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Package 40/419HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.0.6
Mark Dunning
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/beadarray
Last Changed Rev: 53565 / Revision: 54588
Last Changed Date: 2011-03-10 02:48:20 -0800 (Thu, 10 Mar 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 

Summary

Package: beadarray
Version: 2.0.6
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings beadarray_2.0.6.tar.gz
StartedAt: 2011-04-07 06:05:34 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 06:10:03 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 269.1 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/beadarray.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '2.0.6'
* 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
createBeadSummaryData: no visible global function definition for
  'NoBeads'
createBeadSummaryData: no visible global function definition for
  'NoBeads<-'
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'
getArrayData,BeadLevelList: no visible global function definition for
  'beadResids'
* 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 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

beadarray.Rcheck/00install.out:

* installing *source* package 'beadarray' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c BASH.c -o BASH.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c HULK.c -o HULK.o
gcc -I"E:/biocbld/BBS-2˜1.7-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˜1.7-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˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:68:35: warning: statement with no effect
imageProcessing.c:70:0: warning: ignoring #pragma omp parallel
imageProcessing.c:51:9: warning: unused variable 'tmp'
imageProcessing.c:49:48: warning: unused variable 'k'
imageProcessing.c:49:45: warning: unused variable 'j'
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:166:0: warning: ignoring #pragma omp parallel
imageProcessing.c:168:0: warning: ignoring #pragma omp for
imageProcessing.c:175:0: warning: ignoring #pragma omp for
imageProcessing.c:154:22: warning: unused variable 'chunk'
imageProcessing.c:154:12: warning: unused variable 'nthreads'
imageProcessing.c:154:7: warning: unused variable 'tid'
gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LE:/biocbld/BBS-2˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-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
  'openVignette()'. 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 2.0.6
There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details

* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH46.62 0.1247.00
BASHCompact4.180.114.30
BASHDiffuse7.760.027.87
BASHExtended6.600.016.66
ExpressionControlData0.030.000.06
HULK5.680.035.85
backgroundCorrectSingleSection2.860.022.90
beadStatusVector2.580.002.58
beadarrayUsersGuide000
calculateDetection0.280.010.30
calculateOutlierStats6.050.036.11
class-beadLevelData2.530.022.60
class-illuminaChannel8.360.078.48
controlProbeDetection2.940.052.99
controlProfile0.010.000.01
createTargetsFile000
expressionQCPipeline2.570.022.59
generateNeighbours2.700.032.74
getBeadData2.590.012.62
illuminaOutlierMethod2.580.002.58
imageplot11.99 0.0812.13
insertSectionData3.230.053.28
makeQCTable3.160.033.22
medianNormalise0.030.000.03
normaliseIllumina4.200.064.40
numBeads3.810.003.82
outlierplot5.640.025.65
plotBeadIntensities2.610.032.64
plotBeadLocations2.670.062.77
plotChipLayout000
plotMAXY000
poscontPlot3.020.053.09
quickSummary2.680.012.72
readBeadSummaryData000
sectionNames2.660.022.70
showArrayMask9.480.069.59
summarize9.100.059.19
transformationFunctions4.140.174.33