Package: beadarray

Version: 2.6.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.6.0.tar.gz

StartedAt: 2012-03-31 23:45:59 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:52:57 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 418.0 seconds

RetCode: 0

Status:  OK

CheckDir: beadarray.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/beadarray.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.6.0'
* 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  5.7Mb
  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
.onAttach: warning in packageDescription("beadarray", field =
  "Version"): partial argument match of 'field' to 'fields'
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'
expressionQCPipeline: warning in ggsave(im, file = fname.im, width = 4,
  height = 1): partial argument match of 'file' to 'filename'
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'
makeControlProfile: warning in packageDescription(annoPkg, field =
  "Version"): partial argument match of 'field' to 'fields'
plotMAXY: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
processSwathData: warning in assignToImage(t1, an, inputDir = inputDir,
  twocolour = twoColour, locs = locslist, GrnTiffSuffix1 =
  GrnTiffSuffix1, GrnTiffSuffix2 = GrnTiffSuffix2, verbose = verbose):
  partial argument match of 'locs' to 'locslist'
summarize: warning in packageDescription(annoPkg, field = "Version"):
  partial argument match of 'field' to 'fields'
* 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 installed files from '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

NOTE: There were 3 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/beadarray.Rcheck/00check.log'
for details.

* installing *source* package 'beadarray' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c findAllOutliers.c -o findAllOutliers.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c imageProcessing.c -o imageProcessing.o
gcc -std=gnu99 -shared -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/beadarray.Rcheck/beadarray/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ImageProcessing.rnw' 
   'beadarray.rnw' 
   'beadlevel.rnw' 
   'beadsummary.rnw' 
** testing if installed package can be loaded

* DONE (beadarray)

name	user	system	elapsed
BASH	0	0	0
BASHCompact	0	0	0
BASHDiffuse	0	0	0
BASHExtended	0	0	0
HULK	0	0	0
addFeatureData	10.220	0.104	10.419
annotationInterface	7.081	0.240	7.365
backgroundCorrectSingleSection	0.004	0.000	0.000
beadarrayUsersGuide	0.004	0.000	0.012
boxplot	4.300	0.020	4.369
calculateDetection	11.777	0.036	11.840
calculateOutlierStats	16.953	0.880	17.862
class-beadLevelData	2.296	0.032	2.351
class-illuminaChannel	0.004	0.000	0.003
combine	6.480	0.196	6.711
controlProbeDetection	12.985	0.096	13.142
createTargetsFile	0	0	0
expressionQCPipeline	0.036	0.004	0.054
generateNeighbours	0	0	0
getBeadData	2.372	0.016	2.411
identifyControlBeads	11.553	0.064	11.675
illuminaOutlierMethod	3.036	0.040	3.099
imageplot	6.965	0.040	7.040
insertBeadData	2.524	0.044	2.595
insertSectionData	10.421	0.044	10.528
makeControlProfile	0.556	0.016	0.605
makeQCTable	10.916	0.208	11.199
medianNormalise	2.120	0.012	2.153
metrics	1.713	0.000	1.737
noOutlierMethod	1.928	0.016	1.965
normaliseIllumina	16.113	0.112	16.542
numBeads	2.076	0.008	2.107
outlierplot	16.661	0.140	16.835
plotBeadIntensities	2.936	0.108	3.064
plotBeadLocations	2.704	0.084	2.806
plotChipLayout	0	0	0
plotMAXY	2.972	0.024	3.017
poscontPlot	11.253	0.204	11.517
quickSummary	7.797	0.096	7.948
readBeadSummaryData	0	0	0
sectionNames	2.368	0.036	2.427
showArrayMask	6.920	0.272	7.217
squeezedVarOutlierMethod	54.396	0.080	54.506
summarize	35.846	0.680	36.611
transformationFunctions	3.012	0.168	3.206
weightsOutlierMethod	0.000	0.000	0.001