BioC 3.1: CHECK report for limma on morelia

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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_3.24.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘3.24.15’
* 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 ... [5s/5s] 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’ [6s/6s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...1318d1317
< Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
 [6s/6s] 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-3.1-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-3.1-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	0.001	0.000	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	4.372	0.192	4.670
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.002
avearrays	0.001	0.000	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.007	0.000	0.008
barcodeplot	0.036	0.006	0.042
beadCountWeights	0.001	0.001	0.001
blockDiag	0.001	0.000	0.002
camera	0.030	0.002	0.031
cbind	0.004	0.000	0.005
changelog	0.001	0.000	0.001
channel2M	0.001	0.000	0.001
classifytests	0.001	0.000	0.002
contrastAsCoef	0.005	0.000	0.005
contrasts.fit	0.013	0.000	0.014
controlStatus	0.008	0.000	0.008
diffSplice	0.001	0.000	0.001
dim	0.002	0.001	0.003
dupcor	0.001	0.000	0.001
ebayes	0.017	0.001	0.019
fitGammaIntercept	0.001	0.000	0.002
fitfdist	0.001	0.000	0.002
genas	0.116	0.016	0.132
geneSetTest	0.001	0.000	0.001
getSpacing	0.002	0.000	0.001
getlayout	0	0	0
goana	0.001	0.001	0.001
heatdiagram	0.000	0.000	0.001
helpMethods	0.000	0.000	0.001
ids2indices	0.001	0.000	0.001
imageplot	0.039	0.003	0.044
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.001	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.001	0.001	0.001
lm.series	0.000	0.000	0.001
lmFit	0.578	0.034	0.633
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.001	0.008
ma3x3	0.001	0.000	0.002
makeContrasts	0.001	0.000	0.002
makeunique	0.001	0.000	0.001
mdplot	0.003	0.001	0.004
merge	0.006	0.000	0.006
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.001	0.000	0.002
modifyWeights	0.000	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.018	0.001	0.020
normalizeVSN	0.250	0.010	0.281
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.001	0.000	0.001
plotExons	0.001	0.000	0.001
plotMD	0.025	0.003	0.028
plotMDS	0.010	0.001	0.011
plotRLDF	0.199	0.007	0.206
plotSplice	0	0	0
plotWithHighlights	0.009	0.001	0.010
plotma	0.024	0.003	0.028
poolvar	0.001	0.000	0.001
predFCm	0.021	0.001	0.022
printorder	0.005	0.003	0.008
printtipWeights	0.000	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0.000	0.000	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.002	0.000	0.002
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.006	0.001	0.006
read.idat	0.001	0.000	0.000
read.ilmn	0.001	0.000	0.000
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.003	0.000	0.003
removeext	0.000	0.000	0.001
roast	0.029	0.001	0.029
romer	0.029	0.001	0.030
selectmodel	0.014	0.000	0.014
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.001	0.001
subsetting	0.006	0.000	0.006
targetsA2C	0.007	0.001	0.006
topGO	0.001	0.000	0.001
topRomer	0.001	0.000	0.000
topSplice	0.001	0.000	0.000
toptable	0	0	0
tricubeMovingAverage	0.002	0.001	0.003
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	0.002
venn	0.018	0.001	0.019
volcanoplot	0	0	0
weightedLowess	0.006	0.000	0.008
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.002

BioC 3.1: CHECK report for limma on morelia

Summary

Command output