BioC 3.5: CHECK report for limma on veracruz2

Package: limma

Version: 3.32.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.32.10.tar.gz

StartedAt: 2017-10-18 05:21:07 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:22:30 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 83.1 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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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_3.32.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/limma.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘3.32.10’
* 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 ... 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 ... 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: OK

* 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-3.5-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	0.001	0.000	0.001
TestResults	0.001	0.000	0.001
alias2Symbol	3.337	0.105	3.523
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.026	0.001	0.027
auROC	0.030	0.001	0.032
avearrays	0.001	0.000	0.002
avereps	0.001	0.000	0.001
backgroundcorrect	0.125	0.001	0.129
barcodeplot	0.346	0.007	0.362
beadCountWeights	0	0	0
blockDiag	0.001	0.000	0.001
camera	0.379	0.006	0.393
cbind	0.003	0.000	0.003
changelog	0.001	0.001	0.002
channel2M	0.001	0.000	0.002
classifytests	0.047	0.001	0.049
contrastAsCoef	0.005	0.001	0.005
contrasts.fit	0.227	0.006	0.242
controlStatus	0.005	0.000	0.005
coolmap	0.306	0.012	0.330
cumOverlap	0.001	0.000	0.001
detectionPValue	0	0	0
diffSplice	0.000	0.000	0.001
dim	0.001	0.001	0.001
dupcor	0.809	0.024	0.852
ebayes	0.021	0.002	0.024
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
fitmixture	0.003	0.000	0.004
genas	0.165	0.006	0.176
geneSetTest	0.001	0.000	0.002
getSpacing	0.010	0.000	0.011
getlayout	0.001	0.000	0.001
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	0.023	0.002	0.025
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.000	0.001
isnumeric	0.002	0.000	0.002
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.002	0.000	0.002
lm.series	0.000	0.000	0.001
lmFit	0.399	0.006	0.419
lmscFit	0.002	0.000	0.002
loessfit	0.229	0.003	0.240
logcosh	0.001	0.000	0.001
ma3x3	0.023	0.001	0.025
makeContrasts	0.033	0.001	0.034
makeunique	0.000	0.000	0.001
mdplot	0.041	0.001	0.044
merge	0.060	0.002	0.064
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.029	0.001	0.030
modifyWeights	0.000	0.000	0.001
nec	0.000	0.001	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.016	0.001	0.017
normalizeVSN	0.306	0.014	0.618
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.000	0.001	0.000
plotExons	0.000	0.000	0.001
plotMD	0.025	0.002	0.027
plotMDS	0.038	0.001	0.040
plotRLDF	0.006	0.001	0.007
plotSplice	0	0	0
plotWithHighlights	0.005	0.001	0.006
plotma	0.017	0.002	0.019
poolvar	0.001	0.001	0.001
predFCm	0.011	0.000	0.011
printorder	0.004	0.004	0.008
printtipWeights	0.001	0.000	0.000
propTrueNull	0.001	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	0.000	0.001	0.000
rankSumTestwithCorrelation	0.042	0.000	0.043
read.idat	0.000	0.000	0.001
read.ilmn	0	0	0
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.013	0.001	0.014
removeext	0.009	0.000	0.009
roast	0.086	0.001	0.090
romer	0.036	0.002	0.038
selectmodel	0.009	0.000	0.010
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.004	0.000	0.004
targetsA2C	0.005	0.000	0.006
topGO	0.000	0.000	0.001
topRomer	0.001	0.000	0.000
topSplice	0.000	0.000	0.001
toptable	0	0	0
tricubeMovingAverage	0.002	0.000	0.003
trigammainverse	0	0	0
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.000	0.000	0.001
venn	0.372	0.006	0.385
volcanoplot	0.000	0.000	0.001
weightedLowess	0.024	0.001	0.025
weightedmedian	0.001	0.000	0.001
zscore	0.010	0.000	0.009