BioC 3.4: CHECK report for limma on malbec1

Package: limma

Version: 3.30.13

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.30.13.tar.gz

StartedAt: 2017-04-14 23:28:42 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:29:52 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 70.9 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.30.13.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/limma.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 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
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c normexp.c -o normexp.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c weighted_lowess.c -o weighted_lowess.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o limma.so normexp.o weighted_lowess.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/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	0.000	0.000	0.001
PrintLayout	0.000	0.000	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	3.096	0.036	3.135
arrayWeights	0	0	0
arrayWeightsQuick	0	0	0
asMatrixWeights	0.000	0.000	0.001
auROC	0	0	0
avearrays	0.000	0.000	0.001
avereps	0.000	0.000	0.001
backgroundcorrect	0.004	0.000	0.005
barcodeplot	0.024	0.004	0.026
beadCountWeights	0	0	0
blockDiag	0.000	0.000	0.001
camera	0.016	0.000	0.017
cbind	0.004	0.004	0.005
changelog	0.000	0.000	0.002
channel2M	0.000	0.004	0.002
classifytests	0.000	0.000	0.002
contrastAsCoef	0.008	0.000	0.006
contrasts.fit	0.008	0.004	0.011
controlStatus	0.016	0.000	0.015
coolmap	0.128	0.004	0.133
cumOverlap	0.000	0.000	0.001
detectionPValue	0.000	0.000	0.001
diffSplice	0.000	0.000	0.001
dim	0.000	0.000	0.001
dupcor	0.32	0.00	0.32
ebayes	0.024	0.000	0.022
fitGammaIntercept	0	0	0
fitfdist	0.004	0.000	0.000
fitmixture	0.004	0.000	0.003
genas	0.096	0.000	0.096
geneSetTest	0.004	0.000	0.002
getSpacing	0.000	0.000	0.001
getlayout	0.000	0.000	0.001
goana	0.004	0.000	0.002
heatdiagram	0.000	0.000	0.001
helpMethods	0	0	0
ids2indices	0.000	0.000	0.001
imageplot	0.036	0.004	0.039
intraspotCorrelation	0	0	0
isfullrank	0.000	0.000	0.001
isnumeric	0.000	0.000	0.001
kooperberg	0	0	0
limmaUsersGuide	0.004	0.000	0.001
lm.series	0	0	0
lmFit	0.364	0.000	0.365
lmscFit	0.000	0.000	0.001
loessfit	0.000	0.004	0.005
logcosh	0.004	0.000	0.000
ma3x3	0.000	0.000	0.001
makeContrasts	0.000	0.000	0.001
makeunique	0.000	0.000	0.001
mdplot	0.004	0.000	0.003
merge	0.004	0.000	0.005
mergeScansRG	0	0	0
modelMatrix	0.000	0.000	0.001
modifyWeights	0.000	0.000	0.001
nec	0.004	0.000	0.001
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0.020	0.000	0.019
normalizeVSN	0.540	0.020	1.103
normalizebetweenarrays	0.000	0.000	0.002
normalizeprintorder	0	0	0
normexpfit	0.000	0.000	0.001
normexpfitcontrol	0.004	0.000	0.001
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0	0	0
plotExons	0.000	0.000	0.001
plotMD	0.016	0.004	0.022
plotMDS	0.036	0.004	0.042
plotRLDF	0.008	0.000	0.007
plotSplice	0	0	0
plotWithHighlights	0.004	0.000	0.007
plotma	0.020	0.000	0.021
poolvar	0	0	0
predFCm	0.028	0.000	0.025
printorder	0.008	0.000	0.007
printtipWeights	0.000	0.000	0.001
propTrueNull	0.004	0.000	0.002
propexpr	0	0	0
protectMetachar	0.000	0.000	0.001
qqt	0.004	0.000	0.003
qualwt	0	0	0
rankSumTestwithCorrelation	0.004	0.000	0.006
read.idat	0	0	0
read.ilmn	0	0	0
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0	0	0
removeBatchEffect	0.012	0.000	0.012
removeext	0.000	0.000	0.001
roast	0.008	0.000	0.011
romer	0.172	0.000	0.173
selectmodel	0.004	0.004	0.009
squeezeVar	0.004	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.004	0.000	0.003
targetsA2C	0.004	0.000	0.003
topGO	0	0	0
topRomer	0	0	0
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.000	0.000	0.002
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0.004	0.000	0.001
uniquegenelist	0.000	0.000	0.001
unwrapdups	0	0	0
venn	0.020	0.000	0.019
volcanoplot	0.000	0.000	0.001
weightedLowess	0.012	0.000	0.009
weightedmedian	0	0	0
zscore	0.000	0.000	0.001