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BioC 3.0: CHECK report for beadarray on oaxaca

This page was generated on 2015-04-10 10:01:58 -0700 (Fri, 10 Apr 2015).

Package 73/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.16.0
Mark Dunning
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/beadarray
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: beadarray
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.16.0.tar.gz
StartedAt: 2015-04-09 21:36:51 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:47:23 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 631.3 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 --no-multiarch beadarray_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/beadarray.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.16.0’
* 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 ... [21s/21s] 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’
* 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 ... [417s/431s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 52.590  0.818  55.975
summarize                43.664  3.181  48.658
limmaDE                  34.456  0.382  35.256
calculateOutlierStats    21.396  1.827  23.366
outlierplot              20.510  0.996  21.726
calculateDetection       20.024  0.867  20.993
normaliseIllumina        18.393  0.867  19.556
maplots                  16.162  2.244  18.600
controlProbeDetection    13.345  0.912  14.396
makeQCTable              12.632  1.383  14.121
insertSectionData        12.248  1.107  13.444
identifyControlBeads     11.494  0.440  12.047
addFeatureData           11.564  0.316  12.586
poscontPlot              10.886  0.767  11.992
annotationInterface       9.995  0.513  10.543
quickSummary              8.934  0.969  11.318
showArrayMask             8.520  0.961  10.074
imageplot                 8.452  0.786   9.561
combine                   7.031  0.693   7.769
boxplot                   4.990  0.304   5.329
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-3.0-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
BASH0.0020.0000.002
BASHCompact0.0010.0000.001
BASHDiffuse0.0010.0000.001
BASHExtended0.0010.0000.001
GEO0.0010.0010.001
GEOtemplate0.0210.0020.023
HULK0.0010.0000.001
addFeatureData11.564 0.31612.586
annotationInterface 9.995 0.51310.543
backgroundCorrectSingleSection0.0010.0000.002
beadarrayUsersGuide0.0070.0010.009
boxplot4.9900.3045.329
calculateDetection20.024 0.86720.993
calculateOutlierStats21.396 1.82723.366
class-beadLevelData3.0210.3643.393
class-illuminaChannel0.0040.0010.004
combine7.0310.6937.769
controlProbeDetection13.345 0.91214.396
createTargetsFile000
expressionQCPipeline0.0480.0030.063
generateNeighbours0.0010.0000.001
getBeadData2.9440.3373.479
identifyControlBeads11.494 0.44012.047
illuminaOutlierMethod4.0500.4554.548
imageplot8.4520.7869.561
insertBeadData3.1930.3983.599
insertSectionData12.248 1.10713.444
limmaDE34.456 0.38235.256
makeControlProfile0.8050.0310.838
makeQCTable12.632 1.38314.121
maplots16.162 2.24418.600
medianNormalise2.3080.2152.920
metrics1.9110.1262.037
noOutlierMethod2.0900.1192.210
normaliseIllumina18.393 0.86719.556
numBeads2.4270.1602.673
outlierplot20.510 0.99621.726
plotBeadIntensities3.9040.5394.466
plotBeadLocations3.2820.4263.970
plotChipLayout0.0010.0000.001
plotMAXY0.0010.0000.000
poscontPlot10.886 0.76711.992
quickSummary 8.934 0.96911.318
readBeadSummaryData0.0010.0010.001
sectionNames2.4780.1524.473
showArrayMask 8.520 0.96110.074
squeezedVarOutlierMethod52.590 0.81855.975
summarize43.664 3.18148.658
transformationFunctions4.0370.5774.645
weightsOutlierMethod0.0010.0000.001