BioC 3.2: CHECK report for limma on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.26.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/limma.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 ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.26.9’
* 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 ‘limma’ can be installed ... [5s/19s] 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' call to ‘GO.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [7s/10s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [7s/11s] OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/limma.Rcheck/00check.log’
for details.

* installing *source* package ‘limma’ ...
** 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 normexp.c -o normexp.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 weighted_lowess.c -o weighted_lowess.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 limma.so normexp.o weighted_lowess.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)

name	user	system	elapsed
LargeDataObject	0.000	0.000	0.001
PrintLayout	0.001	0.000	0.002
TestResults	0	0	0
alias2Symbol	4.207	0.096	4.575
arrayWeights	0.001	0.000	0.000
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.000	0.000	0.001
auROC	0.001	0.000	0.001
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.005	0.001	0.005
barcodeplot	0.026	0.003	0.061
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.001
camera	0.039	0.001	0.040
cbind	0.007	0.000	0.006
changelog	0.001	0.000	0.002
channel2M	0.001	0.000	0.001
classifytests	0.003	0.000	0.002
contrastAsCoef	0.008	0.000	0.008
contrasts.fit	0.016	0.000	0.016
controlStatus	0.006	0.000	0.007
diffSplice	0	0	0
dim	0.002	0.000	0.002
dupcor	0.000	0.000	0.001
ebayes	0.012	0.001	0.014
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
genas	0.105	0.005	0.114
geneSetTest	0.001	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
goana	0.002	0.000	0.002
heatdiagram	0.001	0.000	0.001
helpMethods	0	0	0
ids2indices	0.000	0.000	0.001
imageplot	0.025	0.002	0.027
intraspotCorrelation	0.001	0.000	0.000
isfullrank	0.001	0.001	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.001	0.000	0.001
lm.series	0	0	0
lmFit	0.520	0.018	0.563
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.001	0.009
ma3x3	0.001	0.000	0.002
makeContrasts	0.002	0.000	0.002
makeunique	0.001	0.000	0.001
mdplot	0.004	0.000	0.004
merge	0.007	0.001	0.007
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.002	0.001	0.003
modifyWeights	0.001	0.000	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.023	0.001	0.025
normalizeVSN	0.488	0.012	0.501
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0	0	0
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.000
normexpsignal	0	0	0
plotDensities	0.000	0.000	0.001
plotExons	0	0	0
plotMD	0.018	0.002	0.022
plotMDS	0.010	0.001	0.011
plotRLDF	0.021	0.001	0.021
plotSplice	0	0	0
plotWithHighlights	0.008	0.001	0.009
plotma	0.018	0.002	0.022
poolvar	0.001	0.000	0.002
predFCm	0.021	0.001	0.022
printorder	0.006	0.004	0.010
printtipWeights	0.001	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0	0	0
protectMetachar	0.001	0.000	0.001
qqt	0.002	0.000	0.003
qualwt	0	0	0
rankSumTestwithCorrelation	0.006	0.001	0.007
read.idat	0.001	0.000	0.001
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.000	0.000	0.001
readgal	0.001	0.000	0.001
removeBatchEffect	0.005	0.001	0.006
removeext	0.002	0.000	0.002
roast	0.043	0.001	0.044
romer	0.210	0.001	0.211
selectmodel	0.015	0.000	0.015
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.005	0.000	0.005
targetsA2C	0.008	0.000	0.007
topGO	0	0	0
topRomer	0	0	0
topSplice	0.001	0.000	0.000
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.002	0.000	0.003
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0	0	0
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.000	0.000	0.001
venn	0.019	0.001	0.019
volcanoplot	0.000	0.000	0.001
weightedLowess	0.006	0.000	0.006
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.002

BioC 3.2: CHECK report for limma on oaxaca

Summary

Command output