’
setAnnotation: no visible binding for global variable
  ‘ExpressionControlData’
showArrayMask: no visible binding for global variable ‘SAM’
summarize: no visible binding for global variable
  ‘ExpressionControlData’
viewBeads: no visible global function definition for ‘getArrayData’
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘beadlevel.pdf’ from 2296Kb to 393Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* 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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c BASH.c -o BASH.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c HULK.c -o HULK.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c findAllOutliers.c -o findAllOutliers.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c imageProcessing.c -o imageProcessing.o
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 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
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Creating a new generic function for "boxplot" in "beadarray"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘ImageProcessing.rnw’ 
   ‘beadarray.rnw’ 
   ‘beadlevel.rnw’ 
** testing if installed package can be loaded
Welcome to beadarray version 2.3.1
There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details

* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.0000.0010.001
BASHCompact5.9890.9276.965
BASHDiffuse8.6030.7109.345
BASHExtended8.3230.3048.709
ExpressionControlData0.0390.0020.041
HULK 7.863 0.34312.923
backgroundCorrectSingleSection3.1600.4586.512
beadStatusVector2.9550.2285.826
beadarrayUsersGuide0.0060.0020.009
calculateDetection0.2180.0140.330
calculateOutlierStats4.0940.5678.272
class-beadLevelData2.9560.2275.795
class-illuminaChannel 6.530 0.89313.215
combine3.7230.5056.130
controlProbeDetection3.5130.6025.754
controlProfile0.0110.0040.025
createTargetsFile0.0000.0010.000
expressionQCPipeline2.9530.2225.930
generateNeighbours3.2410.2224.147
getBeadData2.9300.2104.902
illuminaOutlierMethod3.0010.2545.824
imageplot 7.311 0.59113.846
insertSectionData3.8930.9558.656
makeQCTable3.9170.9458.762
medianNormalise0.0430.0080.070
normaliseIllumina 6.238 0.20911.349
numBeads4.1380.1966.599
outlierplot4.7420.3185.280
plotBeadIntensities3.0760.2373.339
plotBeadLocations3.0060.2173.268
plotChipLayout000
plotMAXY0.0010.0000.001
poscontPlot3.8650.3194.264
quickSummary3.0420.2303.302
readBeadSummaryData000
sectionNames2.9910.1963.593
showArrayMask12.003 0.75112.822
summarize7.5041.0598.902
transformationFunctions3.0580.2463.441