BioC 3.0: CHECK report for limma on zin1

Package: limma

Version: 3.22.7

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.22.7.tar.gz

StartedAt: 2015-04-10 01:27:31 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:29:24 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 113.0 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.22.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/limma.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘3.22.7’
* 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 ... [4s/5s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/10s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.048  0.084   6.104
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [7s/8s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [7s/8s] 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/limma.Rcheck/00check.log’
for details.

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-bioc/R/lib -L/usr/local/lib -o limma.so normexp.o weighted_lowess.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/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	0.000	0.000	0.001
PrintLayout	0.000	0.000	0.001
TestResults	0.004	0.000	0.000
alias2Symbol	5.048	0.084	6.104
arrayWeights	0.000	0.000	0.001
arrayWeightsQuick	0.004	0.000	0.001
asMatrixWeights	0.000	0.000	0.001
auROC	0.000	0.004	0.149
avearrays	0.004	0.000	0.002
avereps	0.000	0.000	0.002
backgroundcorrect	0.008	0.000	0.009
barcodeplot	0.164	0.004	0.168
beadCountWeights	0.000	0.000	0.001
blockDiag	0.000	0.000	0.001
camera	0.024	0.000	0.024
cbind	0.004	0.000	0.005
changelog	0.004	0.000	0.003
channel2M	0.004	0.000	0.001
classifytests	0.004	0.000	0.013
contrastAsCoef	0.008	0.000	0.008
contrasts.fit	0.020	0.000	0.075
controlStatus	0.016	0.000	0.014
diffSplice	0.000	0.000	0.001
dim	0.004	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	0.112	0.000	0.112
geneSetTest	0.000	0.000	0.001
getSpacing	0.004	0.000	0.001
getlayout	0	0	0
goana.MArrayLM	0.004	0.000	0.001
goana	0.000	0.000	0.001
heatdiagram	0.000	0.000	0.001
helpMethods	0	0	0
ids2indices	0.000	0.000	0.001
imageplot	0.160	0.004	0.168
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.004	0.000	0.002
isnumeric	0.000	0.000	0.001
kooperberg	0.004	0.000	0.001
limmaUsersGuide	0.004	0.000	0.003
lm.series	0	0	0
lmFit	0.556	0.004	0.610
lmscFit	0.000	0.000	0.001
loessfit	0.008	0.000	0.008
ma3x3	0.004	0.000	0.002
makeContrasts	0.004	0.000	0.002
makeunique	0.000	0.000	0.001
merge	0.008	0.000	0.007
mergeScansRG	0.004	0.000	0.001
modelMatrix	0.004	0.000	0.003
modifyWeights	0.000	0.000	0.001
nec	0.004	0.000	0.001
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.024	0.008	0.052
normalizeVSN	0.444	0.012	0.531
normalizebetweenarrays	0.004	0.000	0.003
normalizeprintorder	0	0	0
normexpfit	0.000	0.000	0.002
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0	0	0
normexpsignal	0.004	0.000	0.000
plot	0.012	0.000	0.011
plotDensities	0	0	0
plotExons	0.004	0.000	0.000
plotMDS	0.016	0.000	0.016
plotRLDF	0.048	0.012	0.069
plotSplice	0	0	0
plotma	0.168	0.000	0.170
poolvar	0.000	0.000	0.001
predFCm	0.028	0.000	0.027
printorder	0.000	0.008	0.008
printtipWeights	0.000	0.000	0.001
propTrueNull	0.004	0.000	0.002
propexpr	0.000	0.000	0.001
protectMetachar	0.004	0.000	0.001
qqt	0.000	0.000	0.002
qualwt	0.000	0.000	0.001
rankSumTestwithCorrelation	0.008	0.000	0.007
read.idat	0	0	0
read.ilmn	0.004	0.000	0.001
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0	0	0
readgal	0.000	0.000	0.001
removeBatchEffect	0.004	0.000	0.004
removeext	0.000	0.000	0.001
roast	0.044	0.000	0.044
romer	0.028	0.000	0.028
selectmodel	0.016	0.000	0.015
squeezeVar	0.004	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.008	0.000	0.005
targetsA2C	0.004	0.000	0.006
topGO	0.000	0.000	0.001
topRomer	0	0	0
topSplice	0	0	0
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.004	0.000	0.002
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.000	0.000	0.001
unwrapdups	0.000	0.000	0.001
venn	0.024	0.000	0.024
volcanoplot	0	0	0
weightedLowess	0.012	0.000	0.010
weightedmedian	0	0	0
zscore	0.000	0.000	0.002