BioC 3.6: CHECK report for limma on veracruz1

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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_3.33.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/limma.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.33.7’
* 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 ... 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 ... OK
* 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 ... WARNING
Missing link or links in documentation object 'normalizeVSN.Rd':
  ‘[vsn:vsn]{vsn}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.6-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   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c normexp.c -o normexp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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 init.o normexp.o weighted_lowess.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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	0.000	0.001	0.000
PrintLayout	0.001	0.000	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	2.978	0.083	3.091
arrayWeights	0	0	0
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.02	0.00	0.02
auROC	0.024	0.000	0.024
avearrays	0.001	0.000	0.001
avereps	0.002	0.001	0.001
backgroundcorrect	0.104	0.002	0.107
barcodeplot	0.368	0.004	0.375
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.001
camera	0.414	0.003	0.421
cbind	0.003	0.000	0.003
changelog	0.002	0.000	0.002
channel2M	0.001	0.000	0.002
classifytests	0.056	0.000	0.057
contrastAsCoef	0.006	0.001	0.005
contrasts.fit	0.236	0.001	0.241
controlStatus	0.007	0.000	0.007
coolmap	0.493	0.006	0.501
cumOverlap	0.001	0.001	0.001
detectionPValue	0.001	0.000	0.001
diffSplice	0.000	0.000	0.001
dim	0.002	0.000	0.002
dupcor	0.678	0.014	0.693
ebayes	0.017	0.001	0.018
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
fitmixture	0.003	0.001	0.003
genas	0.182	0.006	0.189
geneSetTest	0.002	0.000	0.001
getSpacing	0.012	0.000	0.013
getlayout	0	0	0
goana	0.001	0.000	0.002
heatdiagram	0.000	0.001	0.001
helpMethods	0	0	0
ids2indices	0.001	0.000	0.001
imageplot	0.028	0.003	0.031
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.002	0.000	0.002
isnumeric	0.002	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.000	0.002
lm.series	0.001	0.000	0.001
lmFit	0.352	0.003	0.357
lmscFit	0	0	0
loessfit	0.059	0.001	0.060
logcosh	0.000	0.000	0.001
ma3x3	0.028	0.001	0.028
makeContrasts	0.043	0.000	0.043
makeunique	0.001	0.001	0.002
mdplot	0.068	0.000	0.069
merge	0.048	0.001	0.049
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.030	0.001	0.030
modifyWeights	0.000	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.015	0.000	0.016
normalizeVSN	0.397	0.014	0.725
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.002	0.000	0.001
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0.000	0.000	0.001
plotDensities	0.001	0.001	0.002
plotExons	0.001	0.000	0.001
plotMD	0.028	0.003	0.036
plotMDS	0.037	0.001	0.039
plotRLDF	0.008	0.001	0.010
plotSplice	0.001	0.000	0.000
plotWithHighlights	0.006	0.000	0.007
plotma	0.020	0.003	0.022
poolvar	0.001	0.000	0.002
predFCm	0.026	0.001	0.028
printorder	0.004	0.004	0.008
printtipWeights	0.001	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0.000	0.001	0.001
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.000	0.002
qualwt	0.001	0.001	0.001
rankSumTestwithCorrelation	0.046	0.000	0.046
read.idat	0.001	0.000	0.000
read.ilmn	0.001	0.001	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.010	0.001	0.011
removeext	0.013	0.000	0.013
roast	0.105	0.001	0.106
romer	0.032	0.001	0.032
selectmodel	0.011	0.001	0.011
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.002	0.001	0.003
targetsA2C	0.005	0.000	0.004
topGO	0.001	0.000	0.000
topRomer	0	0	0
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.002	0.000	0.002
trigammainverse	0	0	0
trimWhiteSpace	0.001	0.001	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.477	0.002	0.490
volcanoplot	0.001	0.001	0.000
weightedLowess	0.027	0.000	0.028
weightedmedian	0.000	0.000	0.001
zscore	0.012	0.000	0.012

BioC 3.6: CHECK report for limma on veracruz1

Summary

Command output