BioC 3.5: CHECK report for limma on toluca2

Package: limma

Version: 3.31.22

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.31.22.tar.gz

StartedAt: 2017-04-23 05:52:10 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:54:00 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 110.2 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_3.31.22.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/limma.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘3.31.22’
* 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 init.c -o init.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 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 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	0.000
PrintLayout	0.001	0.000	0.001
TestResults	0.001	0.000	0.001
alias2Symbol	4.287	0.117	4.439
arrayWeights	0.000	0.000	0.001
arrayWeightsQuick	0.001	0.001	0.001
asMatrixWeights	0.044	0.001	0.045
auROC	0.043	0.000	0.044
avearrays	0.001	0.000	0.002
avereps	0.002	0.000	0.001
backgroundcorrect	0.172	0.001	0.174
barcodeplot	0.544	0.005	0.554
beadCountWeights	0.001	0.000	0.001
blockDiag	0.002	0.000	0.002
camera	0.687	0.003	0.693
cbind	0.006	0.001	0.007
changelog	0.002	0.000	0.002
channel2M	0.001	0.001	0.002
classifytests	0.087	0.000	0.089
contrastAsCoef	0.008	0.001	0.008
contrasts.fit	0.346	0.001	0.348
controlStatus	0.007	0.000	0.008
coolmap	0.437	0.007	0.444
cumOverlap	0.001	0.000	0.002
detectionPValue	0.001	0.000	0.001
diffSplice	0	0	0
dim	0.002	0.000	0.001
dupcor	1.308	0.005	1.316
ebayes	0.022	0.002	0.024
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.002	0.000	0.001
fitmixture	0.003	0.000	0.004
genas	0.278	0.020	0.300
geneSetTest	0.001	0.000	0.001
getSpacing	0.013	0.000	0.014
getlayout	0.001	0.000	0.000
goana	0.001	0.000	0.001
heatdiagram	0.001	0.000	0.001
helpMethods	0.001	0.000	0.001
ids2indices	0.001	0.000	0.001
imageplot	0.028	0.002	0.029
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.000	0.002
isnumeric	0.001	0.000	0.001
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.002	0.000	0.001
lm.series	0	0	0
lmFit	0.443	0.005	0.449
lmscFit	0.001	0.001	0.001
loessfit	0.102	0.001	0.102
logcosh	0.001	0.000	0.001
ma3x3	0.036	0.001	0.036
makeContrasts	0.058	0.000	0.058
makeunique	0.000	0.000	0.001
mdplot	0.084	0.000	0.083
merge	0.083	0.001	0.083
mergeScansRG	0	0	0
modelMatrix	0.047	0.000	0.047
modifyWeights	0.001	0.000	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.002	0.000	0.001
normalizeRobustSpline	0.025	0.001	0.026
normalizeVSN	0.564	0.017	1.082
normalizebetweenarrays	0.002	0.000	0.003
normalizeprintorder	0.000	0.001	0.000
normexpfit	0.002	0.000	0.001
normexpfitcontrol	0.001	0.000	0.000
normexpfitdetectionp	0.001	0.000	0.000
normexpsignal	0	0	0
plotDensities	0.001	0.000	0.001
plotExons	0.001	0.000	0.001
plotMD	0.039	0.003	0.041
plotMDS	0.055	0.001	0.058
plotRLDF	0.009	0.001	0.010
plotSplice	0	0	0
plotWithHighlights	0.006	0.001	0.008
plotma	0.021	0.002	0.023
poolvar	0.002	0.001	0.002
predFCm	0.027	0.000	0.027
printorder	0.006	0.005	0.011
printtipWeights	0.001	0.000	0.001
propTrueNull	0.003	0.000	0.002
propexpr	0.000	0.001	0.001
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.000	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.064	0.000	0.065
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	0.015	0.001	0.016
removeext	0.009	0.000	0.010
roast	0.143	0.001	0.145
romer	0.035	0.001	0.037
selectmodel	0.01	0.00	0.01
squeezeVar	0.001	0.000	0.002
strsplit2	0.002	0.000	0.001
subsetting	0.004	0.000	0.005
targetsA2C	0.006	0.000	0.006
topGO	0.001	0.000	0.000
topRomer	0.000	0.000	0.001
topSplice	0.001	0.001	0.001
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.003	0.000	0.003
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.000	0.000
unwrapdups	0.001	0.000	0.001
venn	0.594	0.002	0.596
volcanoplot	0.001	0.000	0.000
weightedLowess	0.042	0.001	0.043
weightedmedian	0.001	0.000	0.001
zscore	0.017	0.000	0.018