BioC 2.14: CHECK report for limma on petty

Package: limma

Version: 3.20.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.20.9.tar.gz

StartedAt: 2014-10-07 22:42:04 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:45:05 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 181.0 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 --no-multiarch limma_3.20.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/limma.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [10s/10s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 8.805  0.205   9.153
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [3s/3s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [4s/4s] 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c normexp.c -o normexp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c weighted_lowess.c -o weighted_lowess.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-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	0.001	0.000	0.001
PrintLayout	0.002	0.000	0.003
TestResults	0.001	0.000	0.001
alias2Symbol	8.805	0.205	9.153
arrayWeights	0.002	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.002	0.000	0.002
auROC	0.003	0.000	0.002
avearrays	0.003	0.001	0.003
avereps	0.003	0.000	0.003
backgroundcorrect	0.016	0.001	0.017
barcodeplot	0.021	0.003	0.024
beadCountWeights	0.001	0.000	0.002
blockDiag	0.002	0.000	0.002
camera	0.041	0.003	0.045
cbind	0.030	0.001	0.031
changelog	0.005	0.002	0.006
channel2M	0.004	0.000	0.004
classifytests	0.004	0.001	0.005
contrastAsCoef	0.015	0.001	0.014
contrasts.fit	0.034	0.001	0.035
controlStatus	0.014	0.001	0.015
diffSplice	0.001	0.000	0.001
dim	0.005	0.000	0.005
dupcor	0.001	0.001	0.001
ebayes	0.028	0.002	0.030
fitGammaIntercept	0.002	0.000	0.003
fitfdist	0.002	0.000	0.002
genas	0.491	0.009	0.506
geneSetTest	0.003	0.000	0.003
getSpacing	0.002	0.000	0.002
getlayout	0.001	0.001	0.001
heatdiagram	0.001	0.000	0.001
helpMethods	0.000	0.001	0.001
imageplot	0.059	0.004	0.064
intraspotCorrelation	0.001	0.001	0.001
isfullrank	0.003	0.000	0.003
isnumeric	0.002	0.000	0.003
kooperberg	0.001	0.001	0.002
limmaUsersGuide	0.005	0.001	0.006
lm.series	0.001	0.001	0.001
lmFit	1.060	0.027	1.101
lmscFit	0.001	0.000	0.002
loessfit	0.012	0.002	0.022
ma3x3	0.003	0.000	0.003
makeContrasts	0.003	0.000	0.003
makeunique	0.002	0.001	0.002
merge	0.013	0.001	0.014
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.005	0.000	0.005
modifyWeights	0.001	0.001	0.002
nec	0.001	0.000	0.002
normalizeMedianAbsValues	0.002	0.000	0.002
normalizeRobustSpline	0.142	0.015	0.271
normalizeVSN	0.879	0.040	0.920
normalizebetweenarrays	0.005	0.000	0.006
normalizeprintorder	0.001	0.000	0.001
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.002
normexpsignal	0.000	0.000	0.001
plot	0.024	0.003	0.028
plotDensities	0.001	0.000	0.001
plotMDS	0.022	0.001	0.027
plotRLDF	0.572	0.007	0.581
plotSplice	0.001	0.000	0.001
plotma	0.024	0.003	0.028
poolvar	0.003	0.000	0.003
predFCm	0.056	0.001	0.057
printorder	0.013	0.010	0.023
printtipWeights	0.002	0.000	0.002
propTrueNull	0.005	0.000	0.005
propexpr	0.001	0.001	0.001
protectMetachar	0.001	0.000	0.002
qqt	0.003	0.001	0.004
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.014	0.000	0.014
read.idat	0.001	0.000	0.002
read.ilmn	0.001	0.000	0.001
read.maimages	0.002	0.001	0.002
readImaGeneHeader	0.001	0.000	0.001
readgal	0.001	0.000	0.001
removeBatchEffect	0.008	0.001	0.009
removeext	0.002	0.000	0.001
roast	0.315	0.003	0.318
romer	0.050	0.003	0.051
selectmodel	0.023	0.000	0.024
squeezeVar	0.002	0.000	0.002
strsplit2	0.002	0.000	0.002
subsetting	0.010	0.001	0.011
targetsA2C	0.011	0.001	0.012
topRomer	0.001	0.000	0.001
topSplice	0.001	0.000	0.001
toptable	0.001	0.000	0.001
tricubeMovingAverage	0.004	0.002	0.006
trigammainverse	0.002	0.000	0.001
trimWhiteSpace	0.001	0.001	0.002
uniquegenelist	0.002	0.000	0.003
unwrapdups	0.002	0.000	0.002
venn	0.046	0.008	0.054
volcanoplot	0.001	0.001	0.001
weightedLowess	0.011	0.002	0.013
weightedmedian	0.001	0.000	0.002
zscore	0.003	0.000	0.003