Package: beadarray

Version: 2.0.6

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.0.6.tar.gz

StartedAt: 2011-03-31 04:30:56 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:34:12 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 196.0 seconds

RetCode: 0

Status:  OK

CheckDir: beadarray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/beadarray.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘2.0.6’
* 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 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
createBeadSummaryData: no visible global function definition for
  ‘NoBeads’
createBeadSummaryData: no visible global function definition for
  ‘NoBeads<-’
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’
getArrayData,BeadLevelList: no visible global function definition for
  ‘beadResids’
* 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 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c findAllOutliers.c -o findAllOutliers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/beadarray.Rcheck/beadarray/libs
** 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)'.

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 2.0.6
There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details

* DONE (beadarray)

name	user	system	elapsed
BASH	42.774	0.196	44.381
BASHCompact	2.916	0.056	2.972
BASHDiffuse	5.037	0.036	5.078
BASHExtended	4.868	0.020	4.890
ExpressionControlData	0.016	0.000	0.017
HULK	4.204	0.052	4.259
backgroundCorrectSingleSection	1.680	0.036	1.716
beadStatusVector	1.537	0.032	1.566
beadarrayUsersGuide	0.004	0.000	0.005
calculateDetection	0.136	0.000	0.136
calculateOutlierStats	2.372	0.028	2.399
class-beadLevelData	1.552	0.032	1.585
class-illuminaChannel	3.924	0.028	3.955
controlProbeDetection	1.98	0.04	2.02
controlProfile	0.004	0.000	0.007
createTargetsFile	0	0	0
expressionQCPipeline	1.500	0.040	1.539
generateNeighbours	1.720	0.024	1.744
getBeadData	1.512	0.032	1.544
illuminaOutlierMethod	1.785	0.036	1.819
imageplot	4.960	0.052	5.012
insertSectionData	2.532	0.032	2.565
makeQCTable	2.492	0.028	2.523
medianNormalise	0.020	0.000	0.021
normaliseIllumina	4.416	0.036	4.459
numBeads	3.601	0.036	3.638
outlierplot	3.256	0.068	3.326
plotBeadIntensities	1.684	0.036	1.722
plotBeadLocations	2.068	0.024	2.090
plotChipLayout	0	0	0
plotMAXY	0	0	0
poscontPlot	2.800	0.048	2.848
quickSummary	1.680	0.036	1.714
readBeadSummaryData	0	0	0
sectionNames	1.653	0.024	1.673
showArrayMask	7.376	0.052	7.426
summarize	4.800	0.048	4.860
transformationFunctions	1.956	0.292	2.250