BioC 3.4: CHECK report for limma on morelia

Package: limma

Version: 3.30.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.30.13.tar.gz

StartedAt: 2017-04-15 04:11:36 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 04:13:57 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 140.2 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_3.30.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/limma.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘3.30.13’
* 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
Examples with CPU or elapsed time > 5s
             user system elapsed
alias2Symbol  3.4  0.117  18.092
* 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	0.000	0.000	0.001
alias2Symbol	3.400	0.117	18.092
arrayWeights	0.001	0.000	0.000
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.001	0.001
auROC	0.001	0.000	0.001
avearrays	0.002	0.000	0.002
avereps	0.001	0.001	0.001
backgroundcorrect	0.006	0.000	0.006
barcodeplot	0.034	0.004	0.286
beadCountWeights	0.001	0.000	0.001
blockDiag	0.000	0.000	0.001
camera	0.015	0.001	0.016
cbind	0.006	0.001	0.009
changelog	0.001	0.000	0.001
channel2M	0.001	0.000	0.001
classifytests	0.002	0.000	0.002
contrastAsCoef	0.016	0.000	0.017
contrasts.fit	0.019	0.001	0.020
controlStatus	0.006	0.001	0.006
coolmap	0.160	0.008	0.194
cumOverlap	0.001	0.000	0.001
detectionPValue	0.000	0.000	0.001
diffSplice	0.000	0.001	0.001
dim	0.002	0.000	0.002
dupcor	0.335	0.007	0.342
ebayes	0.022	0.002	0.164
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.002	0.000	0.001
fitmixture	0.003	0.000	0.032
genas	0.068	0.003	0.120
geneSetTest	0.001	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
goana	0.001	0.000	0.001
heatdiagram	0.000	0.000	0.001
helpMethods	0.001	0.000	0.001
ids2indices	0.001	0.001	0.001
imageplot	0.022	0.001	0.067
intraspotCorrelation	0.000	0.000	0.005
isfullrank	0.001	0.000	0.001
isnumeric	0.002	0.000	0.001
kooperberg	0.000	0.001	0.000
limmaUsersGuide	0.001	0.000	0.002
lm.series	0.001	0.000	0.001
lmFit	0.439	0.005	0.595
lmscFit	0.001	0.000	0.001
loessfit	0.008	0.001	0.035
logcosh	0.000	0.000	0.001
ma3x3	0.002	0.000	0.003
makeContrasts	0.002	0.000	0.003
makeunique	0.001	0.001	0.002
mdplot	0.005	0.000	0.006
merge	0.008	0.000	0.010
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.003	0.000	0.004
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.001	0.002
normalizeRobustSpline	0.028	0.002	0.030
normalizeVSN	0.518	0.022	0.846
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.000	0.001
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.000	0.001	0.001
normexpsignal	0.001	0.000	0.000
plotDensities	0.001	0.000	0.002
plotExons	0.001	0.000	0.001
plotMD	0.033	0.003	0.038
plotMDS	0.018	0.002	0.020
plotRLDF	0.013	0.001	0.015
plotSplice	0	0	0
plotWithHighlights	0.008	0.001	0.009
plotma	0.041	0.003	0.129
poolvar	0.001	0.000	0.001
predFCm	0.014	0.001	0.015
printorder	0.008	0.006	0.013
printtipWeights	0.001	0.000	0.000
propTrueNull	0.002	0.001	0.002
propexpr	0.001	0.000	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.001	0.033
qualwt	0	0	0
rankSumTestwithCorrelation	0.008	0.000	0.009
read.idat	0	0	0
read.ilmn	0.001	0.000	0.000
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0.000	0.000	0.001
removeBatchEffect	0.017	0.001	0.083
removeext	0.001	0.000	0.001
roast	0.188	0.000	0.189
romer	0.020	0.001	0.022
selectmodel	0.011	0.000	0.011
squeezeVar	0.001	0.000	0.001
strsplit2	0.002	0.001	0.001
subsetting	0.004	0.000	0.005
targetsA2C	0.007	0.001	0.007
topGO	0	0	0
topRomer	0.001	0.000	0.001
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.003	0.000	0.008
trigammainverse	0.001	0.001	0.001
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.001	0.001
venn	0.026	0.001	0.044
volcanoplot	0.001	0.000	0.001
weightedLowess	0.007	0.000	0.036
weightedmedian	0.001	0.000	0.002
zscore	0.001	0.000	0.002