BioC 3.3: CHECK report for limma on morelia

Package: limma

Version: 3.27.19

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.27.19.tar.gz

StartedAt: 2016-04-21 04:23:36 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:25:07 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 90.8 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_3.27.19.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/limma.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.27.19’
* 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 ... [4s/4s] 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 ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [6s/6s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [6s/6s] 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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c normexp.c -o normexp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 normexp.o weighted_lowess.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-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	0.001	0.000	0.001
TestResults	0.001	0.000	0.000
alias2Symbol	4.127	0.099	4.253
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.001	0.001
auROC	0.001	0.000	0.002
avearrays	0.002	0.000	0.002
avereps	0.001	0.000	0.001
backgroundcorrect	0.008	0.001	0.008
barcodeplot	0.035	0.003	0.039
beadCountWeights	0.001	0.000	0.000
blockDiag	0.001	0.000	0.001
camera	0.029	0.001	0.030
cbind	0.004	0.000	0.004
changelog	0.002	0.001	0.001
channel2M	0.002	0.000	0.001
classifytests	0.002	0.000	0.002
contrastAsCoef	0.005	0.001	0.006
contrasts.fit	0.018	0.000	0.018
controlStatus	0.008	0.000	0.008
diffSplice	0.001	0.000	0.001
dim	0.003	0.001	0.002
dupcor	0.001	0.000	0.001
ebayes	0.014	0.001	0.016
fitGammaIntercept	0.002	0.000	0.001
fitfdist	0	0	0
genas	0.094	0.006	0.099
geneSetTest	0.001	0.000	0.002
getSpacing	0.001	0.000	0.002
getlayout	0.001	0.000	0.001
goana	0.002	0.000	0.002
heatdiagram	0.001	0.000	0.000
helpMethods	0	0	0
ids2indices	0.001	0.000	0.001
imageplot	0.038	0.003	0.042
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.002	0.000	0.001
isnumeric	0.002	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.000	0.002
lm.series	0.000	0.001	0.000
lmFit	0.566	0.017	0.596
lmscFit	0.001	0.000	0.002
loessfit	0.007	0.001	0.009
ma3x3	0.002	0.000	0.002
makeContrasts	0.001	0.001	0.003
makeunique	0.001	0.000	0.002
mdplot	0.004	0.001	0.005
merge	0.007	0.000	0.007
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.003	0.000	0.003
modifyWeights	0.001	0.001	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.030	0.002	0.033
normalizeVSN	0.494	0.012	0.509
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.001	0.000
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.000	0.001	0.001
normexpsignal	0.000	0.000	0.001
plotDensities	0.000	0.000	0.001
plotExons	0.000	0.000	0.001
plotMD	0.030	0.003	0.034
plotMDS	0.015	0.001	0.016
plotRLDF	0.024	0.002	0.031
plotSplice	0.000	0.000	0.001
plotWithHighlights	0.009	0.001	0.010
plotma	0.029	0.003	0.034
poolvar	0.001	0.000	0.001
predFCm	0.058	0.001	0.061
printorder	0.008	0.006	0.014
printtipWeights	0.001	0.001	0.001
propTrueNull	0.003	0.000	0.003
propexpr	0.000	0.000	0.001
protectMetachar	0.001	0.001	0.001
qqt	0.003	0.000	0.004
qualwt	0.001	0.001	0.000
rankSumTestwithCorrelation	0.008	0.000	0.008
read.idat	0.001	0.000	0.001
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.000	0.000
readgal	0.001	0.000	0.000
removeBatchEffect	0.006	0.001	0.006
removeext	0.001	0.000	0.002
roast	0.053	0.002	0.055
romer	0.022	0.001	0.024
selectmodel	0.015	0.001	0.016
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.002
subsetting	0.005	0.001	0.006
targetsA2C	0.006	0.000	0.007
topGO	0.001	0.000	0.001
topRomer	0.001	0.000	0.001
topSplice	0.001	0.000	0.000
toptable	0	0	0
tricubeMovingAverage	0.003	0.001	0.003
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.002	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.037	0.001	0.039
volcanoplot	0	0	0
weightedLowess	0.008	0.000	0.009
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.000	0.002