Package: beadarray

Version: 2.3.5

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.3.5.tar.gz

StartedAt: 2011-07-06 23:38:28 -0700 (Wed, 06 Jul 2011)

EndedAt: 2011-07-06 23:41:35 -0700 (Wed, 06 Jul 2011)

EllapsedTime: 186.9 seconds

RetCode: 0

Status:  OK

CheckDir: beadarray.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/beadarray.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘2.3.5’
* 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 12.9Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    data      7.0Mb
    doc       1.5Mb
* 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 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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
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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/beadarray.Rcheck/beadarray/libs
** 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 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’ 
** testing if installed package can be loaded
Welcome to beadarray version 2.3.5
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	0.004	0.000	0.000
BASHCompact	4.224	0.108	4.332
BASHDiffuse	5.380	0.080	5.465
BASHExtended	5.513	0.040	5.558
ExpressionControlData	0.02	0.00	0.02
HULK	4.860	0.056	4.922
backgroundCorrectSingleSection	1.640	0.044	1.706
beadStatusVector	1.468	0.044	1.561
beadarrayUsersGuide	0.008	0.000	0.006
calculateDetection	0.156	0.000	0.161
calculateOutlierStats	2.304	0.048	2.363
class-beadLevelData	1.472	0.056	1.532
class-illuminaChannel	4.037	0.048	4.085
combine	2.044	0.072	2.123
controlProbeDetection	2.068	0.040	2.111
controlProfile	0.008	0.000	0.007
createTargetsFile	0	0	0
expressionQCPipeline	1.468	0.068	1.547
generateNeighbours	1.668	0.064	1.935
getBeadData	1.480	0.052	2.708
illuminaOutlierMethod	1.548	0.032	2.914
imageplot	4.720	0.088	8.292
insertSectionData	2.301	0.052	3.891
makeQCTable	2.272	0.032	3.728
medianNormalise	0.020	0.000	0.051
normaliseIllumina	4.924	0.044	7.751
numBeads	3.132	0.096	3.950
outlierplot	3.669	0.060	4.262
plotBeadIntensities	1.868	0.044	2.188
plotBeadLocations	1.636	0.032	1.727
plotChipLayout	0	0	0
plotMAXY	0	0	0
poscontPlot	1.752	0.060	1.812
quickSummary	1.608	0.036	1.654
readBeadSummaryData	0	0	0
sectionNames	1.552	0.048	1.623
showArrayMask	7.817	0.108	8.767
summarize	5.408	0.072	6.139
transformationFunctions	1.652	0.052	3.417