BioC 3.0: 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 --no-multiarch limma_3.22.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/limma.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘3.22.7’
* 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 ... [8s/13s] 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 ... [12s/13s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 7.401  0.192   7.593
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [10s/10s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [10s/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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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-3.0-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	0.001	0.000
PrintLayout	0.002	0.000	0.001
TestResults	0.001	0.001	0.000
alias2Symbol	7.401	0.192	7.593
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.000	0.001
auROC	0.002	0.000	0.001
avearrays	0.001	0.001	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.007	0.001	0.008
barcodeplot	0.245	0.004	0.261
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.001	0.001
camera	0.029	0.004	0.032
cbind	0.007	0.000	0.007
changelog	0.003	0.001	0.004
channel2M	0.002	0.000	0.003
classifytests	0.003	0.000	0.003
contrastAsCoef	0.009	0.001	0.009
contrasts.fit	0.019	0.002	0.022
controlStatus	0.026	0.001	0.028
diffSplice	0.001	0.001	0.001
dim	0.002	0.000	0.002
dupcor	0.001	0.000	0.001
ebayes	0.016	0.001	0.021
fitGammaIntercept	0.001	0.000	0.002
fitfdist	0.001	0.000	0.001
genas	0.126	0.004	0.139
geneSetTest	0.002	0.000	0.002
getSpacing	0.002	0.001	0.002
getlayout	0.001	0.000	0.000
goana.MArrayLM	0.001	0.001	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	0.001	0.001
imageplot	0.291	0.003	0.303
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.001	0.000	0.002
isnumeric	0.001	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.001	0.003
lm.series	0.000	0.001	0.000
lmFit	0.595	0.016	0.640
lmscFit	0.001	0.000	0.002
loessfit	0.008	0.002	0.022
ma3x3	0.002	0.000	0.002
makeContrasts	0.002	0.001	0.002
makeunique	0.001	0.000	0.001
merge	0.008	0.001	0.008
mergeScansRG	0.001	0.001	0.001
modelMatrix	0.003	0.000	0.004
modifyWeights	0.001	0.000	0.001
nec	0.001	0.001	0.001
normalizeMedianAbsValues	0.001	0.000	0.002
normalizeRobustSpline	0.038	0.004	0.043
normalizeVSN	0.437	0.023	0.463
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.001	0.001
normexpfit	0.004	0.000	0.004
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.001	0.001
normexpsignal	0.000	0.000	0.001
plot	0.012	0.002	0.017
plotDensities	0.001	0.000	0.001
plotExons	0.001	0.001	0.000
plotMDS	0.018	0.002	0.029
plotRLDF	0.390	0.008	0.406
plotSplice	0.000	0.001	0.001
plotma	0.039	0.003	0.057
poolvar	0.002	0.000	0.002
predFCm	0.032	0.001	0.033
printorder	0.008	0.007	0.015
printtipWeights	0.001	0.000	0.001
propTrueNull	0.004	0.000	0.003
propexpr	0.001	0.000	0.000
protectMetachar	0.001	0.001	0.001
qqt	0.003	0.001	0.013
qualwt	0.000	0.000	0.001
rankSumTestwithCorrelation	0.008	0.001	0.008
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	0.006
removeext	0.001	0.000	0.001
roast	0.326	0.003	0.330
romer	0.029	0.002	0.031
selectmodel	0.020	0.001	0.020
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.001	0.001
subsetting	0.006	0.001	0.007
targetsA2C	0.007	0.000	0.007
topGO	0.001	0.001	0.000
topRomer	0.001	0.000	0.001
topSplice	0.000	0.001	0.000
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.002	0.001	0.012
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.001	0.001
unwrapdups	0.002	0.000	0.002
venn	0.029	0.005	0.037
volcanoplot	0	0	0
weightedLowess	0.007	0.002	0.016
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.002

BioC 3.0: CHECK report for limma on perceval

Summary

Command output