Package: beadarray

Version: 2.1.12

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings beadarray_2.1.12.tar.gz

StartedAt: 2011-02-24 17:03:46 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:07:37 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 231.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: beadarray.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/beadarray.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.1.12'
* 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 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
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 ... WARNING
Codoc mismatches from documentation object 'processSwathData':
processSwathData
  Code: function(twoColour = NULL, textstring = "_perBeadFile.txt",
                 segmentHeight = 326, segmentWidth = 397, swathOverlap
                 = 81, fullOutput = TRUE, newTextString = ".txt",
                 verbose = TRUE)
  Docs: function(twoColour = TRUE, textstring = "_perBeadFile.txt",
                 segmentHeight = 326, segmentWidth = 397, swathOverlap
                 = 81, fullOutput = TRUE, newTextString = ".txt",
                 verbose = TRUE)
  Mismatches in argument default values:
    Name: 'twoColour' Code: NULL Docs: TRUE

* 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.8-bioc/meat/beadarray.Rcheck/00check.log'
for details

* installing *source* package 'beadarray' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c BASH.c -o BASH.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c HULK.c -o HULK.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function 'roundLocsFileValues':
determiningGridPositions.c:7:12: warning: unused variable 'vecLength'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:161:9: warning: 'm' may be used uninitialized in this function
findAllOutliers.c:161:12: warning: 'ma' may be used uninitialized in this function
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:234:20: warning: 'status' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:82:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:126:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:224:0: warning: ignoring #pragma omp parallel
imageProcessing.c:231:0: warning: ignoring #pragma omp parallel
gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/beadarray.Rcheck/beadarray/libs/i386
** 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 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 2.1.12
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	44.66	0.34	45.23
BASHCompact	4.29	0.11	4.44
BASHDiffuse	6.11	0.02	6.19
BASHExtended	6.36	0.01	6.37
ExpressionControlData	0.03	0.00	0.03
HULK	5.27	0.00	5.27
backgroundCorrectSingleSection	2.86	0.05	2.91
beadStatusVector	2.53	0.12	2.65
beadarrayUsersGuide	0.02	0.00	0.02
calculateDetection	0.15	0.00	0.15
calculateOutlierStats	3.81	0.05	3.86
class-beadLevelData	2.57	0.08	2.67
class-illuminaChannel	5.47	0.06	5.54
controlProbeDetection	3.07	0.03	3.11
controlProfile	0.02	0.00	0.01
createTargetsFile	0	0	0
expressionQCPipeline	2.52	0.02	2.53
generateNeighbours	2.78	0.00	2.78
getBeadData	2.54	0.00	2.55
illuminaOutlierMethod	2.58	0.01	2.59
imageplot	6.53	0.03	6.60
insertSectionData	3.25	0.07	3.33
makeQCTable	3.35	0.03	3.39
medianNormalise	0.02	0.00	0.02
normaliseIllumina	3.83	0.20	4.20
numBeads	4.20	0.03	4.27
outlierplot	4.87	0.05	4.94
plotBeadIntensities	2.74	0.03	2.77
plotBeadLocations	2.73	0.02	2.75
plotChipLayout	0	0	0
plotMAXY	0	0	0
poscontPlot	2.86	0.04	2.92
quickSummary	2.88	0.07	2.93
readBeadSummaryData	0.00	0.01	0.02
sectionNames	2.61	0.00	2.61
showArrayMask	9.73	0.05	9.80
summarize	6.00	0.08	6.09
transformationFunctions	3.05	0.15	3.20