Package: beadarray

Version: 2.3.5

Command: mkdir beadarray.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.3.5.tar.gz >beadarray-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.3.5.tar.gz && mv beadarray.buildbin-libdir/* beadarray.Rcheck/ && rmdir beadarray.buildbin-libdir

StartedAt: 2011-07-07 04:13:00 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:18:30 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 330.3 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 2.14.0 Under development (unstable) (2011-06-20 r56188)
* 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 '2.3.5'
* 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:
    data      7.0Mb
    doc       1.5Mb
    extdata   4.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

install for i386

* installing *source* package 'beadarray' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -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
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -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
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/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/beadarray.buildbin-libdir/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 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

add DLL for x64

* 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.buildbin-libdir/beadarray/libs/x64
** 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
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.3.5.zip

* DONE (beadarray)

name	user	system	elapsed
BASH	0	0	0
BASHCompact	3.76	0.07	4.17
BASHDiffuse	6.44	0.03	6.47
BASHExtended	5.91	0.02	5.93
ExpressionControlData	0.02	0.00	0.02
HULK	5.27	0.02	5.30
backgroundCorrectSingleSection	1.67	0.03	1.70
beadStatusVector	1.56	0.01	1.58
beadarrayUsersGuide	0	0	0
calculateDetection	0.14	0.00	0.14
calculateOutlierStats	2.61	0.08	2.68
class-beadLevelData	1.65	0.03	1.69
class-illuminaChannel	4.02	0.05	4.07
combine	1.95	0.05	2.35
controlProbeDetection	2.14	0.10	2.25
controlProfile	0	0	0
createTargetsFile	0	0	0
expressionQCPipeline	1.51	0.04	1.54
generateNeighbours	1.74	0.04	1.78
getBeadData	1.57	0.03	1.61
illuminaOutlierMethod	1.56	0.05	1.60
imageplot	4.93	0.02	6.03
insertSectionData	2.17	0.03	2.20
makeQCTable	2.10	0.03	2.14
medianNormalise	0.03	0.00	0.03
normaliseIllumina	4.04	0.06	4.12
numBeads	2.56	0.00	2.59
outlierplot	3.89	0.05	4.05
plotBeadIntensities	1.85	0.01	1.88
plotBeadLocations	1.64	0.03	1.68
plotChipLayout	0	0	0
plotMAXY	0	0	0
poscontPlot	1.84	0.08	1.93
quickSummary	1.72	0.02	1.74
readBeadSummaryData	0	0	0
sectionNames	1.62	0.04	1.70
showArrayMask	9.55	0.07	9.62
summarize	4.94	0.04	4.99
transformationFunctions	1.75	0.00	1.75