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_3.25.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/limma.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘3.25.15’
* 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 ... [6s/8s] 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 ... [8s/12s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 4.671   0.11   7.694
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [6s/8s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [7s/9s] 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	0	0
PrintLayout	0.002	0.000	0.001
TestResults	0.001	0.000	0.001
alias2Symbol	4.671	0.110	7.694
arrayWeights	0.001	0.000	0.002
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.002	0.000	0.001
avearrays	0.001	0.001	0.001
avereps	0.001	0.000	0.002
backgroundcorrect	0.007	0.001	0.009
barcodeplot	0.034	0.003	0.039
beadCountWeights	0.000	0.000	0.001
blockDiag	0.002	0.000	0.001
camera	0.032	0.002	0.034
cbind	0.007	0.000	0.008
changelog	0.002	0.000	0.001
channel2M	0.002	0.000	0.002
classifytests	0.002	0.001	0.003
contrastAsCoef	0.007	0.000	0.009
contrasts.fit	0.017	0.001	0.018
controlStatus	0.008	0.000	0.012
diffSplice	0.001	0.000	0.001
dim	0.002	0.001	0.002
dupcor	0.000	0.000	0.001
ebayes	0.014	0.001	0.023
fitGammaIntercept	0.002	0.000	0.002
fitfdist	0.001	0.000	0.001
genas	0.104	0.007	0.137
geneSetTest	0.001	0.000	0.002
getSpacing	0.001	0.000	0.001
getlayout	0.001	0.000	0.001
goana	0.001	0.000	0.001
heatdiagram	0.001	0.001	0.001
helpMethods	0.001	0.000	0.000
ids2indices	0.001	0.000	0.001
imageplot	0.038	0.003	0.051
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.001	0.000	0.004
isnumeric	0.001	0.000	0.001
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.000	0.002
lm.series	0.001	0.000	0.001
lmFit	0.533	0.017	0.735
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.001	0.010
ma3x3	0.002	0.001	0.002
makeContrasts	0.002	0.000	0.003
makeunique	0.001	0.000	0.001
mdplot	0.004	0.000	0.007
merge	0.008	0.001	0.009
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.003	0.000	0.003
modifyWeights	0.001	0.000	0.001
nec	0.002	0.001	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.032	0.002	0.041
normalizeVSN	0.618	0.016	0.834
normalizebetweenarrays	0.003	0.000	0.005
normalizeprintorder	0.001	0.000	0.001
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.000	0.000	0.004
normexpsignal	0.000	0.000	0.001
plotDensities	0.001	0.000	0.001
plotExons	0.000	0.000	0.001
plotMD	0.027	0.003	0.038
plotMDS	0.014	0.002	0.023
plotRLDF	0.226	0.004	0.304
plotSplice	0.001	0.000	0.000
plotWithHighlights	0.008	0.001	0.009
plotma	0.027	0.003	0.070
poolvar	0.001	0.001	0.002
predFCm	0.036	0.001	0.038
printorder	0.008	0.005	0.012
printtipWeights	0.001	0.000	0.001
propTrueNull	0.004	0.000	0.004
propexpr	0.001	0.000	0.001
protectMetachar	0.002	0.000	0.001
qqt	0.004	0.000	0.005
qualwt	0.001	0.000	0.000
rankSumTestwithCorrelation	0.009	0.000	0.013
read.idat	0.001	0.000	0.001
read.ilmn	0.001	0.001	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.000	0.001
readgal	0.000	0.000	0.001
removeBatchEffect	0.005	0.001	0.011
removeext	0.001	0.000	0.001
roast	0.040	0.002	0.047
romer	0.045	0.001	0.059
selectmodel	0.017	0.001	0.022
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.005	0.000	0.005
targetsA2C	0.006	0.000	0.009
topGO	0.000	0.000	0.001
topRomer	0.001	0.000	0.001
topSplice	0.001	0.000	0.000
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.002	0.001	0.005
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.001	0.000	0.002
unwrapdups	0.001	0.000	0.001
venn	0.026	0.002	0.027
volcanoplot	0.001	0.000	0.001
weightedLowess	0.009	0.001	0.011
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.012

BioC 3.2: CHECK report for limma on oaxaca

Summary

Command output