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Package 40/419HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.0.6
Mark Dunning
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/beadarray
Last Changed Rev: 53565 / Revision: 54281
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: beadarray
Version: 2.0.6
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.0.6.tar.gz
StartedAt: 2011-03-31 04:39:13 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 04:45:44 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 391.2 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/beadarray.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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 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
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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c BASH.c -o BASH.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c HULK.c -o HULK.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function ‘roundLocsFileValues’:
determiningGridPositions.c:7: warning: unused variable ‘vecLength’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:161: warning: ‘ma’ may be used uninitialized in this function
findAllOutliers.c:161: warning: ‘m’ may be used uninitialized in this function
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:234: warning: ‘status’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:68: warning: statement with no effect
imageProcessing.c:70: warning: ignoring #pragma omp parallel
imageProcessing.c:51: warning: unused variable ‘tmp’
imageProcessing.c:49: warning: unused variable ‘k’
imageProcessing.c:49: warning: unused variable ‘j’
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:166: warning: ignoring #pragma omp parallel
imageProcessing.c:168: warning: ignoring #pragma omp for
imageProcessing.c:175: warning: ignoring #pragma omp for
imageProcessing.c:154: warning: unused variable ‘chunk’
imageProcessing.c:154: warning: unused variable ‘nthreads’
imageProcessing.c:154: warning: unused variable ‘tid’
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/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
BASH68.913 3.88074.015
BASHCompact5.7221.1557.243
BASHDiffuse 8.975 0.83010.112
BASHExtended9.0890.4179.920
ExpressionControlData0.0350.0010.037
HULK8.3350.4319.589
backgroundCorrectSingleSection3.7650.5684.389
beadStatusVector3.3210.2753.667
beadarrayUsersGuide0.0070.0020.008
calculateDetection0.2140.0170.233
calculateOutlierStats4.5340.6875.322
class-beadLevelData3.3050.2794.203
class-illuminaChannel 6.843 1.05210.391
controlProbeDetection3.9760.6975.840
controlProfile0.0120.0030.065
createTargetsFile0.0000.0000.001
expressionQCPipeline3.2800.2834.314
generateNeighbours3.6460.3005.511
getBeadData3.3170.3044.698
illuminaOutlierMethod3.3560.3194.474
imageplot7.7590.7029.078
insertSectionData4.4171.1835.754
makeQCTable4.4141.2105.979
medianNormalise0.0410.0070.059
normaliseIllumina5.7000.2266.609
numBeads4.7410.2575.107
outlierplot5.3660.4477.181
plotBeadIntensities3.4990.3264.429
plotBeadLocations3.4250.2913.773
plotChipLayout0.0000.0000.001
plotMAXY0.0000.0010.000
poscontPlot3.9110.4444.737
quickSummary3.5960.4305.218
readBeadSummaryData0.0000.0000.001
sectionNames3.4810.3114.459
showArrayMask13.084 1.00015.663
summarize7.7551.2489.115
transformationFunctions3.9420.8114.807