Back to Multiple platform build/check report for BioC 3.7
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CHECK report for beadarray on merida2

This page was generated on 2018-10-17 08:46:51 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:beadarray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings beadarray_2.30.0.tar.gz
StartedAt: 2018-10-16 20:02:49 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:12:35 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 585.9 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:beadarray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings beadarray_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/beadarray.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
maplots                  102.171  4.135 107.028
squeezedVarOutlierMethod  58.516  1.146  60.242
summarize                 38.027  4.072  42.444
limmaDE                   26.593  0.451  27.519
outlierplot               18.352  1.703  20.278
calculateOutlierStats     14.741  1.831  16.705
normaliseIllumina         13.815  0.861  15.279
calculateDetection        12.497  0.891  13.494
insertSectionData         10.362  1.422  12.180
controlProbeDetection     10.579  0.900  11.579
makeQCTable                8.876  1.383  10.323
poscontPlot                8.875  0.871   9.800
identifyControlBeads       9.263  0.472   9.791
showArrayMask              8.213  0.894   9.189
annotationInterface        7.321  0.568   8.026
addFeatureData             7.356  0.363   7.844
imageplot                  6.862  0.855   7.848
quickSummary               6.904  0.772   7.735
boxplot                    5.109  0.319   5.514
* 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
  ‘/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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL beadarray
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘beadarray’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BASH.c -o BASH.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c HULK.c -o HULK.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c findAllOutliers.c -o findAllOutliers.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c imageProcessing.c -o imageProcessing.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beadarray)

Tests output

Example timings

beadarray.Rcheck/beadarray-Ex.timings

nameusersystemelapsed
BASH0.0050.0000.006
BASHCompact0.0020.0000.003
BASHDiffuse0.0030.0000.003
BASHExtended0.0030.0010.003
GEO0.0030.0000.003
GEOtemplate0.0050.0010.007
HULK0.0020.0000.003
addFeatureData7.3560.3637.844
annotationInterface7.3210.5688.026
backgroundCorrectSingleSection0.0030.0000.003
beadarrayUsersGuide0.0040.0000.005
boxplot5.1090.3195.514
calculateDetection12.497 0.89113.494
calculateOutlierStats14.741 1.83116.705
class-beadLevelData3.0530.3723.451
class-illuminaChannel0.0040.0010.004
combine3.7360.5104.270
controlProbeDetection10.579 0.90011.579
createTargetsFile0.0010.0000.001
expressionQCPipeline0.0290.0010.029
generateNeighbours0.0020.0000.002
getBeadData2.4760.2722.764
identifyControlBeads9.2630.4729.791
illuminaOutlierMethod3.0320.4173.471
imageplot6.8620.8557.848
insertBeadData3.0140.4533.477
insertSectionData10.362 1.42212.180
limmaDE26.593 0.45127.519
makeControlProfile0.3680.0030.372
makeQCTable 8.876 1.38310.323
maplots102.171 4.135107.028
medianNormalise1.7970.1381.951
metrics2.3870.1892.611
noOutlierMethod2.3590.1172.494
normaliseIllumina13.815 0.86115.279
numBeads2.3190.1812.513
outlierplot18.352 1.70320.278
plotBeadIntensities3.9180.5814.540
plotBeadLocations3.3210.3803.737
plotChipLayout0.0010.0000.001
plotMAXY0.0010.0000.001
poscontPlot8.8750.8719.800
quickSummary6.9040.7727.735
readBeadSummaryData0.0010.0000.001
sectionNames2.3660.2532.656
showArrayMask8.2130.8949.189
squeezedVarOutlierMethod58.516 1.14660.242
summarize38.027 4.07242.444
transformationFunctions3.8680.7904.674
weightsOutlierMethod0.0010.0010.001