BioC 3.3: CHECK report for limma on oaxaca

Package: limma

Version: 3.28.21

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.28.21.tar.gz

StartedAt: 2016-10-13 03:09:25 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:11:29 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 123.8 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_3.28.21.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘3.28.21’
* 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-3.3-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	0.000
TestResults	0.001	0.000	0.000
alias2Symbol	3.670	0.090	3.846
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.001
avearrays	0.002	0.000	0.001
avereps	0.002	0.000	0.001
backgroundcorrect	0.006	0.001	0.006
barcodeplot	0.041	0.003	0.056
beadCountWeights	0.001	0.000	0.001
blockDiag	0.002	0.000	0.002
camera	0.021	0.002	0.023
cbind	0.006	0.001	0.006
changelog	0.002	0.000	0.003
channel2M	0.002	0.000	0.002
classifytests	0.002	0.000	0.003
contrastAsCoef	0.007	0.001	0.007
contrasts.fit	0.013	0.001	0.014
controlStatus	0.008	0.001	0.008
cumOverlap	0.001	0.000	0.001
detectionPValue	0.001	0.000	0.001
diffSplice	0.001	0.001	0.001
dim	0.002	0.000	0.003
dupcor	0.460	0.018	0.652
ebayes	0.013	0.001	0.447
fitGammaIntercept	0.000	0.000	0.001
fitfdist	0.001	0.001	0.001
fitmixture	0.004	0.000	0.005
genas	0.083	0.003	0.086
geneSetTest	0.001	0.001	0.002
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
goana	0.001	0.000	0.001
heatdiagram	0	0	0
helpMethods	0.000	0.000	0.001
ids2indices	0.001	0.000	0.001
imageplot	0.038	0.002	0.040
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.002	0.000	0.002
isnumeric	0.001	0.000	0.002
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.001	0.000	0.001
lm.series	0.000	0.000	0.001
lmFit	0.466	0.004	0.472
lmscFit	0.001	0.001	0.001
loessfit	0.016	0.001	0.018
logcosh	0	0	0
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.000	0.002
makeunique	0.001	0.000	0.001
mdplot	0.002	0.000	0.003
merge	0.004	0.000	0.004
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.002	0.001	0.001
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.002
normalizeRobustSpline	0.023	0.001	0.024
normalizeVSN	0.479	0.019	0.791
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.001	0.001
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.000	0.000	0.001
plotExons	0.000	0.000	0.001
plotMD	0.022	0.002	0.026
plotMDS	0.028	0.002	0.030
plotRLDF	0.007	0.001	0.007
plotSplice	0.000	0.000	0.001
plotWithHighlights	0.005	0.000	0.005
plotma	0.024	0.003	0.028
poolvar	0.002	0.000	0.002
predFCm	0.048	0.001	0.049
printorder	0.008	0.005	0.013
printtipWeights	0.001	0.001	0.001
propTrueNull	0.002	0.000	0.003
propexpr	0.000	0.000	0.001
protectMetachar	0.001	0.000	0.000
qqt	0.003	0.000	0.004
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.009	0.000	0.009
read.idat	0.001	0.000	0.001
read.ilmn	0.001	0.000	0.000
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.014	0.000	0.014
removeext	0.002	0.001	0.002
roast	0.017	0.000	0.018
romer	0.039	0.001	0.041
selectmodel	0.013	0.000	0.013
squeezeVar	0.001	0.000	0.001
strsplit2	0.002	0.000	0.002
subsetting	0.004	0.001	0.005
targetsA2C	0.007	0.000	0.007
topGO	0.001	0.000	0.001
topRomer	0.000	0.000	0.001
topSplice	0.000	0.000	0.001
toptable	0.001	0.000	0.001
tricubeMovingAverage	0.003	0.001	0.004
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.000	0.000	0.001
venn	0.018	0.001	0.020
volcanoplot	0.001	0.000	0.001
weightedLowess	0.008	0.000	0.009
weightedmedian	0.000	0.001	0.001
zscore	0.001	0.000	0.001