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CHECK report for beadarray on tokay2

This page was generated on 2018-10-17 08:32:44 -0400 (Wed, 17 Oct 2018).

Package 105/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.30.0
Mark Dunning
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/beadarray
Branch: RELEASE_3_7
Last Commit: 73dd490
Last Changed Date: 2018-04-30 10:35:04 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarray
Version: 2.30.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:beadarray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings beadarray_2.30.0.tar.gz
StartedAt: 2018-10-17 00:39:14 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:57:59 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1124.3 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:beadarray.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings beadarray_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/beadarray.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.30.0'
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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-3.7-bioc/R/library/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
maplots                  83.23  12.15   95.41
squeezedVarOutlierMethod 52.60   0.08   52.68
summarize                37.31   0.22   37.53
outlierplot              36.89   0.17   37.08
calculateOutlierStats    18.29   1.27   19.56
controlProbeDetection    18.84   0.72   19.56
showArrayMask            17.44   0.14   17.58
limmaDE                  17.19   0.15   17.34
normaliseIllumina        11.10   5.19   22.74
insertSectionData        14.10   1.18   15.28
identifyControlBeads     14.48   0.27   14.75
calculateDetection       12.81   0.79   13.61
makeQCTable              12.10   0.99   13.08
poscontPlot              10.87   0.06   10.94
imageplot                 8.58   0.72    9.30
annotationInterface       7.76   0.37    8.14
quickSummary              7.52   0.08    7.60
addFeatureData            6.91   0.21    7.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
maplots                  115.78   3.44  120.32
squeezedVarOutlierMethod  55.56   0.11   55.68
summarize                 40.38   0.18   40.56
outlierplot               30.37   0.05   30.42
limmaDE                   24.51   0.21   24.78
calculateOutlierStats     20.76   1.92   22.75
controlProbeDetection     16.22   0.63   16.91
identifyControlBeads      15.95   0.30   16.27
calculateDetection        13.72   0.47   14.19
insertSectionData         12.61   1.20   13.90
makeQCTable               11.64   1.09   12.73
showArrayMask             11.91   0.14   12.04
poscontPlot               11.58   0.09   11.67
normaliseIllumina         10.55   0.34   12.25
annotationInterface        8.24   0.56    8.80
imageplot                  7.86   0.57    8.43
addFeatureData             8.20   0.19    8.39
quickSummary               7.10   0.10    7.20
metrics                    6.26   0.08    6.35
plotBeadIntensities        5.27   0.06    5.33
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/beadarray.Rcheck/00check.log'
for details.

Installation output

beadarray.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/beadarray_2.30.0.tar.gz && rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=beadarray.buildbin-libdir beadarray_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL beadarray_2.30.0.zip && rm beadarray_2.30.0.tar.gz beadarray_2.30.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  9 1317k    9  128k    0     0  1892k      0 --:--:-- --:--:-- --:--:-- 2064k
100 1317k  100 1317k    0     0  16.6M      0 --:--:-- --:--:-- --:--:-- 17.8M

install for i386

* installing *source* package 'beadarray' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c BASH.c -o BASH.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c HULK.c -o HULK.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c determiningGridPositions.c -o determiningGridPositions.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'beadarray'
    finding HTML links ... done
    BASH                                    html  
    BASHCompact                             html  
    BASHDiffuse                             html  
    BASHExtended                            html  
    GEO                                     html  
    GEOtemplate                             html  
    HULK                                    html  
    addFeatureData                          html  
    annotationInterface                     html  
    backgroundCorrectSingleSection          html  
    beadarray-package                       html  
    beadarrayUsersGuide                     html  
    boxplot                                 html  
    calculateDetection                      html  
    calculateOutlierStats                   html  
    checkRegistration                       html  
    class-BeadLevelList                     html  
    class-ExpressionSetIllumina             html  
    class-beadLevelData                     html  
    class-beadRegistrationData              html  
    class-illuminaChannel                   html  
    class-limmaResults                      html  
    combine                                 html  
    controlProbeDetection                   html  
    convertBeadLevelList                    html  
    createTargetsFile                       html  
    deprecatedFunctions                     html  
    dim                                     html  
    expressionQCPipeline                    html  
    generateNeighbours                      html  
    getBeadData                             html  
    identifyControlBeads                    html  
    illuminaOutlierMethod                   html  
    imageProcessing                         html  
    imageplot                               html  
    insertBeadData                          html  
    insertSectionData                       html  
    limmaDE                                 html  
    makeControlProfile                      html  
    makeQCTable                             html  
    maplots                                 html  
    medianNormalise                         html  
    metrics                                 html  
    noOutlierMethod                         html  
    normaliseIllumina                       html  
    numBeads                                html  
    outlierplot                             html  
    platformSigs                            html  
    plotBeadIntensities                     html  
    plotBeadLocations                       html  
    plotChipLayout                          html  
    plotMAXY                                html  
    plotTIFF                                html  
    poscontPlot                             html  
    processSwathData                        html  
    quickSummary                            html  
    readBeadSummaryData                     html  
    readIdatFiles                           html  
    readIllumina                            html  
    readLocsFile                            html  
    readTIFF                                html  
    sampleSheet                             html  
    sectionNames                            html  
    setWeights                              html  
    show                                    html  
    showArrayMask                           html  
    squeezedVarOutlierMethod                html  
    summarize                               html  
    transformationFunctions                 html  
    weightsOutlierMethod                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'beadarray' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c BASH.c -o BASH.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c HULK.c -o HULK.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c determiningGridPositions.c -o determiningGridPositions.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.30.0.zip
* DONE (beadarray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'beadarray' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

beadarray.Rcheck/examples_i386/beadarray-Ex.timings

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate000
HULK000
addFeatureData6.910.217.11
annotationInterface7.760.378.14
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot4.390.214.60
calculateDetection12.81 0.7913.61
calculateOutlierStats18.29 1.2719.56
class-beadLevelData2.940.123.06
class-illuminaChannel000
combine4.050.394.44
controlProbeDetection18.84 0.7219.56
createTargetsFile000
expressionQCPipeline0.010.000.01
generateNeighbours000
getBeadData2.970.143.11
identifyControlBeads14.48 0.2714.75
illuminaOutlierMethod4.380.234.61
imageplot8.580.729.30
insertBeadData3.930.314.24
insertSectionData14.10 1.1815.28
limmaDE17.19 0.1517.34
makeControlProfile0.250.000.25
makeQCTable12.10 0.9913.08
maplots83.2312.1595.41
medianNormalise2.560.172.73
metrics3.100.093.19
noOutlierMethod2.620.112.73
normaliseIllumina11.10 5.1922.74
numBeads2.590.132.71
outlierplot36.89 0.1737.08
plotBeadIntensities3.440.083.52
plotBeadLocations3.760.063.83
plotChipLayout000
plotMAXY000
poscontPlot10.87 0.0610.94
quickSummary7.520.087.60
readBeadSummaryData000
sectionNames2.700.112.81
showArrayMask17.44 0.1417.58
squeezedVarOutlierMethod52.60 0.0852.68
summarize37.31 0.2237.53
transformationFunctions3.870.063.94
weightsOutlierMethod0.020.000.01

beadarray.Rcheck/examples_x64/beadarray-Ex.timings

nameusersystemelapsed
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO0.010.000.02
GEOtemplate000
HULK000
addFeatureData8.200.198.39
annotationInterface8.240.568.80
backgroundCorrectSingleSection000
beadarrayUsersGuide000
boxplot4.420.314.73
calculateDetection13.72 0.4714.19
calculateOutlierStats20.76 1.9222.75
class-beadLevelData3.390.223.61
class-illuminaChannel000
combine4.220.564.78
controlProbeDetection16.22 0.6316.91
createTargetsFile000
expressionQCPipeline0.030.000.03
generateNeighbours000
getBeadData3.020.363.39
identifyControlBeads15.95 0.3016.27
illuminaOutlierMethod3.650.434.10
imageplot7.860.578.43
insertBeadData2.690.373.07
insertSectionData12.61 1.2013.90
limmaDE24.51 0.2124.78
makeControlProfile0.470.000.47
makeQCTable11.64 1.0912.73
maplots115.78 3.44120.32
medianNormalise2.080.062.15
metrics6.260.086.35
noOutlierMethod2.500.082.57
normaliseIllumina10.55 0.3412.25
numBeads2.080.062.14
outlierplot30.37 0.0530.42
plotBeadIntensities5.270.065.33
plotBeadLocations3.510.083.61
plotChipLayout000
plotMAXY000
poscontPlot11.58 0.0911.67
quickSummary7.10.17.2
readBeadSummaryData000
sectionNames3.310.083.39
showArrayMask11.91 0.1412.04
squeezedVarOutlierMethod55.56 0.1155.68
summarize40.38 0.1840.56
transformationFunctions4.530.164.69
weightsOutlierMethod000