beadarray 2.22.2
Mark Dunning
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/beadarray | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings beadarray_2.22.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/beadarray.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.22.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 ... 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘Nozzle.R1’ ‘affy’ ‘ggbio’ ‘hwriter’ ‘lumi’ ‘vsn’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘ggplot2’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘BeadDataPackR:::combineFiles’ ‘BeadDataPackR:::readHeader’
‘Biobase:::assayDataStorageMode’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘illuminaForeground_6x6’ ‘locsIndicesToGrid’ ‘obtainLocs’
‘simpleXMLparse’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for
‘packageDescription’
analyseDirectory: no visible global function definition for
‘read.table’
calculateDetection: no visible global function definition for
‘txtProgressBar’
calculateDetection: no visible global function definition for
‘setTxtProgressBar’
combinedControlPlot: no visible binding for global variable ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
combinedControlPlot: no visible global function definition for
‘density’
combinedControlPlot: no visible global function definition for ‘ggplot’
combinedControlPlot: no visible global function definition for ‘aes’
combinedControlPlot: no visible binding for global variable ‘ID’
combinedControlPlot: no visible binding for global variable
‘Log2Intensity’
combinedControlPlot: no visible binding for global variable
‘ControlType’
combinedControlPlot: no visible global function definition for
‘geom_boxplot’
combinedControlPlot: no visible global function definition for
‘geom_hline’
combinedControlPlot: no visible global function definition for
‘facet_wrap’
combinedControlPlot: no visible global function definition for
‘geom_point’
combinedControlPlot: no visible binding for global variable ‘Masked’
createGEOMatrix: no visible global function definition for
‘write.table’
createGEOMeta: no visible global function definition for ‘data’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
createTargetsFile: no visible global function definition for
‘read.table’
expressionQCPipeline: no visible global function definition for
‘ggsave’
expressionQCPipeline: no visible global function definition for ‘jpeg’
expressionQCPipeline: no visible global function definition for ‘pdf’
expressionQCPipeline: no visible global function definition for ‘png’
expressionQCPipeline: no visible global function definition for
‘dev.off’
expressionQCPipeline: no visible global function definition for
‘openPage’
expressionQCPipeline: no visible global function definition for
‘hwrite’
expressionQCPipeline: no visible global function definition for
‘hwriteImage’
expressionQCPipeline: no visible global function definition for
‘closePage’
expressionQCPipeline: no visible global function definition for
‘write.csv’
generateE: no visible global function definition for ‘aggregate’
genericBeadIntensityPlot: no visible global function definition for
‘runif’
getPlatformSigs: no visible global function definition for
‘lumiHumanIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
‘dbListTables’
getPlatformSigs: no visible global function definition for
‘dbListFields’
getPlatformSigs: no visible global function definition for ‘dbGetQuery’
getPlatformSigs: no visible global function definition for
‘lumiMouseIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
‘lumiRatIDMapping_dbconn’
imageplot: no visible global function definition for ‘ggplot’
imageplot: no visible global function definition for ‘aes’
imageplot: no visible binding for global variable ‘Var1’
imageplot: no visible binding for global variable ‘Var2’
imageplot: no visible binding for global variable ‘value’
imageplot: no visible global function definition for ‘geom_tile’
imageplot: no visible global function definition for
‘scale_fill_gradient’
imageplot: no visible global function definition for ‘theme’
imageplot: no visible global function definition for ‘element_blank’
limmaDE: no visible global function definition for ‘model.matrix’
makeControlProfile: no visible global function definition for
‘packageDescription’
makeReport: no visible global function definition for ‘newCustomReport’
makeReport: no visible global function definition for ‘newSection’
makeReport: no visible global function definition for ‘newTable’
makeReport: no visible global function definition for ‘newParagraph’
makeReport: no visible global function definition for ‘addTo’
makeReport: no visible global function definition for ‘autoplot’
makeReport: no visible global function definition for ‘plotIdeogram’
makeReport: no visible global function definition for ‘tracks’
makeReport: no visible global function definition for ‘ggsave’
makeReport: no visible global function definition for ‘newFigure’
makeReport: no visible binding for global variable ‘IMAGE.TYPE.RASTER’
makeReport: no visible binding for global variable ‘PROTECTION.PUBLIC’
makeReport: no visible global function definition for ‘ggplot’
makeReport: no visible global function definition for ‘aes’
makeReport: no visible binding for global variable ‘value’
makeReport: no visible global function definition for ‘geom_boxplot’
makeReport: no visible global function definition for ‘facet_wrap’
makeReport: no visible global function definition for ‘writeReport’
maplots: no visible global function definition for ‘ggplot’
maplots: no visible global function definition for ‘aes’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
maplots: no visible global function definition for ‘stat_binhex’
maplots: no visible global function definition for ‘theme_bw’
maplots: no visible global function definition for ‘xlab’
maplots: no visible global function definition for ‘ylab’
maplots: no visible global function definition for ‘facet_wrap’
maplots: no visible global function definition for ‘theme’
maplots: no visible global function definition for ‘ggtitle’
normaliseIllumina: no visible global function definition for ‘lumiT’
normaliseIllumina: no visible global function definition for
‘normalize.qspline’
normaliseIllumina: no visible global function definition for ‘vsn2’
normaliseIllumina: no visible global function definition for ‘rsn’
numberOfChannels: no visible global function definition for
‘read.table’
numberOfColumns: no visible global function definition for ‘read.table’
outlierplot2: no visible global function definition for ‘geom_vline’
outlierplot2: no visible global function definition for ‘geom_hline’
plot.smooth.line: no visible global function definition for ‘approx’
plot.smooth.line: no visible global function definition for ‘lowess’
plotBeadIntensities: no visible global function definition for
‘rainbow’
plotBeadLocations2: no visible global function definition for ‘qplot’
plotBeadLocations2: no visible global function definition for ‘opts’
plotBeadLocations2: no visible global function definition for
‘theme_blank’
plotChipLayout: no visible global function definition for ‘rgb’
plotProbe: no visible global function definition for ‘data’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible global function definition for ‘aes’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
plotTIFF: no visible global function definition for ‘col2rgb’
plotTIFF: no visible global function definition for ‘rgb’
poscontPlot: no visible global function definition for ‘rainbow’
rankInvariantNormalise: no visible global function definition for
‘normalize.invariantset’
rankInvariantNormalise: no visible global function definition for
‘predict’
readBeadSummaryData: no visible global function definition for
‘read.table’
readQC: no visible global function definition for ‘read.table’
readSampleSheet: no visible global function definition for ‘read.csv’
setFeatureData: no visible global function definition for
‘packageDescription’
squeezedVarOutlierMethod: no visible global function definition for
‘loess’
squeezedVarOutlierMethod: no visible global function definition for
‘predict’
suggestAnnotation: no visible binding for global variable
‘platformSigs’
suggestAnnotation_Vector: no visible global function definition for
‘data’
suggestAnnotation_Vector: no visible binding for global variable
‘platformSigs’
summarize: no visible global function definition for
‘packageDescription’
viewBeads: no visible global function definition for ‘col2rgb’
viewBeads: no visible global function definition for ‘menu’
viewBeads: no visible global function definition for ‘rgb’
writeOutFiles: no visible global function definition for ‘write.table’
[,ExpressionSetIllumina-ANY: no visible global function definition for
‘assayDataEnvLock’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘ggplot’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘aes’
boxplot,ExpressionSetIllumina: no visible binding for global variable
‘Var2’
boxplot,ExpressionSetIllumina: no visible binding for global variable
‘value’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘geom_boxplot’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘scale_fill_discrete’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘facet_wrap’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘theme’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘element_blank’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘element_text’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘ylab’
plot,limmaResults-ANY: no visible global function definition for
‘ggplot’
plot,limmaResults-ANY: no visible global function definition for ‘aes’
plot,limmaResults-ANY: no visible global function definition for
‘geom_point’
plot,limmaResults-ANY: no visible global function definition for
‘facet_wrap’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘ggplot’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘aes’
plotMA,ExpressionSetIllumina: no visible binding for global variable
‘value.1’
plotMA,ExpressionSetIllumina: no visible binding for global variable
‘value’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘stat_binhex’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘theme_bw’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘xlab’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘ylab’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘facet_wrap’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘theme’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘ggtitle’
show,limmaResults: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
Negative PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo aes aggregate
approx assayDataEnvLock autoplot closePage col2rgb data dbGetQuery
dbListFields dbListTables density dev.off element_blank element_text
facet_wrap genesymbol geom_boxplot geom_hline geom_point geom_tile
geom_vline ggplot ggsave ggtitle hwrite hwriteImage jpeg loess lowess
lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn
lumiRatIDMapping_dbconn lumiT menu metaTemplate model.matrix
newCustomReport newFigure newParagraph newSection newTable
normalize.invariantset normalize.qspline openPage opts p.adjust
packageDescription pdf platformSigs plotIdeogram png predict qplot
rainbow read.csv read.table rgb rsn runif scale_fill_discrete
scale_fill_gradient setTxtProgressBar stat_binhex theme theme_blank
theme_bw tracks txtProgressBar value value.1 vsn2 write.csv
write.table writeReport xlab ylab
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
"rainbow", "rgb")
importFrom("stats", "aggregate", "approx", "density", "loess",
"lowess", "model.matrix", "p.adjust", "predict", "runif")
importFrom("utils", "data", "menu", "packageDescription", "read.csv",
"read.table", "setTxtProgressBar", "txtProgressBar",
"write.csv", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 48.077 0.635 48.771
summarize 28.621 2.828 31.470
limmaDE 29.662 0.455 30.183
outlierplot 16.630 0.956 17.623
calculateOutlierStats 15.842 1.649 17.514
calculateDetection 16.220 0.767 17.870
maplots 12.013 2.772 14.804
normaliseIllumina 12.394 0.664 13.384
controlProbeDetection 11.478 0.790 12.299
insertSectionData 9.298 1.269 10.577
identifyControlBeads 10.020 0.364 10.396
makeQCTable 8.898 1.195 10.106
poscontPlot 8.881 0.719 9.616
addFeatureData 9.001 0.291 9.813
quickSummary 7.242 0.730 7.985
annotationInterface 7.113 0.567 8.779
showArrayMask 6.527 0.997 7.564
imageplot 6.396 0.707 7.302
combine 5.234 0.683 5.928
boxplot 4.465 0.223 5.352
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/beadarray.Rcheck/00check.log’
for details.
* installing *source* package ‘beadarray’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BASH.c -o BASH.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c HULK.c -o HULK.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c findAllOutliers.c -o findAllOutliers.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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 /Users/biocbuild/bbs-3.3-bioc/meat/beadarray.Rcheck/beadarray/libs
** 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
* DONE (beadarray)