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BioC 3.2: CHECK report for beadarray on moscato1

This page was generated on 2016-04-23 10:15:53 -0700 (Sat, 23 Apr 2016).

Package 79/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.20.1
Mark Dunning
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/beadarray
Last Changed Rev: 112515 / Revision: 116712
Last Changed Date: 2016-01-13 08:34:26 -0800 (Wed, 13 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarray
Version: 2.20.1
Command: rm -rf beadarray.buildbin-libdir beadarray.Rcheck && mkdir beadarray.buildbin-libdir beadarray.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.20.1.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.20.1.tar.gz
StartedAt: 2016-04-22 23:49:50 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-23 00:12:39 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1369.1 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf beadarray.buildbin-libdir beadarray.Rcheck && mkdir beadarray.buildbin-libdir beadarray.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.20.1.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/beadarray.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.20.1'
* 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 whether package 'beadarray' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'Nozzle.R1' 'affy' 'ggbio' 'hwriter' 'lumi' 'vsn'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'ggplot2' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'BeadDataPackR:::combineFiles' 'BeadDataPackR:::readHeader'
  'Biobase:::assayDataStorageMode'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'illuminaForeground_6x6' 'locsIndicesToGrid' 'obtainLocs'
  'simpleXMLparse'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
combinedControlPlot: no visible binding for global variable 'Control'
combinedControlPlot: no visible binding for global variable 'Negative'
combinedControlPlot: no visible global function definition for 'ggplot'
combinedControlPlot: no visible global function definition for 'aes'
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 global function definition for
  'geom_boxplot'
combinedControlPlot: no visible global function definition for
  'geom_hline'
combinedControlPlot: no visible global function definition for
  'facet_wrap'
combinedControlPlot: no visible global function definition for
  'geom_point'
combinedControlPlot: no visible binding for global variable 'Masked'
createGEOMeta: no visible binding for global variable 'metaTemplate'
expressionQCPipeline: no visible global function definition for
  'ggsave'
expressionQCPipeline: no visible global function definition for
  'openPage'
expressionQCPipeline: no visible global function definition for
  'hwrite'
expressionQCPipeline: no visible global function definition for
  'hwriteImage'
expressionQCPipeline: no visible global function definition for
  'closePage'
getPlatformSigs: no visible global function definition for
  'lumiHumanIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'dbListTables'
getPlatformSigs: no visible global function definition for
  'dbListFields'
getPlatformSigs: no visible global function definition for 'dbGetQuery'
getPlatformSigs: no visible global function definition for
  'lumiMouseIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiRatIDMapping_dbconn'
imageplot: no visible global function definition for 'ggplot'
imageplot: no visible global function definition for 'aes'
imageplot: no visible binding for global variable 'Var1'
imageplot: no visible binding for global variable 'Var2'
imageplot: no visible binding for global variable 'value'
imageplot: no visible global function definition for 'geom_tile'
imageplot: no visible global function definition for
  'scale_fill_gradient'
imageplot: no visible global function definition for 'theme'
imageplot: no visible global function definition for 'element_blank'
makeReport: no visible global function definition for 'newCustomReport'
makeReport: no visible global function definition for 'newSection'
makeReport: no visible global function definition for 'newTable'
makeReport: no visible global function definition for 'newParagraph'
makeReport: no visible global function definition for 'addTo'
makeReport: no visible global function definition for 'autoplot'
makeReport: no visible global function definition for 'plotIdeogram'
makeReport: no visible global function definition for 'tracks'
makeReport: no visible global function definition for 'ggsave'
makeReport: no visible global function definition for 'newFigure'
makeReport: no visible binding for global variable 'IMAGE.TYPE.RASTER'
makeReport: no visible binding for global variable 'PROTECTION.PUBLIC'
makeReport: no visible global function definition for 'ggplot'
makeReport: no visible global function definition for 'aes'
makeReport: no visible binding for global variable 'value'
makeReport: no visible global function definition for 'geom_boxplot'
makeReport: no visible global function definition for 'facet_wrap'
makeReport: no visible global function definition for 'writeReport'
maplots: no visible global function definition for 'ggplot'
maplots: no visible global function definition for 'aes'
maplots: no visible binding for global variable 'value.1'
maplots: no visible binding for global variable 'value'
maplots: no visible global function definition for 'stat_binhex'
maplots: no visible global function definition for 'theme_bw'
maplots: no visible global function definition for 'xlab'
maplots: no visible global function definition for 'ylab'
maplots: no visible global function definition for 'facet_wrap'
maplots: no visible global function definition for 'theme'
maplots: no visible global function definition for 'ggtitle'
normaliseIllumina: no visible global function definition for 'lumiT'
normaliseIllumina: no visible global function definition for
  'normalize.qspline'
normaliseIllumina: no visible global function definition for 'vsn2'
normaliseIllumina: no visible global function definition for 'rsn'
outlierplot2: no visible global function definition for 'geom_vline'
outlierplot2: no visible global function definition for 'geom_hline'
plotBeadLocations2: no visible global function definition for 'qplot'
plotBeadLocations2: no visible global function definition for 'opts'
plotBeadLocations2: no visible global function definition for
  'theme_blank'
plotProbe: no visible global function definition for 'autoplot'
plotProbe: no visible binding for global variable 'genesymbol'
plotProbe: no visible global function definition for 'tracks'
plotProbe: no visible global function definition for 'aes'
plotProbe: no visible binding for global variable 'PROBEQUALITY'
rankInvariantNormalise: no visible global function definition for
  'normalize.invariantset'
suggestAnnotation: no visible binding for global variable
  'platformSigs'
suggestAnnotation_Vector: no visible binding for global variable
  'platformSigs'
[,ExpressionSetIllumina-ANY: no visible global function definition for
  'assayDataEnvLock'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'ggplot'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'aes'
boxplot,ExpressionSetIllumina : .local: no visible binding for global
  variable 'Var2'
boxplot,ExpressionSetIllumina : .local: no visible binding for global
  variable 'value'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'geom_boxplot'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'scale_fill_discrete'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'facet_wrap'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'theme'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'element_blank'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'element_text'
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for 'ylab'
plot,limmaResults-ANY : .local: no visible global function definition
  for 'ggplot'
plot,limmaResults-ANY : .local: no visible global function definition
  for 'aes'
plot,limmaResults-ANY : .local: no visible global function definition
  for 'geom_point'
plot,limmaResults-ANY : .local: no visible global function definition
  for 'facet_wrap'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'ggplot'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'aes'
plotMA,ExpressionSetIllumina : .local: no visible binding for global
  variable 'value.1'
plotMA,ExpressionSetIllumina : .local: no visible binding for global
  variable 'value'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'stat_binhex'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'theme_bw'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'xlab'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'ylab'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'facet_wrap'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'theme'
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for 'ggtitle'
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64/beadarray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [549s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 79.52   0.13   79.64
outlierplot              57.11   0.58   57.69
summarize                42.40   0.70   43.11
limmaDE                  30.74   0.11   30.85
calculateOutlierStats    26.93   0.90   28.33
identifyControlBeads     20.85   0.22   21.08
controlProbeDetection    20.45   0.28   20.73
showArrayMask            18.93   0.51   19.45
calculateDetection       18.83   0.16   18.99
insertSectionData        18.22   0.59   18.81
makeQCTable              17.87   0.58   18.45
poscontPlot              17.96   0.25   18.21
maplots                  16.63   0.98   17.61
normaliseIllumina        16.58   0.25   17.80
quickSummary             11.88   0.34   12.22
imageplot                11.38   0.33   11.72
addFeatureData            9.26   0.26   34.95
annotationInterface       8.28   0.30   13.00
combine                   6.66   0.38    7.04
boxplot                   5.01   0.12    5.13
** running examples for arch 'x64' ... [557s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 79.39   0.36   79.75
outlierplot              58.52   0.71   59.21
summarize                52.60   1.20   53.80
limmaDE                  36.46   0.09   36.55
calculateOutlierStats    29.12   0.92   30.07
controlProbeDetection    22.36   0.33   22.90
calculateDetection       21.43   0.22   21.65
insertSectionData        20.67   0.85   21.51
makeQCTable              20.70   0.79   21.49
showArrayMask            20.20   0.61   20.81
maplots                  19.08   1.28   20.36
identifyControlBeads     19.61   0.23   19.85
normaliseIllumina        19.25   0.33   19.66
poscontPlot              17.98   0.48   18.48
quickSummary             12.64   0.45   13.08
imageplot                11.75   0.55   12.29
annotationInterface       9.19   0.26    9.45
addFeatureData            8.94   0.06    9.00
combine                   7.70   0.47    8.18
plotBeadIntensities       5.93   0.37    6.31
insertBeadData            5.36   0.31    5.68
transformationFunctions   5.27   0.36    5.63
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/beadarray.Rcheck/00check.log'
for details.

beadarray.Rcheck/00install.out:


install for i386

* installing *source* package 'beadarray' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:247:13: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/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 [-Wunknown-pragmas]
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m32 -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'beadarray' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:247:13: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/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 [-Wunknown-pragmas]
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.20.1.zip
* DONE (beadarray)

beadarray.Rcheck/examples_i386/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.020.000.02
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate0.020.000.01
HULK000
addFeatureData 9.26 0.2634.95
annotationInterface 8.28 0.3013.00
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot5.010.125.13
calculateDetection18.83 0.1618.99
calculateOutlierStats26.93 0.9028.33
class-beadLevelData3.030.163.18
class-illuminaChannel000
combine6.660.387.04
controlProbeDetection20.45 0.2820.73
createTargetsFile000
expressionQCPipeline0.050.000.05
generateNeighbours000
getBeadData3.640.183.82
identifyControlBeads20.85 0.2221.08
illuminaOutlierMethod3.580.313.88
imageplot11.38 0.3311.72
insertBeadData3.870.244.10
insertSectionData18.22 0.5918.81
limmaDE30.74 0.1130.85
makeControlProfile0.870.030.90
makeQCTable17.87 0.5818.45
maplots16.63 0.9817.61
medianNormalise2.250.012.27
metrics3.130.073.19
noOutlierMethod3.220.043.26
normaliseIllumina16.58 0.2517.80
numBeads3.370.083.45
outlierplot57.11 0.5857.69
plotBeadIntensities4.700.154.85
plotBeadLocations3.630.213.84
plotChipLayout000
plotMAXY000
poscontPlot17.96 0.2518.21
quickSummary11.88 0.3412.22
readBeadSummaryData000
sectionNames2.690.052.73
showArrayMask18.93 0.5119.45
squeezedVarOutlierMethod79.52 0.1379.64
summarize42.40 0.7043.11
transformationFunctions3.570.173.74
weightsOutlierMethod000

beadarray.Rcheck/examples_x64/beadarray-Ex.timings:

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate000
HULK000
addFeatureData8.940.069.00
annotationInterface9.190.269.45
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot4.260.164.42
calculateDetection21.43 0.2221.65
calculateOutlierStats29.12 0.9230.07
class-beadLevelData3.530.173.69
class-illuminaChannel000
combine7.700.478.18
controlProbeDetection22.36 0.3322.90
createTargetsFile000
expressionQCPipeline0.070.000.07
generateNeighbours000
getBeadData3.520.143.66
identifyControlBeads19.61 0.2319.85
illuminaOutlierMethod3.880.234.17
imageplot11.75 0.5512.29
insertBeadData5.360.315.68
insertSectionData20.67 0.8521.51
limmaDE36.46 0.0936.55
makeControlProfile0.840.000.84
makeQCTable20.70 0.7921.49
maplots19.08 1.2820.36
medianNormalise2.400.072.46
metrics2.340.112.45
noOutlierMethod2.780.072.85
normaliseIllumina19.25 0.3319.66
numBeads2.980.093.08
outlierplot58.52 0.7159.21
plotBeadIntensities5.930.376.31
plotBeadLocations3.820.194.00
plotChipLayout000
plotMAXY000
poscontPlot17.98 0.4818.48
quickSummary12.64 0.4513.08
readBeadSummaryData000
sectionNames3.650.113.76
showArrayMask20.20 0.6120.81
squeezedVarOutlierMethod79.39 0.3679.75
summarize52.6 1.253.8
transformationFunctions5.270.365.63
weightsOutlierMethod000