BioC 2.14: CHECK report for limma on morelia

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 23:43:36 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:45:16 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 99.7 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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


* 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-darwin13.1.0 (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 ... [6s/6s] 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 ... [8s/8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [2s/2s]
  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
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/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	0.000
PrintLayout	0.002	0.000	0.001
TestResults	0.001	0.000	0.001
alias2Symbol	4.640	0.097	4.756
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.000	0.001
auROC	0.002	0.000	0.001
avearrays	0.002	0.000	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.009	0.000	0.010
barcodeplot	0.013	0.002	0.014
beadCountWeights	0.001	0.000	0.001
blockDiag	0.002	0.000	0.001
camera	0.021	0.001	0.023
cbind	0.019	0.001	0.020
changelog	0.004	0.000	0.005
channel2M	0.002	0.000	0.002
classifytests	0.003	0.000	0.003
contrastAsCoef	0.008	0.000	0.008
contrasts.fit	0.020	0.001	0.021
controlStatus	0.008	0.000	0.008
diffSplice	0	0	0
dim	0.002	0.000	0.001
dupcor	0.000	0.000	0.001
ebayes	0.015	0.002	0.016
fitGammaIntercept	0.001	0.000	0.002
fitfdist	0.001	0.000	0.002
genas	0.150	0.008	0.157
geneSetTest	0.001	0.000	0.001
getSpacing	0.002	0.000	0.001
getlayout	0.001	0.000	0.000
heatdiagram	0.001	0.000	0.001
helpMethods	0.001	0.000	0.000
imageplot	0.048	0.002	0.050
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.002	0.000	0.002
isnumeric	0.002	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.004	0.001	0.004
lm.series	0.001	0.000	0.001
lmFit	0.676	0.012	0.691
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.002	0.010
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.000	0.001
makeunique	0.002	0.000	0.001
merge	0.008	0.000	0.009
mergeScansRG	0.001	0.000	0.000
modelMatrix	0.003	0.000	0.003
modifyWeights	0.001	0.001	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.002
normalizeRobustSpline	0.070	0.004	0.075
normalizeVSN	0.455	0.020	0.476
normalizebetweenarrays	0.002	0.001	0.003
normalizeprintorder	0.001	0.000	0.001
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.001
normexpsignal	0	0	0
plot	0.016	0.002	0.018
plotDensities	0.001	0.000	0.001
plotMDS	0.015	0.002	0.016
plotRLDF	0.160	0.004	0.164
plotSplice	0	0	0
plotma	0.010	0.001	0.014
poolvar	0.001	0.001	0.001
predFCm	0.029	0.000	0.029
printorder	0.007	0.005	0.012
printtipWeights	0	0	0
propTrueNull	0.002	0.000	0.002
propexpr	0.000	0.000	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.001	0.004
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.021	0.001	0.022
read.idat	0.000	0.000	0.001
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.000	0.000	0.001
readgal	0.001	0.000	0.001
removeBatchEffect	0.003	0.000	0.004
removeext	0.001	0.000	0.000
roast	0.035	0.002	0.037
romer	0.019	0.001	0.020
selectmodel	0.012	0.000	0.013
squeezeVar	0.001	0.000	0.001
strsplit2	0.000	0.001	0.001
subsetting	0.004	0.000	0.004
targetsA2C	0.004	0.000	0.004
topRomer	0	0	0
topSplice	0	0	0
toptable	0.001	0.000	0.001
tricubeMovingAverage	0.002	0.000	0.003
trigammainverse	0.001	0.000	0.000
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.028	0.001	0.028
volcanoplot	0.001	0.000	0.001
weightedLowess	0.009	0.001	0.009
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.002