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BioC 3.3: CHECK report for beadarray on moscato2

This page was generated on 2016-10-13 12:47:45 -0700 (Thu, 13 Oct 2016).

Package 84/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.22.2
Mark Dunning
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/beadarray
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (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: 2.22.2
Command: rm -rf beadarray.buildbin-libdir beadarray.Rcheck && mkdir beadarray.buildbin-libdir beadarray.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.22.2.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out && E:\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_2.22.2.tar.gz
StartedAt: 2016-10-13 01:17:16 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:38:57 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1301.0 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.22.2.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out  && E:\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_2.22.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/beadarray.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.22.2'
* 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
.onAttach: no visible global function definition for
  'packageDescription'
analyseDirectory: no visible global function definition for
  'read.table'
calculateDetection: no visible global function definition for
  'txtProgressBar'
calculateDetection: no visible global function definition for
  'setTxtProgressBar'
combinedControlPlot: no visible binding for global variable 'Control'
combinedControlPlot: no visible binding for global variable 'Negative'
combinedControlPlot: no visible global function definition for
  'density'
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'
createGEOMatrix: no visible global function definition for
  'write.table'
createGEOMeta: no visible global function definition for 'data'
createGEOMeta: no visible binding for global variable 'metaTemplate'
createTargetsFile: no visible global function definition for
  'read.table'
expressionQCPipeline: no visible global function definition for
  'ggsave'
expressionQCPipeline: no visible global function definition for 'jpeg'
expressionQCPipeline: no visible global function definition for 'pdf'
expressionQCPipeline: no visible global function definition for 'png'
expressionQCPipeline: no visible global function definition for
  'dev.off'
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'
expressionQCPipeline: no visible global function definition for
  'write.csv'
generateE: no visible global function definition for 'aggregate'
genericBeadIntensityPlot: no visible global function definition for
  'runif'
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'
limmaDE: no visible global function definition for 'model.matrix'
makeControlProfile: no visible global function definition for
  'packageDescription'
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'
numberOfChannels: no visible global function definition for
  'read.table'
numberOfColumns: no visible global function definition for 'read.table'
outlierplot2: no visible global function definition for 'geom_vline'
outlierplot2: no visible global function definition for 'geom_hline'
plot.smooth.line: no visible global function definition for 'approx'
plot.smooth.line: no visible global function definition for 'lowess'
plotBeadIntensities: no visible global function definition for
  'rainbow'
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'
plotChipLayout: no visible global function definition for 'rgb'
plotProbe: no visible global function definition for 'data'
plotProbe: no visible binding for global variable 'genesymbol'
plotProbe: no visible global function definition for 'autoplot'
plotProbe: no visible global function definition for 'tracks'
plotProbe: no visible global function definition for 'aes'
plotProbe: no visible binding for global variable 'PROBEQUALITY'
plotTIFF: no visible global function definition for 'col2rgb'
plotTIFF: no visible global function definition for 'rgb'
poscontPlot: no visible global function definition for 'rainbow'
rankInvariantNormalise: no visible global function definition for
  'normalize.invariantset'
rankInvariantNormalise: no visible global function definition for
  'predict'
readBeadSummaryData: no visible global function definition for
  'read.table'
readQC: no visible global function definition for 'read.table'
readSampleSheet: no visible global function definition for 'read.csv'
setFeatureData: no visible global function definition for
  'packageDescription'
squeezedVarOutlierMethod: no visible global function definition for
  'loess'
squeezedVarOutlierMethod: no visible global function definition for
  'predict'
suggestAnnotation: no visible binding for global variable
  'platformSigs'
suggestAnnotation_Vector: no visible global function definition for
  'data'
suggestAnnotation_Vector: no visible binding for global variable
  'platformSigs'
summarize: no visible global function definition for
  'packageDescription'
viewBeads: no visible global function definition for 'col2rgb'
viewBeads: no visible global function definition for 'menu'
viewBeads: no visible global function definition for 'rgb'
writeOutFiles: no visible global function definition for 'write.table'
[,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'
show,limmaResults: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
  Negative PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo aes aggregate
  approx assayDataEnvLock autoplot closePage col2rgb data dbGetQuery
  dbListFields dbListTables density dev.off element_blank element_text
  facet_wrap genesymbol geom_boxplot geom_hline geom_point geom_tile
  geom_vline ggplot ggsave ggtitle hwrite hwriteImage jpeg loess lowess
  lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn
  lumiRatIDMapping_dbconn lumiT menu metaTemplate model.matrix
  newCustomReport newFigure newParagraph newSection newTable
  normalize.invariantset normalize.qspline openPage opts p.adjust
  packageDescription pdf platformSigs plotIdeogram png predict qplot
  rainbow read.csv read.table rgb rsn runif scale_fill_discrete
  scale_fill_gradient setTxtProgressBar stat_binhex theme theme_blank
  theme_bw tracks txtProgressBar value value.1 vsn2 write.csv
  write.table writeReport xlab ylab
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
             "rainbow", "rgb")
  importFrom("stats", "aggregate", "approx", "density", "loess",
             "lowess", "model.matrix", "p.adjust", "predict", "runif")
  importFrom("utils", "data", "menu", "packageDescription", "read.csv",
             "read.table", "setTxtProgressBar", "txtProgressBar",
             "write.csv", "write.table")
to your NAMESPACE file.
* 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 'E:/biocbld/bbs-3.3-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386/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' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 71.20   0.16   71.37
outlierplot              54.64   0.87   55.52
summarize                49.84   1.48   51.34
limmaDE                  29.67   0.11   29.80
calculateOutlierStats    26.66   1.28   28.05
calculateDetection       26.01   0.20   27.17
controlProbeDetection    21.30   0.43   21.78
makeQCTable              17.21   0.68   17.89
identifyControlBeads     16.94   0.21   17.14
poscontPlot              15.89   0.49   16.38
showArrayMask            15.44   0.59   16.13
insertSectionData        14.84   0.92   15.75
maplots                  13.48   0.96   17.10
normaliseIllumina        13.95   0.33   15.21
quickSummary             11.42   0.43   11.86
imageplot                 9.91   0.37   13.86
annotationInterface       9.60   0.39   12.77
addFeatureData            9.31   0.15   24.18
boxplot                   7.89   0.22    8.11
combine                   6.78   0.39    7.32
plotBeadLocations         3.69   0.28    5.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 76.86   0.31   77.17
outlierplot              63.27   0.93   64.21
summarize                47.57   1.50   49.08
limmaDE                  35.71   0.08   35.79
calculateOutlierStats    25.29   0.82   26.93
controlProbeDetection    22.65   0.51   23.17
calculateDetection       20.11   0.15   20.26
showArrayMask            19.19   0.57   19.76
identifyControlBeads     19.08   0.27   19.34
insertSectionData        17.08   0.78   17.86
maplots                  16.31   1.35   18.43
poscontPlot              16.09   0.39   16.47
makeQCTable              15.45   0.82   16.30
normaliseIllumina        15.19   0.28   16.50
quickSummary             12.23   0.41   12.63
imageplot                 9.91   0.36   10.41
addFeatureData            9.79   0.15    9.94
annotationInterface       8.72   0.24    9.03
combine                   6.55   0.33    8.59
illuminaOutlierMethod     5.14   0.34    5.49
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/beadarray.Rcheck/00check.log'
for details.

beadarray.Rcheck/00install.out:


install for i386

* installing *source* package 'beadarray' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/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 [-Wmaybe-uninitialized]
   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
                             ^
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
                                                     ^
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized]
  beadStatusStruct *status; 
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/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]
     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
 ^
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
 ^
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
 ^
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
 ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/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
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/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 [-Wmaybe-uninitialized]
   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
                             ^
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
                                                     ^
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226:20: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized]
  beadStatusStruct *status; 
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/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]
     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
 ^
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
 ^
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
 ^
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
 ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/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_2.22.2.zip
* DONE (beadarray)

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

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse0.020.000.02
BASHExtended000
GEO000
GEOtemplate000
HULK000
addFeatureData 9.31 0.1524.18
annotationInterface 9.60 0.3912.77
backgroundCorrectSingleSection000
beadarrayUsersGuide0.000.020.02
boxplot7.890.228.11
calculateDetection26.01 0.2027.17
calculateOutlierStats26.66 1.2828.05
class-beadLevelData3.790.304.09
class-illuminaChannel0.020.000.01
combine6.780.397.32
controlProbeDetection21.30 0.4321.78
createTargetsFile000
expressionQCPipeline0.040.000.04
generateNeighbours000
getBeadData3.310.113.42
identifyControlBeads16.94 0.2117.14
illuminaOutlierMethod4.600.234.83
imageplot 9.91 0.3713.86
insertBeadData3.580.383.96
insertSectionData14.84 0.9215.75
limmaDE29.67 0.1129.80
makeControlProfile0.730.000.73
makeQCTable17.21 0.6817.89
maplots13.48 0.9617.10
medianNormalise2.010.042.06
metrics2.450.072.51
noOutlierMethod2.500.062.55
normaliseIllumina13.95 0.3315.21
numBeads3.490.143.64
outlierplot54.64 0.8755.52
plotBeadIntensities3.580.343.91
plotBeadLocations3.690.285.13
plotChipLayout000
plotMAXY000
poscontPlot15.89 0.4916.38
quickSummary11.42 0.4311.86
readBeadSummaryData0.000.020.01
sectionNames3.470.113.57
showArrayMask15.44 0.5916.13
squeezedVarOutlierMethod71.20 0.1671.37
summarize49.84 1.4851.34
transformationFunctions4.340.234.57
weightsOutlierMethod000

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

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate0.000.020.01
HULK000
addFeatureData9.790.159.94
annotationInterface8.720.249.03
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot4.530.144.66
calculateDetection20.11 0.1520.26
calculateOutlierStats25.29 0.8226.93
class-beadLevelData3.040.263.31
class-illuminaChannel000
combine6.550.338.59
controlProbeDetection22.65 0.5123.17
createTargetsFile000
expressionQCPipeline0.040.000.03
generateNeighbours000
getBeadData4.210.224.43
identifyControlBeads19.08 0.2719.34
illuminaOutlierMethod5.140.345.49
imageplot 9.91 0.3610.41
insertBeadData4.480.374.85
insertSectionData17.08 0.7817.86
limmaDE35.71 0.0835.79
makeControlProfile0.830.020.84
makeQCTable15.45 0.8216.30
maplots16.31 1.3518.43
medianNormalise1.950.001.95
metrics3.270.103.38
noOutlierMethod3.170.053.22
normaliseIllumina15.19 0.2816.50
numBeads2.940.163.09
outlierplot63.27 0.9364.21
plotBeadIntensities4.650.284.93
plotBeadLocations3.740.163.90
plotChipLayout000
plotMAXY000
poscontPlot16.09 0.3916.47
quickSummary12.23 0.4112.63
readBeadSummaryData000
sectionNames2.240.082.33
showArrayMask19.19 0.5719.76
squeezedVarOutlierMethod76.86 0.3177.17
summarize47.57 1.5049.08
transformationFunctions3.670.223.89
weightsOutlierMethod000