Package: beadarray

Version: 2.4.1

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch beadarray_2.4.1.tar.gz

StartedAt: 2012-01-09 01:24:28 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:35:23 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 655.5 seconds

RetCode: 0

Status:  OK

CheckDir: beadarray.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/beadarray.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.4.1'
* 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 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 'X1'
imageplot: no visible binding for global variable 'X2'
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 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

* installing *source* package 'beadarray' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:155:9: warning: 'm' may be used uninitialized in this function
findAllOutliers.c:155:12: warning: 'ma' may be used uninitialized in this function
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:238:0: warning: ignoring #pragma omp parallel
imageProcessing.c:245:0: warning: ignoring #pragma omp parallel
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/beadarray.Rcheck/beadarray/libs/x64
** 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)

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	14.83	0.23	16.69
annotationInterface	13.70	0.39	15.06
backgroundCorrectSingleSection	0	0	0
beadarrayUsersGuide	0	0	0
boxplot	7.66	0.77	8.42
calculateDetection	17.01	0.45	17.47
calculateOutlierStats	29.38	1.53	30.91
class-beadLevelData	6.77	0.27	7.05
class-illuminaChannel	0	0	0
combine	12.48	0.97	13.45
controlProbeDetection	20.82	0.78	21.63
createTargetsFile	0	0	0
expressionQCPipeline	0.03	0.00	0.03
generateNeighbours	0	0	0
getBeadData	6.68	0.22	6.89
identifyControlBeads	19.40	0.37	19.79
illuminaOutlierMethod	7.49	0.46	8.00
imageplot	13.48	0.70	14.21
insertBeadData	7.28	0.34	7.66
insertSectionData	18.21	0.91	19.11
makeControlProfile	0.75	0.01	0.77
makeQCTable	18.28	0.96	19.25
medianNormalise	3.37	0.25	3.62
metrics	6.30	0.12	6.42
noOutlierMethod	6.36	0.10	6.46
normaliseIllumina	15.37	0.57	16.59
numBeads	6.80	0.13	6.93
outlierplot	50.70	0.94	51.67
plotBeadIntensities	7.59	0.31	7.90
plotBeadLocations	6.88	0.16	7.04
plotChipLayout	0	0	0
plotMAXY	4.43	0.21	4.65
poscontPlot	17.49	0.43	18.05
quickSummary	14.67	0.54	15.22
readBeadSummaryData	0	0	0
sectionNames	6.53	0.08	6.61
showArrayMask	20.34	0.58	20.92
squeezedVarOutlierMethod	70.58	0.34	70.94
summarize	49.77	2.47	52.25
transformationFunctions	7.90	0.27	8.17
weightsOutlierMethod	0	0	0