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BioC 3.2: CHECK report for beadarray on oaxaca

This page was generated on 2016-04-23 10:23:16 -0700 (Sat, 23 Apr 2016).

Package 79/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.20.1
Mark Dunning
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/beadarray
Last Changed Rev: 112515 / Revision: 116712
Last Changed Date: 2016-01-13 08:34:26 -0800 (Wed, 13 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarray
Version: 2.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings beadarray_2.20.1.tar.gz
StartedAt: 2016-04-22 22:02:29 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:11:17 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 528.7 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings beadarray_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/beadarray.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.20.1’
* 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 ... [15s/15s] 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
combinedControlPlot: no visible binding for global variable ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
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’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
expressionQCPipeline: no visible global function definition for
  ‘ggsave’
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’
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’
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’
outlierplot2: no visible global function definition for ‘geom_vline’
outlierplot2: no visible global function definition for ‘geom_hline’
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’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible global function definition for ‘aes’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
rankInvariantNormalise: no visible global function definition for
  ‘normalize.invariantset’
suggestAnnotation: no visible binding for global variable
  ‘platformSigs’
suggestAnnotation_Vector: no visible binding for global variable
  ‘platformSigs’
[,ExpressionSetIllumina-ANY: no visible global function definition for
  ‘assayDataEnvLock’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘ggplot’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘aes’
boxplot,ExpressionSetIllumina : .local: no visible binding for global
  variable ‘Var2’
boxplot,ExpressionSetIllumina : .local: no visible binding for global
  variable ‘value’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘geom_boxplot’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘scale_fill_discrete’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘facet_wrap’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘theme’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘element_blank’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘element_text’
boxplot,ExpressionSetIllumina : .local: no visible global function
  definition for ‘ylab’
plot,limmaResults-ANY : .local: no visible global function definition
  for ‘ggplot’
plot,limmaResults-ANY : .local: no visible global function definition
  for ‘aes’
plot,limmaResults-ANY : .local: no visible global function definition
  for ‘geom_point’
plot,limmaResults-ANY : .local: no visible global function definition
  for ‘facet_wrap’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘ggplot’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘aes’
plotMA,ExpressionSetIllumina : .local: no visible binding for global
  variable ‘value.1’
plotMA,ExpressionSetIllumina : .local: no visible binding for global
  variable ‘value’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘stat_binhex’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘theme_bw’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘xlab’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘ylab’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘facet_wrap’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘theme’
plotMA,ExpressionSetIllumina : .local: no visible global function
  definition for ‘ggtitle’
* 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 ... [371s/376s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 49.652  0.782  51.347
summarize                39.963  3.298  43.424
limmaDE                  28.002  0.358  28.379
calculateOutlierStats    19.826  1.912  21.782
outlierplot              17.533  0.875  18.447
maplots                  15.017  3.060  18.110
calculateDetection       16.033  0.804  16.858
normaliseIllumina        15.600  0.714  16.353
controlProbeDetection    12.071  0.932  13.027
makeQCTable              11.083  1.389  12.483
insertSectionData        11.148  1.172  12.333
poscontPlot               9.954  0.809  10.849
identifyControlBeads     10.287  0.429  10.723
showArrayMask             8.291  0.892   9.283
addFeatureData            8.549  0.258  10.044
quickSummary              7.491  0.629   8.126
annotationInterface       7.368  0.559   8.007
imageplot                 7.153  0.702   8.277
combine                   6.322  0.626   6.953
* 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-3.2-bioc/meat/beadarray.Rcheck/00check.log’
for details.

beadarray.Rcheck/00install.out:

* 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-3.2-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)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.0020.0010.002
BASHCompact0.0010.0000.001
BASHDiffuse0.0010.0010.001
BASHExtended0.0010.0000.001
GEO0.0010.0000.001
GEOtemplate0.0030.0010.004
HULK0.0000.0000.001
addFeatureData 8.549 0.25810.044
annotationInterface7.3680.5598.007
backgroundCorrectSingleSection0.0020.0010.002
beadarrayUsersGuide0.0040.0000.003
boxplot4.0650.2124.300
calculateDetection16.033 0.80416.858
calculateOutlierStats19.826 1.91221.782
class-beadLevelData3.1340.3953.532
class-illuminaChannel0.0040.0000.004
combine6.3220.6266.953
controlProbeDetection12.071 0.93213.027
createTargetsFile0.0010.0000.000
expressionQCPipeline0.0440.0000.045
generateNeighbours0.0010.0000.001
getBeadData2.6450.2672.913
identifyControlBeads10.287 0.42910.723
illuminaOutlierMethod3.6690.4994.169
imageplot7.1530.7028.277
insertBeadData3.4800.3553.838
insertSectionData11.148 1.17212.333
limmaDE28.002 0.35828.379
makeControlProfile0.6310.0030.635
makeQCTable11.083 1.38912.483
maplots15.017 3.06018.110
medianNormalise1.8010.1101.911
metrics2.2400.1422.385
noOutlierMethod2.3430.1552.499
normaliseIllumina15.600 0.71416.353
numBeads2.0450.1412.190
outlierplot17.533 0.87518.447
plotBeadIntensities3.4950.4733.973
plotBeadLocations3.4210.4113.835
plotChipLayout0.0000.0000.001
plotMAXY0.0000.0000.001
poscontPlot 9.954 0.80910.849
quickSummary7.4910.6298.126
readBeadSummaryData0.0000.0000.001
sectionNames2.4250.1852.643
showArrayMask8.2910.8929.283
squeezedVarOutlierMethod49.652 0.78251.347
summarize39.963 3.29843.424
transformationFunctions3.8020.5424.346
weightsOutlierMethod0.0010.0000.001