BioC 3.0: CHECK report for limma on oaxaca

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.22.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/limma.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.22.7’
* 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/7s] 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 ... NOTE
'library' or 'require' call to ‘GO.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... [9s/10s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.988  0.129   6.541
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [8s/9s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [8s/10s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/limma.Rcheck/00check.log’
for details.

* 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/Library/Frameworks/R.framework/Resources/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-3.0-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	0.001	0.000	0.000
alias2Symbol	5.988	0.129	6.541
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.001	0.001
auROC	0.001	0.000	0.001
avearrays	0.002	0.000	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.007	0.000	0.007
barcodeplot	0.171	0.003	0.189
beadCountWeights	0.001	0.000	0.000
blockDiag	0.001	0.000	0.001
camera	0.023	0.001	0.025
cbind	0.005	0.000	0.005
changelog	0.002	0.001	0.004
channel2M	0.002	0.000	0.003
classifytests	0.003	0.001	0.003
contrastAsCoef	0.008	0.000	0.008
contrasts.fit	0.021	0.001	0.022
controlStatus	0.017	0.001	0.017
diffSplice	0.001	0.000	0.001
dim	0.003	0.000	0.003
dupcor	0.000	0.000	0.001
ebayes	0.014	0.001	0.016
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
genas	0.106	0.004	0.110
geneSetTest	0.001	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0.001	0.000	0.000
goana.MArrayLM	0.001	0.000	0.001
goana	0.001	0.000	0.000
heatdiagram	0.000	0.001	0.001
helpMethods	0.000	0.000	0.001
ids2indices	0.001	0.000	0.001
imageplot	0.182	0.003	0.186
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.000	0.001
isnumeric	0.002	0.000	0.001
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.003	0.001	0.004
lm.series	0.001	0.000	0.000
lmFit	0.684	0.011	0.712
lmscFit	0.001	0.001	0.001
loessfit	0.005	0.001	0.007
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.000	0.001
makeunique	0.001	0.000	0.002
merge	0.007	0.000	0.007
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.002	0.000	0.003
modifyWeights	0.001	0.000	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.028	0.002	0.030
normalizeVSN	0.298	0.017	0.316
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0.000	0.000	0.001
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.000	0.000	0.001
normexpsignal	0	0	0
plot	0.010	0.001	0.011
plotDensities	0.000	0.000	0.001
plotExons	0.001	0.000	0.001
plotMDS	0.011	0.001	0.013
plotRLDF	0.071	0.003	0.074
plotSplice	0.000	0.001	0.000
plotma	0.157	0.002	0.161
poolvar	0.001	0.000	0.002
predFCm	0.025	0.000	0.025
printorder	0.006	0.005	0.010
printtipWeights	0.001	0.000	0.001
propTrueNull	0.001	0.000	0.002
propexpr	0.001	0.001	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.001	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.007	0.000	0.007
read.idat	0.001	0.000	0.001
read.ilmn	0	0	0
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.000	0.000
readgal	0.000	0.000	0.001
removeBatchEffect	0.005	0.000	0.006
removeext	0.001	0.000	0.001
roast	0.043	0.001	0.044
romer	0.026	0.001	0.027
selectmodel	0.019	0.001	0.019
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.001	0.002
subsetting	0.006	0.000	0.006
targetsA2C	0.006	0.001	0.007
topGO	0	0	0
topRomer	0.001	0.000	0.000
topSplice	0.001	0.000	0.000
toptable	0.000	0.001	0.000
tricubeMovingAverage	0.002	0.000	0.003
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0	0	0
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.025	0.001	0.027
volcanoplot	0	0	0
weightedLowess	0.009	0.001	0.010
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.000	0.001

BioC 3.0: CHECK report for limma on oaxaca

Summary

Command output