Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.3: CHECK report for beadarray on windows2.bioconductor.org

This page was generated on 2015-10-27 12:14:06 -0400 (Tue, 27 Oct 2015).

Package 79/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.21.0
Mark Dunning
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarray
Version: 2.21.0
Command: rm -rf beadarray.buildbin-libdir beadarray.Rcheck && mkdir beadarray.buildbin-libdir beadarray.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.21.0.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.21.0.tar.gz
StartedAt: 2015-10-27 00:46:07 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 00:59:39 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 811.9 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 && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.21.0.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/beadarray.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '2.21.0'
* 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: no visible global function definition
  for 'ggplot'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'aes'
boxplot,ExpressionSetIllumina: no visible binding for global variable
  'Var2'
boxplot,ExpressionSetIllumina: no visible binding for global variable
  'value'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'geom_boxplot'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'scale_fill_discrete'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'facet_wrap'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'theme'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'element_blank'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'element_text'
boxplot,ExpressionSetIllumina: no visible global function definition
  for 'ylab'
plot,limmaResults-ANY: no visible global function definition for
  'ggplot'
plot,limmaResults-ANY: no visible global function definition for 'aes'
plot,limmaResults-ANY: no visible global function definition for
  'geom_point'
plot,limmaResults-ANY: no visible global function definition for
  'facet_wrap'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'ggplot'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'aes'
plotMA,ExpressionSetIllumina: no visible binding for global variable
  'value.1'
plotMA,ExpressionSetIllumina: no visible binding for global variable
  'value'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'stat_binhex'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'theme_bw'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'xlab'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'ylab'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'facet_wrap'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'theme'
plotMA,ExpressionSetIllumina: no visible global function definition for
  'ggtitle'
Undefined global functions or variables:
  Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
  Negative PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo aes
  assayDataEnvLock autoplot closePage dbGetQuery dbListFields
  dbListTables element_blank element_text facet_wrap genesymbol
  geom_boxplot geom_hline geom_point geom_tile geom_vline ggplot ggsave
  ggtitle hwrite hwriteImage lumiHumanIDMapping_dbconn
  lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT metaTemplate
  newCustomReport newFigure newParagraph newSection newTable
  normalize.invariantset normalize.qspline openPage opts platformSigs
  plotIdeogram qplot rsn scale_fill_discrete scale_fill_gradient
  stat_binhex theme theme_blank theme_bw tracks value value.1 vsn2
  writeReport xlab ylab
* 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 'c:/biocbld/bbs-3.3-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'c:/biocbld/bbs-3.3-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' ... [340s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 46.61   0.22   46.83
outlierplot              31.38   0.64   32.01
summarize                30.29   1.33   31.62
limmaDE                  21.25   0.03   21.28
calculateOutlierStats    17.80   0.92   18.74
controlProbeDetection    14.35   0.47   14.83
identifyControlBeads     14.27   0.15   14.42
calculateDetection       13.60   0.30   13.89
insertSectionData        11.65   0.91   12.57
makeQCTable              11.13   0.58   11.70
showArrayMask            11.06   0.62   11.69
poscontPlot              10.56   0.34   10.91
maplots                   9.86   0.70   10.57
normaliseIllumina         9.81   0.25   10.32
imageplot                 8.57   0.49    9.05
quickSummary              7.66   0.33    7.98
annotationInterface       5.84   0.33    6.28
addFeatureData            5.82   0.22    9.23
combine                   5.37   0.35    5.73
** running examples for arch 'x64' ... [343s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 48.50   0.39   48.90
summarize                32.25   1.86   34.11
outlierplot              31.82   0.79   32.61
limmaDE                  24.47   0.05   24.54
calculateOutlierStats    16.96   1.11   18.06
calculateDetection       14.72   0.14   14.86
controlProbeDetection    14.36   0.47   14.83
identifyControlBeads     12.65   0.23   12.89
insertSectionData        11.25   0.76   12.01
makeQCTable              11.22   0.69   11.91
normaliseIllumina        11.00   0.33   11.33
poscontPlot              10.89   0.40   11.29
showArrayMask            10.66   0.60   11.25
maplots                   9.08   1.27   10.34
quickSummary              8.80   0.41    9.21
imageplot                 6.61   0.47    7.08
addFeatureData            6.76   0.15    6.93
annotationInterface       6.16   0.19    6.34
combine                   4.91   0.34    5.25
* 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
  'c:/biocbld/bbs-3.3-bioc/meat/beadarray.Rcheck/00check.log'
for details.

beadarray.Rcheck/00install.out:


install for i386

* installing *source* package 'beadarray' ...
** libs
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/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"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/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/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-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"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/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"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/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/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.21.0.zip
* DONE (beadarray)

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

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate000
HULK0.010.000.02
addFeatureData5.820.229.23
annotationInterface5.840.336.28
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot3.200.173.38
calculateDetection13.60 0.3013.89
calculateOutlierStats17.80 0.9218.74
class-beadLevelData2.580.192.76
class-illuminaChannel000
combine5.370.355.73
controlProbeDetection14.35 0.4714.83
createTargetsFile000
expressionQCPipeline0.040.000.05
generateNeighbours000
getBeadData3.110.163.26
identifyControlBeads14.27 0.1514.42
illuminaOutlierMethod3.250.313.57
imageplot8.570.499.05
insertBeadData3.030.263.29
insertSectionData11.65 0.9112.57
limmaDE21.25 0.0321.28
makeControlProfile0.50.00.5
makeQCTable11.13 0.5811.70
maplots 9.86 0.7010.57
medianNormalise1.590.071.65
metrics2.220.032.25
noOutlierMethod2.360.072.44
normaliseIllumina 9.81 0.2510.32
numBeads2.120.052.17
outlierplot31.38 0.6432.01
plotBeadIntensities2.990.283.28
plotBeadLocations2.730.182.91
plotChipLayout000
plotMAXY000
poscontPlot10.56 0.3410.91
quickSummary7.660.337.98
readBeadSummaryData000
sectionNames2.170.112.29
showArrayMask11.06 0.6211.69
squeezedVarOutlierMethod46.61 0.2246.83
summarize30.29 1.3331.62
transformationFunctions2.840.203.04
weightsOutlierMethod000

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

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate000
HULK000
addFeatureData6.760.156.93
annotationInterface6.160.196.34
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot3.250.163.40
calculateDetection14.72 0.1414.86
calculateOutlierStats16.96 1.1118.06
class-beadLevelData2.180.202.39
class-illuminaChannel000
combine4.910.345.25
controlProbeDetection14.36 0.4714.83
createTargetsFile000
expressionQCPipeline0.030.000.03
generateNeighbours000
getBeadData2.190.112.30
identifyControlBeads12.65 0.2312.89
illuminaOutlierMethod2.790.243.01
imageplot6.610.477.08
insertBeadData2.650.252.91
insertSectionData11.25 0.7612.01
limmaDE24.47 0.0524.54
makeControlProfile0.590.010.61
makeQCTable11.22 0.6911.91
maplots 9.08 1.2710.34
medianNormalise1.560.031.59
metrics2.430.112.53
noOutlierMethod1.780.081.86
normaliseIllumina11.00 0.3311.33
numBeads1.780.081.86
outlierplot31.82 0.7932.61
plotBeadIntensities3.770.244.00
plotBeadLocations2.780.162.94
plotChipLayout000
plotMAXY000
poscontPlot10.89 0.4011.29
quickSummary8.800.419.21
readBeadSummaryData000
sectionNames2.350.042.39
showArrayMask10.66 0.6011.25
squeezedVarOutlierMethod48.50 0.3948.90
summarize32.25 1.8634.11
transformationFunctions3.050.283.33
weightsOutlierMethod000