BioC 3.4: CHECK report for limma on morelia

Package: limma

Version: 3.29.21

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.29.21.tar.gz

StartedAt: 2016-09-20 08:29:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:31:02 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 72.6 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_3.29.21.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/limma.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.29.21’
* 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 -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-3.4-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	0	0
alias2Symbol	2.846	0.068	2.915
arrayWeights	0.001	0.000	0.000
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.001	0.001
auROC	0.000	0.000	0.001
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.005	0.001	0.005
barcodeplot	0.033	0.002	0.036
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.001
camera	0.021	0.002	0.023
cbind	0.006	0.001	0.007
changelog	0.001	0.000	0.002
channel2M	0.001	0.001	0.002
classifytests	0.002	0.000	0.002
contrastAsCoef	0.008	0.001	0.008
contrasts.fit	0.016	0.001	0.017
controlStatus	0.005	0.000	0.005
cumOverlap	0.001	0.000	0.001
detectionPValue	0.001	0.001	0.000
diffSplice	0.001	0.000	0.001
dim	0.002	0.000	0.002
dupcor	0.324	0.015	0.339
ebayes	0.009	0.001	0.010
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.000	0.000	0.001
fitmixture	0.003	0.001	0.004
genas	0.064	0.003	0.067
geneSetTest	0.001	0.000	0.001
getSpacing	0	0	0
getlayout	0.001	0.000	0.001
goana	0.001	0.000	0.001
heatdiagram	0.001	0.000	0.000
helpMethods	0.001	0.000	0.001
ids2indices	0.001	0.000	0.001
imageplot	0.028	0.002	0.032
intraspotCorrelation	0.001	0.000	0.000
isfullrank	0.001	0.001	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0	0	0
limmaUsersGuide	0.001	0.000	0.001
lm.series	0.000	0.000	0.001
lmFit	0.326	0.002	0.330
lmscFit	0.001	0.000	0.001
loessfit	0.005	0.001	0.006
logcosh	0.001	0.000	0.000
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.000	0.002
makeunique	0.001	0.000	0.001
mdplot	0.003	0.000	0.004
merge	0.004	0.001	0.004
mergeScansRG	0.001	0.000	0.000
modelMatrix	0.001	0.000	0.002
modifyWeights	0.000	0.001	0.000
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.017	0.001	0.019
normalizeVSN	0.314	0.016	0.741
normalizebetweenarrays	0.002	0.000	0.001
normalizeprintorder	0	0	0
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.001	0.001
normexpsignal	0.001	0.000	0.000
plotDensities	0.001	0.000	0.000
plotExons	0.000	0.000	0.001
plotMD	0.040	0.003	0.296
plotMDS	0.011	0.001	0.012
plotRLDF	0.011	0.001	0.012
plotSplice	0.000	0.000	0.001
plotWithHighlights	0.006	0.001	0.773
plotma	0.048	0.003	0.186
poolvar	0.000	0.000	0.001
predFCm	0.012	0.001	0.012
printorder	0.004	0.004	0.008
printtipWeights	0.001	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0.000	0.000	0.001
protectMetachar	0.001	0.000	0.000
qqt	0.003	0.000	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.007	0.000	0.007
read.idat	0.000	0.000	0.001
read.ilmn	0.000	0.000	0.001
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0.000	0.000	0.001
readgal	0.001	0.000	0.000
removeBatchEffect	0.012	0.001	0.012
removeext	0.001	0.000	0.001
roast	0.019	0.001	0.019
romer	0.018	0.001	0.019
selectmodel	0.010	0.000	0.009
squeezeVar	0.000	0.000	0.001
strsplit2	0.001	0.001	0.001
subsetting	0.003	0.000	0.004
targetsA2C	0.004	0.000	0.004
topGO	0	0	0
topRomer	0.000	0.001	0.000
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.002	0.000	0.003
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.000	0.000	0.001
venn	0.017	0.001	0.018
volcanoplot	0	0	0
weightedLowess	0.007	0.001	0.008
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.000	0.001