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_3.26.2.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 (2015-10-08 r69496)
* 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 ‘3.26.2’
* 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/10s] 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/9s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.015  0.121   5.152
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [7s/7s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [7s/7s] 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	0	0
PrintLayout	0.002	0.000	0.001
TestResults	0.001	0.000	0.000
alias2Symbol	5.015	0.121	5.152
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.002
avearrays	0.001	0.001	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.007	0.001	0.008
barcodeplot	0.032	0.004	0.041
beadCountWeights	0.001	0.001	0.001
blockDiag	0.001	0.000	0.001
camera	0.037	0.002	0.039
cbind	0.006	0.001	0.006
changelog	0.002	0.000	0.002
channel2M	0.002	0.001	0.002
classifytests	0.002	0.000	0.003
contrastAsCoef	0.008	0.001	0.008
contrasts.fit	0.017	0.000	0.018
controlStatus	0.007	0.000	0.008
diffSplice	0.000	0.000	0.001
dim	0.003	0.000	0.002
dupcor	0	0	0
ebayes	0.013	0.001	0.015
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
genas	0.108	0.005	0.115
geneSetTest	0.001	0.000	0.002
getSpacing	0.001	0.000	0.001
getlayout	0.001	0.001	0.000
goana	0.002	0.000	0.002
heatdiagram	0.001	0.000	0.001
helpMethods	0.000	0.000	0.001
ids2indices	0.000	0.000	0.001
imageplot	0.037	0.003	0.040
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.002	0.001	0.002
isnumeric	0.001	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.000	0.002
lm.series	0.000	0.000	0.001
lmFit	0.518	0.023	0.543
lmscFit	0.001	0.001	0.001
loessfit	0.006	0.001	0.009
ma3x3	0.001	0.000	0.002
makeContrasts	0.002	0.000	0.003
makeunique	0.002	0.000	0.001
mdplot	0.004	0.000	0.005
merge	0.007	0.000	0.007
mergeScansRG	0.001	0.001	0.001
modelMatrix	0.002	0.000	0.003
modifyWeights	0.001	0.000	0.002
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.029	0.002	0.031
normalizeVSN	0.581	0.017	0.599
normalizebetweenarrays	0.003	0.001	0.003
normalizeprintorder	0.001	0.000	0.001
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.001	0.001	0.000
normexpfitdetectionp	0.001	0.000	0.001
normexpsignal	0.001	0.000	0.001
plotDensities	0.001	0.001	0.001
plotExons	0.000	0.000	0.001
plotMD	0.041	0.003	0.048
plotMDS	0.013	0.002	0.022
plotRLDF	0.281	0.005	0.287
plotSplice	0	0	0
plotWithHighlights	0.008	0.001	0.009
plotma	0.028	0.003	0.037
poolvar	0.001	0.000	0.002
predFCm	0.031	0.000	0.032
printorder	0.008	0.006	0.014
printtipWeights	0.001	0.000	0.001
propTrueNull	0.003	0.000	0.003
propexpr	0.001	0.000	0.001
protectMetachar	0.000	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	0.001	0.000	0.000
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.000	0.001
readgal	0.001	0.000	0.001
removeBatchEffect	0.004	0.000	0.005
removeext	0	0	0
roast	0.047	0.001	0.049
romer	0.033	0.002	0.036
selectmodel	0.026	0.001	0.028
squeezeVar	0.001	0.001	0.001
strsplit2	0.001	0.000	0.002
subsetting	0.005	0.001	0.006
targetsA2C	0.006	0.000	0.006
topGO	0	0	0
topRomer	0.001	0.000	0.000
topSplice	0	0	0
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.003	0.001	0.004
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	0.025	0.001	0.026
volcanoplot	0.001	0.000	0.000
weightedLowess	0.007	0.000	0.007
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.002

BioC 3.2: CHECK report for limma on perceval

Summary

Command output