BioC 2.14: CHECK report for limma on zin2

Package: limma

Version: 3.20.9

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.20.9.tar.gz

StartedAt: 2014-10-08 00:43:32 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:44:49 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 77.4 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.20.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/limma.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.20.9’
* 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 ... [4s/4s] 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [1s/1s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [2s/2s] 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

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-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-2.14-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/usr/local/lib -o limma.so normexp.o weighted_lowess.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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	0.000	0.000	0.001
TestResults	0.004	0.000	0.000
alias2Symbol	3.744	0.072	3.824
arrayWeights	0	0	0
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.000	0.000	0.001
auROC	0.000	0.000	0.001
avearrays	0.004	0.000	0.002
avereps	0.000	0.000	0.001
backgroundcorrect	0.008	0.000	0.007
barcodeplot	0.008	0.004	0.010
beadCountWeights	0.000	0.000	0.001
blockDiag	0.000	0.000	0.001
camera	0.020	0.004	0.024
cbind	0.016	0.000	0.014
changelog	0.004	0.000	0.003
channel2M	0.000	0.000	0.001
classifytests	0.000	0.000	0.003
contrastAsCoef	0.004	0.000	0.006
contrasts.fit	0.012	0.004	0.016
controlStatus	0.004	0.000	0.006
diffSplice	0.004	0.000	0.001
dim	0.000	0.000	0.002
dupcor	0	0	0
ebayes	0.012	0.000	0.014
fitGammaIntercept	0.000	0.000	0.001
fitfdist	0.000	0.000	0.001
genas	0.120	0.004	0.127
geneSetTest	0.000	0.000	0.001
getSpacing	0.000	0.004	0.001
getlayout	0.000	0.000	0.001
heatdiagram	0	0	0
helpMethods	0.000	0.000	0.001
imageplot	0.04	0.00	0.04
intraspotCorrelation	0	0	0
isfullrank	0.000	0.000	0.002
isnumeric	0.000	0.000	0.001
kooperberg	0	0	0
limmaUsersGuide	0.004	0.000	0.003
lm.series	0.000	0.000	0.001
lmFit	0.580	0.008	0.588
lmscFit	0.000	0.000	0.001
loessfit	0.008	0.000	0.008
ma3x3	0.000	0.000	0.002
makeContrasts	0.004	0.000	0.001
makeunique	0.000	0.000	0.001
merge	0.008	0.000	0.006
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.004	0.000	0.002
modifyWeights	0.000	0.000	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.044	0.004	0.049
normalizeVSN	0.312	0.032	0.346
normalizebetweenarrays	0.000	0.000	0.002
normalizeprintorder	0.000	0.000	0.001
normexpfit	0.004	0.000	0.002
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plot	0.012	0.000	0.014
plotDensities	0.000	0.000	0.001
plotMDS	0.012	0.000	0.013
plotRLDF	0.288	0.004	0.295
plotSplice	0.000	0.004	0.000
plotma	0.012	0.000	0.014
poolvar	0.004	0.000	0.001
predFCm	0.024	0.000	0.022
printorder	0.012	0.004	0.014
printtipWeights	0.000	0.000	0.001
propTrueNull	0.004	0.000	0.003
propexpr	0	0	0
protectMetachar	0.000	0.000	0.001
qqt	0.004	0.000	0.003
qualwt	0	0	0
rankSumTestwithCorrelation	0.008	0.000	0.007
read.idat	0	0	0
read.ilmn	0.000	0.000	0.001
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0.000	0.000	0.001
removeBatchEffect	0.000	0.004	0.004
removeext	0.004	0.000	0.001
roast	0.040	0.000	0.039
romer	0.148	0.000	0.148
selectmodel	0.016	0.000	0.014
squeezeVar	0.000	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.000	0.004	0.005
targetsA2C	0.004	0.000	0.005
topRomer	0.000	0.000	0.001
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.004	0.000	0.003
trigammainverse	0	0	0
trimWhiteSpace	0.004	0.000	0.001
uniquegenelist	0.000	0.000	0.001
unwrapdups	0.004	0.000	0.001
venn	0.024	0.000	0.024
volcanoplot	0.000	0.000	0.001
weightedLowess	0.008	0.000	0.009
weightedmedian	0.000	0.000	0.001
zscore	0.000	0.000	0.002