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Package 55/631HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.9.1
Mark Dunning
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray
Last Changed Rev: 71415 / Revision: 72575
Last Changed Date: 2012-11-22 02:00:41 -0800 (Thu, 22 Nov 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: beadarray
Version: 2.9.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.9.1.tar.gz
StartedAt: 2013-01-16 00:50:22 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:00:10 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 588.2 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/beadarray.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘2.9.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘beadarray’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    2.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
expressionQCPipeline: warning in ggsave(im, file = fname.im, width = 4,
  height = 1): partial argument match of 'file' to 'filename'
makeControlProfile: warning in packageDescription(annoPkg, field =
  "Version"): partial argument match of 'field' to 'fields'
plotMAXY: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
summarize: warning in packageDescription(annoPkg, field = "Version"):
  partial argument match of 'field' to 'fields'
combinedControlPlot: no visible binding for global variable ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
combinedControlPlot: no visible binding for global variable ‘ID’
combinedControlPlot: no visible binding for global variable
  ‘Log2Intensity’
combinedControlPlot: no visible binding for global variable
  ‘ControlType’
combinedControlPlot: no visible binding for global variable ‘Masked’
getPlatformSigs: no visible global function definition for
  ‘lumiHumanIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
  ‘lumiMouseIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
  ‘lumiRatIDMapping_dbconn’
imageplot: no visible binding for global variable ‘Var1’
imageplot: no visible binding for global variable ‘Var2’
imageplot: no visible binding for global variable ‘value’
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 66.844  0.232  67.093
summarize                54.139  0.916  55.087
outlierplot              28.486  0.996  29.489
calculateOutlierStats    25.854  0.912  26.766
normaliseIllumina        25.625  0.124  25.768
calculateDetection       17.581  0.052  17.635
addFeatureData           16.017  0.260  16.523
makeQCTable              15.885  0.280  16.165
poscontPlot              15.609  0.492  16.114
insertSectionData        15.217  0.556  15.787
controlProbeDetection    14.409  0.176  14.598
quickSummary             12.381  0.452  12.835
identifyControlBeads     11.605  0.036  11.645
annotationInterface      10.633  0.536  11.192
showArrayMask             9.421  0.480   9.899
imageplot                 9.077  0.108   9.243
combine                   8.300  0.216   8.522
plotBeadIntensities       6.769  0.288   7.057
boxplot                   5.512  0.124   5.646
* 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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/beadarray.Rcheck/00check.log’
for details.

beadarray.Rcheck/00install.out:

* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c findAllOutliers.c -o findAllOutliers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c imageProcessing.c -o imageProcessing.o
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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/beadarray.Rcheck/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ImageProcessing.rnw’ 
   ‘beadarray.rnw’ 
   ‘beadlevel.rnw’ 
   ‘beadsummary.rnw’ 
** testing if installed package can be loaded

* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.040.000.04
BASHCompact0.0120.0000.014
BASHDiffuse0.0280.0000.027
BASHExtended0.0200.0000.017
HULK0.0200.0000.018
addFeatureData16.017 0.26016.523
annotationInterface10.633 0.53611.192
backgroundCorrectSingleSection0.0200.0080.029
beadarrayUsersGuide0.0040.0040.010
boxplot5.5120.1245.646
calculateDetection17.581 0.05217.635
calculateOutlierStats25.854 0.91226.766
class-beadLevelData2.8280.0642.892
class-illuminaChannel0.0280.0000.028
combine8.3000.2168.522
controlProbeDetection14.409 0.17614.598
createTargetsFile0.0000.0000.002
expressionQCPipeline0.0480.0120.058
generateNeighbours0.0040.0000.004
getBeadData2.3840.0442.434
identifyControlBeads11.605 0.03611.645
illuminaOutlierMethod4.4000.0204.421
imageplot9.0770.1089.243
insertBeadData3.3320.1403.478
insertSectionData15.217 0.55615.787
makeControlProfile1.1840.0081.202
makeQCTable15.885 0.28016.165
medianNormalise2.6960.0602.761
metrics2.1720.0362.208
noOutlierMethod2.4970.0482.547
normaliseIllumina25.625 0.12425.768
numBeads3.0040.1003.100
outlierplot28.486 0.99629.489
plotBeadIntensities6.7690.2887.057
plotBeadLocations4.1120.1804.295
plotChipLayout0.0040.0000.003
plotMAXY4.2160.0884.303
poscontPlot15.609 0.49216.114
quickSummary12.381 0.45212.835
readBeadSummaryData0.0320.0000.035
sectionNames2.9000.1123.010
showArrayMask9.4210.4809.899
squeezedVarOutlierMethod66.844 0.23267.093
summarize54.139 0.91655.087
transformationFunctions4.4930.3884.892
weightsOutlierMethod0.0040.0000.004