BioC 3.2: CHECK report for limma on perceval

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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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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/6s] 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 ... [9s/14s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.487  0.189   9.128
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [7s/11s]
  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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c normexp.c -o normexp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c weighted_lowess.c -o weighted_lowess.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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	0.001	0.000	0.001
PrintLayout	0.001	0.001	0.001
TestResults	0.001	0.000	0.001
alias2Symbol	5.487	0.189	9.128
arrayWeights	0.001	0.000	0.002
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.001	0.002
avearrays	0.002	0.000	0.002
avereps	0.001	0.000	0.002
backgroundcorrect	0.007	0.001	0.008
barcodeplot	0.034	0.006	0.053
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.001
camera	0.041	0.002	0.073
cbind	0.007	0.000	0.008
changelog	0.002	0.000	0.002
channel2M	0.002	0.000	0.002
classifytests	0.003	0.000	0.003
contrastAsCoef	0.009	0.000	0.010
contrasts.fit	0.016	0.001	0.018
controlStatus	0.008	0.001	0.016
diffSplice	0.001	0.000	0.009
dim	0.003	0.000	0.004
dupcor	0.001	0.000	0.001
ebayes	0.015	0.001	0.037
fitGammaIntercept	0.001	0.000	0.002
fitfdist	0.002	0.000	0.002
genas	0.117	0.008	0.243
geneSetTest	0.002	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0.000	0.001	0.001
goana	0.001	0.000	0.002
heatdiagram	0.001	0.001	0.001
helpMethods	0	0	0
ids2indices	0.001	0.000	0.001
imageplot	0.036	0.004	0.098
intraspotCorrelation	0.001	0.001	0.001
isfullrank	0.002	0.000	0.005
isnumeric	0.001	0.001	0.001
kooperberg	0	0	0
limmaUsersGuide	0.001	0.000	0.002
lm.series	0.001	0.000	0.001
lmFit	0.507	0.032	0.717
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.002	0.049
ma3x3	0.002	0.001	0.002
makeContrasts	0.001	0.000	0.002
makeunique	0.001	0.000	0.005
mdplot	0.004	0.001	0.015
merge	0.006	0.001	0.007
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.003	0.001	0.003
modifyWeights	0.001	0.000	0.001
nec	0.001	0.001	0.001
normalizeMedianAbsValues	0.002	0.000	0.001
normalizeRobustSpline	0.027	0.003	0.071
normalizeVSN	0.612	0.027	1.018
normalizebetweenarrays	0.004	0.000	0.004
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.000
normexpsignal	0	0	0
plotDensities	0.001	0.000	0.000
plotExons	0.001	0.001	0.001
plotMD	0.029	0.004	0.077
plotMDS	0.014	0.002	0.037
plotRLDF	0.421	0.008	0.600
plotSplice	0.000	0.000	0.001
plotWithHighlights	0.008	0.001	0.009
plotma	0.029	0.005	0.050
poolvar	0.001	0.000	0.002
predFCm	0.038	0.001	0.049
printorder	0.008	0.007	0.015
printtipWeights	0.001	0.000	0.001
propTrueNull	0.003	0.000	0.003
propexpr	0.001	0.000	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.001	0.004
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.008	0.001	0.009
read.idat	0	0	0
read.ilmn	0.000	0.000	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.001	0.000
readgal	0.001	0.000	0.000
removeBatchEffect	0.004	0.001	0.004
removeext	0.001	0.000	0.001
roast	0.032	0.002	0.055
romer	0.045	0.002	0.050
selectmodel	0.014	0.000	0.014
squeezeVar	0.001	0.000	0.002
strsplit2	0.001	0.000	0.002
subsetting	0.005	0.000	0.005
targetsA2C	0.005	0.000	0.006
topGO	0.001	0.000	0.001
topRomer	0.000	0.000	0.001
topSplice	0.001	0.000	0.000
toptable	0.001	0.000	0.001
tricubeMovingAverage	0.003	0.000	0.005
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.026	0.002	0.056
volcanoplot	0.001	0.001	0.000
weightedLowess	0.007	0.001	0.015
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.001	0.005

BioC 3.2: CHECK report for limma on perceval

Summary

Command output