BioC 3.5: CHECK report for limma on veracruz2

Package: limma

Version: 3.32.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.32.5.tar.gz

StartedAt: 2017-08-16 04:36:18 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:37:46 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 88.0 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_3.32.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘3.32.5’
* 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	0.002	0.000	0.002
TestResults	0.001	0.000	0.001
alias2Symbol	3.347	0.094	3.485
arrayWeights	0.001	0.000	0.000
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.02	0.00	0.02
auROC	0.021	0.001	0.022
avearrays	0.002	0.000	0.002
avereps	0.001	0.000	0.000
backgroundcorrect	0.135	0.003	0.140
barcodeplot	0.416	0.004	0.428
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.001
camera	0.509	0.003	0.515
cbind	0.005	0.001	0.006
changelog	0.002	0.000	0.002
channel2M	0.001	0.000	0.002
classifytests	0.050	0.001	0.050
contrastAsCoef	0.006	0.000	0.006
contrasts.fit	0.263	0.001	0.273
controlStatus	0.007	0.001	0.007
coolmap	0.507	0.006	0.520
cumOverlap	0.002	0.000	0.002
detectionPValue	0.000	0.000	0.001
diffSplice	0.000	0.000	0.001
dim	0.001	0.000	0.002
dupcor	0.688	0.015	0.713
ebayes	0.017	0.001	0.020
fitGammaIntercept	0.001	0.000	0.000
fitfdist	0.000	0.000	0.001
fitmixture	0.003	0.001	0.003
genas	0.187	0.005	0.194
geneSetTest	0.001	0.000	0.001
getSpacing	0.007	0.000	0.008
getlayout	0.001	0.000	0.000
goana	0.001	0.000	0.001
heatdiagram	0.001	0.000	0.001
helpMethods	0.000	0.000	0.001
ids2indices	0.001	0.000	0.000
imageplot	0.020	0.002	0.023
intraspotCorrelation	0	0	0
isfullrank	0.002	0.000	0.002
isnumeric	0.001	0.000	0.001
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.001	0.000	0.002
lm.series	0.001	0.000	0.000
lmFit	0.300	0.003	0.305
lmscFit	0.001	0.000	0.001
loessfit	0.081	0.001	0.092
logcosh	0.000	0.000	0.001
ma3x3	0.021	0.000	0.031
makeContrasts	0.037	0.000	0.037
makeunique	0	0	0
mdplot	0.051	0.000	0.052
merge	0.067	0.001	0.067
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.030	0.001	0.030
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.022	0.002	0.023
normalizeVSN	0.365	0.015	0.686
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0	0	0
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0.000	0.001	0.000
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0.000	0.000	0.001
plotDensities	0.001	0.000	0.001
plotExons	0.001	0.000	0.000
plotMD	0.038	0.002	0.040
plotMDS	0.043	0.001	0.045
plotRLDF	0.009	0.001	0.010
plotSplice	0.000	0.001	0.001
plotWithHighlights	0.007	0.000	0.008
plotma	0.023	0.002	0.026
poolvar	0.000	0.001	0.001
predFCm	0.021	0.001	0.023
printorder	0.005	0.003	0.008
printtipWeights	0.000	0.001	0.000
propTrueNull	0.002	0.000	0.002
propexpr	0	0	0
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.001	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.043	0.000	0.043
read.idat	0.000	0.000	0.001
read.ilmn	0	0	0
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.000	0.000
readgal	0.001	0.000	0.000
removeBatchEffect	0.011	0.001	0.011
removeext	0.008	0.000	0.008
roast	0.098	0.001	0.099
romer	0.024	0.001	0.025
selectmodel	0.011	0.000	0.012
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.003	0.000	0.003
targetsA2C	0.003	0.000	0.004
topGO	0.001	0.000	0.001
topRomer	0	0	0
topSplice	0	0	0
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.002	0.001	0.002
trigammainverse	0	0	0
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.001	0.001	0.001
unwrapdups	0.001	0.000	0.001
venn	0.379	0.002	0.383
volcanoplot	0	0	0
weightedLowess	0.023	0.001	0.024
weightedmedian	0.001	0.000	0.000
zscore	0.009	0.000	0.010