BioC 3.3: CHECK report for limma on zin2

Package: limma

Version: 3.28.21

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.28.21.tar.gz

StartedAt: 2016-10-13 03:43:40 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:44:56 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 75.4 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.28.21.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/limma.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.28.21’
* 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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c normexp.c -o normexp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c weighted_lowess.c -o weighted_lowess.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o limma.so normexp.o weighted_lowess.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/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	0.001	0.000	0.000
PrintLayout	0.001	0.000	0.001
TestResults	0	0	0
alias2Symbol	3.118	0.051	3.188
arrayWeights	0.000	0.004	0.001
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.000	0.000	0.001
auROC	0.001	0.000	0.002
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.006	0.000	0.006
barcodeplot	0.036	0.000	0.036
beadCountWeights	0.001	0.000	0.000
blockDiag	0.000	0.000	0.001
camera	0.017	0.000	0.016
cbind	0.004	0.000	0.005
changelog	0.001	0.000	0.001
channel2M	0.002	0.000	0.001
classifytests	0.002	0.000	0.002
contrastAsCoef	0.006	0.000	0.005
contrasts.fit	0.012	0.000	0.013
controlStatus	0.002	0.000	0.006
cumOverlap	0.001	0.004	0.001
detectionPValue	0	0	0
diffSplice	0	0	0
dim	0.001	0.000	0.002
dupcor	0.355	0.012	0.366
ebayes	0.01	0.00	0.01
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
fitmixture	0.004	0.000	0.003
genas	0.077	0.004	0.082
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	0.000
ids2indices	0.001	0.000	0.000
imageplot	0.031	0.000	0.031
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.001	0.000	0.002
lm.series	0.000	0.000	0.001
lmFit	0.360	0.016	0.376
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.001	0.007
logcosh	0	0	0
ma3x3	0.001	0.000	0.001
makeContrasts	0.002	0.000	0.002
makeunique	0.001	0.000	0.001
mdplot	0.003	0.000	0.003
merge	0.005	0.000	0.005
mergeScansRG	0.000	0.003	0.001
modelMatrix	0.000	0.000	0.002
modifyWeights	0	0	0
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.000	0.003	0.001
normalizeRobustSpline	0.019	0.000	0.021
normalizeVSN	0.355	0.001	0.581
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.001	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.001	0.000	0.001
plotExons	0	0	0
plotMD	0.026	0.000	0.026
plotMDS	0.024	0.000	0.024
plotRLDF	0.01	0.00	0.01
plotSplice	0.001	0.000	0.001
plotWithHighlights	0.009	0.000	0.008
plotma	0.022	0.003	0.026
poolvar	0.001	0.000	0.001
predFCm	0.053	0.000	0.053
printorder	0.005	0.004	0.009
printtipWeights	0.001	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0.001	0.000	0.001
protectMetachar	0	0	0
qqt	0.003	0.000	0.003
qualwt	0.001	0.000	0.000
rankSumTestwithCorrelation	0.007	0.000	0.007
read.idat	0.001	0.000	0.001
read.ilmn	0	0	0
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0.001	0.000	0.001
removeBatchEffect	0.013	0.000	0.013
removeext	0.001	0.000	0.001
roast	0.015	0.000	0.015
romer	0.032	0.000	0.032
selectmodel	0.011	0.000	0.011
squeezeVar	0.001	0.000	0.000
strsplit2	0.001	0.000	0.001
subsetting	0.004	0.000	0.005
targetsA2C	0.005	0.000	0.004
topGO	0.000	0.000	0.001
topRomer	0	0	0
topSplice	0.001	0.000	0.001
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.002	0.000	0.002
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.000	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.022	0.000	0.022
volcanoplot	0.001	0.000	0.001
weightedLowess	0.01	0.00	0.01
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.004	0.001