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BioC 3.4: CHECK report for beadarray on tokay1

This page was generated on 2017-04-15 16:14:53 -0400 (Sat, 15 Apr 2017).

Package 92/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.24.0
Mark Dunning
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/beadarray
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarray
Version: 2.24.0
Command: rm -rf beadarray.buildbin-libdir beadarray.Rcheck && mkdir beadarray.buildbin-libdir beadarray.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.24.0.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.24.0.tar.gz
StartedAt: 2017-04-14 21:06:47 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:21:13 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 865.8 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:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.24.0.tar.gz >beadarray.Rcheck\00install.out 2>&1 && cp beadarray.Rcheck\00install.out beadarray-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/beadarray.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '2.24.0'
* 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
.mergePhenodata: no visible global function definition for 'new'
.onAttach: no visible global function definition for
  'packageDescription'
addFeatureData: no visible global function definition for 'is'
addFeatureData: no visible global function definition for 'new'
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'
checkRegistration: no visible global function definition for 'new'
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'
convertBeadLevelList: no visible global function definition for 'new'
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'
limmaDE: no visible global function definition for 'new'
makeControlProfile: no visible global function definition for
  'packageDescription'
makeReport: no visible global function definition for 'as'
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 'new'
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'
readBeadSummaryData: no visible global function definition for 'new'
readIdatFiles: no visible global function definition for 'new'
readIllumina: no visible global function definition for 'new'
readQC: no visible global function definition for 'read.table'
readQC: no visible global function definition for 'new'
readSampleSheet: no visible global function definition for 'read.csv'
setFeatureData: no visible global function definition for
  'packageDescription'
setFeatureData: no visible global function definition for 'new'
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 'new'
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'
channel,ExpressionSetIllumina-ANY: no visible global function
  definition for 'new'
coerce,ExpressionSet-ExpressionSetIllumina: no visible global function
  definition for 'new'
coerce,limmaResults-GRanges: no visible global function definition for
  'new'
combine,beadLevelData-beadLevelData: no visible global function
  definition for 'new'
initialize,ExpressionSetIllumina: no visible global function definition
  for 'new'
initialize,ExpressionSetIllumina: no visible global function definition
  for 'callNextMethod'
initialize,limmaResults: no visible global function definition for
  'new'
initialize,limmaResults: no visible global function definition for
  'callNextMethod'
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,ExpressionSetIllumina: no visible global function definition for
  'callNextMethod'
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 as assayDataEnvLock autoplot callNextMethod 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 is jpeg loess lowess lumiHumanIDMapping_dbconn
  lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT menu
  metaTemplate model.matrix new 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("methods", "as", "callNextMethod", "is", "new")
  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 (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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:/Users/biocbuild/bbs-3.4-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 48.62   0.33   48.95
outlierplot              33.42   0.76   34.18
summarize                31.31   1.42   32.74
calculateOutlierStats    18.11   1.41   19.52
limmaDE                  18.41   0.22   18.63
calculateDetection       15.70   0.41   16.10
controlProbeDetection    14.34   0.48   14.83
identifyControlBeads     13.11   0.22   13.33
maplots                  11.14   1.46   12.60
insertSectionData        11.18   0.78   11.97
showArrayMask            11.25   0.56   11.82
makeQCTable              10.95   0.67   11.62
poscontPlot              10.89   0.37   11.27
normaliseIllumina        10.54   0.42   11.22
addFeatureData            8.45   0.18   14.72
quickSummary              8.21   0.32    8.53
imageplot                 7.60   0.52    8.14
annotationInterface       6.86   0.34   10.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 50.33   0.69   51.01
summarize                31.97   2.34   34.32
outlierplot              30.95   0.97   31.93
limmaDE                  22.43   0.03   22.47
calculateOutlierStats    18.50   1.44   19.94
maplots                  14.12   1.69   15.82
controlProbeDetection    14.83   0.65   15.47
calculateDetection       13.75   0.11   13.85
normaliseIllumina        13.04   0.34   13.75
insertSectionData        11.72   1.05   12.77
showArrayMask            11.74   0.91   12.64
identifyControlBeads     12.12   0.22   12.34
poscontPlot              10.90   0.47   11.38
makeQCTable              10.19   0.84   11.03
quickSummary              8.94   0.57    9.50
addFeatureData            9.16   0.22    9.38
imageplot                 7.22   0.69    7.91
annotationInterface       6.78   0.37    7.16
* 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:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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 -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-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 -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.24.0.zip
* DONE (beadarray)

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

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended0.020.000.02
GEO000
GEOtemplate000
HULK0.010.000.01
addFeatureData 8.45 0.1814.72
annotationInterface 6.86 0.3410.87
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot4.270.304.63
calculateDetection15.70 0.4116.10
calculateOutlierStats18.11 1.4119.52
class-beadLevelData2.830.213.05
class-illuminaChannel0.020.000.01
combine3.420.383.80
controlProbeDetection14.34 0.4814.83
createTargetsFile000
expressionQCPipeline0.030.000.03
generateNeighbours000
getBeadData2.750.132.88
identifyControlBeads13.11 0.2213.33
illuminaOutlierMethod3.540.263.81
imageplot7.600.528.14
insertBeadData3.190.233.42
insertSectionData11.18 0.7811.97
limmaDE18.41 0.2218.63
makeControlProfile0.530.000.53
makeQCTable10.95 0.6711.62
maplots11.14 1.4612.60
medianNormalise1.860.031.89
metrics2.360.092.45
noOutlierMethod2.390.112.50
normaliseIllumina10.54 0.4211.22
numBeads2.310.132.44
outlierplot33.42 0.7634.18
plotBeadIntensities3.180.333.52
plotBeadLocations2.820.303.10
plotChipLayout000
plotMAXY000
poscontPlot10.89 0.3711.27
quickSummary8.210.328.53
readBeadSummaryData000
sectionNames2.320.092.41
showArrayMask11.25 0.5611.82
squeezedVarOutlierMethod48.62 0.3348.95
summarize31.31 1.4232.74
transformationFunctions3.550.363.91
weightsOutlierMethod000

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

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate000
HULK000
addFeatureData9.160.229.38
annotationInterface6.780.377.16
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot3.950.144.10
calculateDetection13.75 0.1113.85
calculateOutlierStats18.50 1.4419.94
class-beadLevelData2.700.232.94
class-illuminaChannel000
combine3.940.534.47
controlProbeDetection14.83 0.6515.47
createTargetsFile000
expressionQCPipeline0.030.000.03
generateNeighbours000
getBeadData2.290.162.44
identifyControlBeads12.12 0.2212.34
illuminaOutlierMethod3.000.333.32
imageplot7.220.697.91
insertBeadData2.940.233.17
insertSectionData11.72 1.0512.77
limmaDE22.43 0.0322.47
makeControlProfile0.610.020.62
makeQCTable10.19 0.8411.03
maplots14.12 1.6915.82
medianNormalise1.750.061.81
metrics2.050.062.11
noOutlierMethod2.060.102.15
normaliseIllumina13.04 0.3413.75
numBeads2.030.112.14
outlierplot30.95 0.9731.93
plotBeadIntensities4.250.344.59
plotBeadLocations3.080.203.28
plotChipLayout000
plotMAXY000
poscontPlot10.90 0.4711.38
quickSummary8.940.579.50
readBeadSummaryData000
sectionNames2.200.072.28
showArrayMask11.74 0.9112.64
squeezedVarOutlierMethod50.33 0.6951.01
summarize31.97 2.3434.32
transformationFunctions3.500.393.89
weightsOutlierMethod000