BioC 3.1: CHECK report for limma on petty

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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 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 ‘3.24.15’
* 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 ... [9s/9s] 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 ... [11s/11s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 6.354  0.158   6.517
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [9s/9s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...1318d1317
< Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
 [9s/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-3.1-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-3.1-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	0.001	0.000	0.001
PrintLayout	0.003	0.001	0.002
TestResults	0.001	0.000	0.001
alias2Symbol	6.354	0.158	6.517
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.001	0.000	0.002
auROC	0.002	0.001	0.003
avearrays	0.002	0.000	0.003
avereps	0.002	0.000	0.001
backgroundcorrect	0.010	0.001	0.012
barcodeplot	0.050	0.006	0.060
beadCountWeights	0.001	0.000	0.002
blockDiag	0.002	0.000	0.002
camera	0.055	0.002	0.058
cbind	0.011	0.000	0.011
changelog	0.003	0.001	0.003
channel2M	0.003	0.000	0.004
classifytests	0.004	0.000	0.005
contrastAsCoef	0.013	0.001	0.014
contrasts.fit	0.026	0.001	0.027
controlStatus	0.012	0.001	0.012
diffSplice	0.002	0.000	0.001
dim	0.003	0.001	0.004
dupcor	0.001	0.000	0.001
ebayes	0.024	0.001	0.026
fitGammaIntercept	0.002	0.000	0.002
fitfdist	0.002	0.001	0.002
genas	0.178	0.010	0.190
geneSetTest	0.002	0.000	0.003
getSpacing	0.001	0.000	0.002
getlayout	0.001	0.000	0.001
goana	0.002	0.000	0.003
heatdiagram	0.002	0.000	0.001
helpMethods	0.001	0.000	0.001
ids2indices	0.001	0.000	0.002
imageplot	0.051	0.004	0.056
intraspotCorrelation	0.002	0.000	0.001
isfullrank	0.002	0.000	0.003
isnumeric	0.003	0.001	0.003
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.001	0.003
lm.series	0.001	0.000	0.001
lmFit	0.751	0.025	0.779
lmscFit	0.002	0.000	0.002
loessfit	0.011	0.002	0.015
ma3x3	0.002	0.001	0.003
makeContrasts	0.003	0.000	0.003
makeunique	0.001	0.001	0.002
mdplot	0.007	0.001	0.008
merge	0.011	0.001	0.011
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.004	0.001	0.005
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.001	0.001
normalizeRobustSpline	0.029	0.002	0.031
normalizeVSN	0.393	0.012	0.405
normalizebetweenarrays	0.004	0.000	0.003
normalizeprintorder	0.001	0.001	0.000
normexpfit	0.003	0.000	0.004
normexpfitcontrol	0.001	0.001	0.002
normexpfitdetectionp	0.001	0.000	0.002
normexpsignal	0.000	0.000	0.001
plotDensities	0.002	0.000	0.002
plotExons	0.001	0.000	0.001
plotMD	0.041	0.004	0.047
plotMDS	0.020	0.001	0.021
plotRLDF	0.326	0.007	0.334
plotSplice	0.000	0.000	0.001
plotWithHighlights	0.013	0.001	0.015
plotma	0.043	0.005	0.062
poolvar	0.003	0.001	0.003
predFCm	0.052	0.000	0.052
printorder	0.011	0.008	0.020
printtipWeights	0.001	0.000	0.001
propTrueNull	0.005	0.000	0.006
propexpr	0.001	0.000	0.002
protectMetachar	0.002	0.001	0.002
qqt	0.004	0.001	0.006
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.011	0.000	0.011
read.idat	0.001	0.001	0.001
read.ilmn	0.001	0.000	0.002
read.maimages	0.001	0.001	0.002
readImaGeneHeader	0.001	0.000	0.001
readgal	0.001	0.001	0.001
removeBatchEffect	0.007	0.001	0.007
removeext	0.001	0.000	0.001
roast	0.052	0.002	0.054
romer	0.064	0.002	0.066
selectmodel	0.025	0.000	0.026
squeezeVar	0.002	0.000	0.002
strsplit2	0.001	0.000	0.001
subsetting	0.008	0.001	0.008
targetsA2C	0.01	0.00	0.01
topGO	0.001	0.000	0.001
topRomer	0.001	0.000	0.001
topSplice	0.000	0.000	0.001
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.004	0.001	0.005
trigammainverse	0.001	0.001	0.002
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.003
venn	0.040	0.002	0.041
volcanoplot	0.001	0.000	0.001
weightedLowess	0.011	0.001	0.016
weightedmedian	0.001	0.000	0.001
zscore	0.003	0.000	0.002

BioC 3.1: CHECK report for limma on petty

Summary

Command output