BioC 3.5: CHECK report for limma on oaxaca

Package: limma

Version: 3.31.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.31.16.tar.gz

StartedAt: 2017-03-04 04:55:49 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:57:20 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 91.6 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_3.31.16.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 r72177)
* 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 ‘3.31.16’
* 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	0	0
PrintLayout	0.001	0.000	0.002
TestResults	0.001	0.000	0.001
alias2Symbol	3.792	0.101	4.076
arrayWeights	0.001	0.000	0.000
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.027	0.001	0.028
auROC	0.024	0.000	0.024
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.105	0.001	0.106
barcodeplot	0.485	0.004	0.490
beadCountWeights	0.000	0.001	0.001
blockDiag	0.001	0.000	0.001
camera	0.518	0.002	0.519
cbind	0.004	0.000	0.004
changelog	0.001	0.000	0.001
channel2M	0.001	0.001	0.002
classifytests	0.001	0.000	0.001
contrastAsCoef	0.006	0.000	0.006
contrasts.fit	0.157	0.001	0.157
controlStatus	0.005	0.001	0.006
coolmap	0.374	0.006	0.380
cumOverlap	0.001	0.000	0.001
detectionPValue	0.001	0.000	0.000
diffSplice	0	0	0
dim	0.001	0.000	0.001
dupcor	1.070	0.004	1.095
ebayes	0.137	0.001	0.142
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
fitmixture	0.004	0.001	0.005
genas	0.348	0.018	0.367
geneSetTest	0.001	0.000	0.001
getSpacing	0.009	0.001	0.010
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	0.000
ids2indices	0.001	0.000	0.000
imageplot	0.021	0.001	0.023
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.001	0.001
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.001	0.000	0.001
lm.series	0.000	0.000	0.001
lmFit	0.368	0.002	0.372
lmscFit	0.000	0.000	0.001
loessfit	0.087	0.001	0.089
logcosh	0.001	0.000	0.001
ma3x3	0.034	0.001	0.035
makeContrasts	0.042	0.000	0.042
makeunique	0.001	0.000	0.001
mdplot	0.082	0.001	0.084
merge	0.067	0.001	0.068
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.047	0.001	0.047
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.018	0.001	0.020
normalizeVSN	0.519	0.016	0.837
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0	0	0
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.001	0.000	0.001
normexpsignal	0.001	0.000	0.000
plotDensities	0.000	0.000	0.001
plotExons	0.000	0.001	0.001
plotMD	0.031	0.002	0.038
plotMDS	0.052	0.001	0.054
plotRLDF	0.010	0.002	0.011
plotSplice	0	0	0
plotWithHighlights	0.008	0.000	0.009
plotma	0.029	0.003	0.033
poolvar	0.002	0.001	0.002
predFCm	0.029	0.001	0.029
printorder	0.005	0.003	0.009
printtipWeights	0.000	0.001	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0.001	0.000	0.001
protectMetachar	0	0	0
qqt	0.002	0.001	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.065	0.001	0.065
read.idat	0.001	0.000	0.001
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.000	0.000
readImaGeneHeader	0.001	0.000	0.001
readgal	0.000	0.000	0.001
removeBatchEffect	0.017	0.000	0.018
removeext	0.01	0.00	0.01
roast	0.132	0.000	0.132
romer	0.032	0.001	0.033
selectmodel	0.008	0.001	0.008
squeezeVar	0.001	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.003	0.000	0.003
targetsA2C	0.005	0.000	0.005
topGO	0	0	0
topRomer	0.000	0.000	0.001
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.002	0.000	0.002
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.001	0.001	0.001
unwrapdups	0.001	0.000	0.001
venn	0.529	0.002	0.530
volcanoplot	0.000	0.000	0.001
weightedLowess	0.037	0.000	0.037
weightedmedian	0.001	0.000	0.001
zscore	0.017	0.000	0.017