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Package 49/467HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.2.0
Mark Dunning
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/beadarray
Last Changed Rev: 55866 / Revision: 59457
Last Changed Date: 2011-05-27 08:12:50 -0700 (Fri, 27 May 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: beadarray
Version: 2.2.0
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.2.0.tar.gz
StartedAt: 2011-10-20 11:47:44 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 11:50:46 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 182.1 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/beadarray.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.2.0’
* checking package namespace 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 14.7Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    doc       3.3Mb
    data      7.0Mb
* 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 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
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 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c findAllOutliers.c -o findAllOutliers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c imageProcessing.c -o imageProcessing.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/beadarray.Rcheck/beadarray/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "boxplot" in "beadarray"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Welcome to beadarray version 2.2.0
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
BASH0.0000.0000.001
BASHCompact4.1840.1124.501
BASHDiffuse5.3960.0485.799
BASHExtended5.4450.0205.558
ExpressionControlData0.0160.0040.048
HULK4.6760.0244.760
backgroundCorrectSingleSection1.6320.0441.690
beadStatusVector1.4720.0401.516
beadarrayUsersGuide0.0040.0000.005
calculateDetection0.1560.0040.159
calculateOutlierStats2.3920.0162.410
class-beadLevelData1.4960.0281.591
class-illuminaChannel4.2570.0444.356
combine2.1720.0642.245
controlProbeDetection1.9240.0401.982
controlProfile0.0080.0000.007
createTargetsFile000
expressionQCPipeline1.4440.0401.481
generateNeighbours1.6520.0361.688
getBeadData1.4320.0601.495
illuminaOutlierMethod1.4720.0401.510
imageplot4.6960.0564.780
insertSectionData2.1490.0722.303
makeQCTable2.1160.0482.204
medianNormalise0.0240.0000.023
normaliseIllumina4.6840.0244.721
numBeads3.1480.0605.281
outlierplot3.6200.0806.077
plotBeadIntensities1.6610.0362.951
plotBeadLocations1.6040.0443.311
plotChipLayout000
plotMAXY000
poscontPlot1.8000.0323.268
quickSummary1.6320.0603.167
readBeadSummaryData0.0000.0000.001
sectionNames1.5800.0602.351
showArrayMask 8.625 0.09213.833
summarize5.9160.0929.022
transformationFunctions1.5880.0242.446