BioC 3.1: CHECK report for limma on zin2

Package: limma

Version: 3.24.15

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.24.15.tar.gz

StartedAt: 2015-10-09 02:58:53 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:00:29 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 96.5 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.24.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/limma.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.24.15’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [4s/6s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...1318d1317
< Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
 [4s/7s] 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/limma.Rcheck/00check.log’
for details.

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o limma.so normexp.o weighted_lowess.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.001	0.000	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	3.385	0.055	4.434
arrayWeights	0	0	0
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.001	0.000	0.009
auROC	0.001	0.000	0.001
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.006	0.000	0.026
barcodeplot	0.029	0.000	0.044
beadCountWeights	0.000	0.000	0.001
blockDiag	0.000	0.000	0.001
camera	0.028	0.000	0.038
cbind	0.004	0.000	0.005
changelog	0.001	0.000	0.001
channel2M	0.002	0.000	0.001
classifytests	0.003	0.000	0.014
contrastAsCoef	0.005	0.000	0.006
contrasts.fit	0.015	0.000	0.041
controlStatus	0.005	0.000	0.005
diffSplice	0.001	0.000	0.001
dim	0.001	0.000	0.002
dupcor	0.001	0.000	0.000
ebayes	0.008	0.004	0.023
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.001
genas	0.091	0.000	0.251
geneSetTest	0.001	0.000	0.002
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
goana	0.001	0.000	0.014
heatdiagram	0.001	0.000	0.001
helpMethods	0.001	0.000	0.000
ids2indices	0.000	0.000	0.001
imageplot	0.033	0.000	0.062
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.000	0.002
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.001	0.000	0.011
lm.series	0.000	0.000	0.001
lmFit	0.393	0.014	0.952
lmscFit	0.001	0.000	0.001
loessfit	0.006	0.000	0.007
ma3x3	0.001	0.000	0.018
makeContrasts	0.002	0.000	0.001
makeunique	0.001	0.000	0.001
mdplot	0.003	0.000	0.003
merge	0.006	0.000	0.013
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.002	0.000	0.002
modifyWeights	0.000	0.000	0.001
nec	0.001	0.000	0.000
normalizeMedianAbsValues	0.000	0.004	0.001
normalizeRobustSpline	0.019	0.000	0.024
normalizeVSN	0.210	0.000	0.252
normalizebetweenarrays	0.002	0.000	0.002
normalizeprintorder	0.000	0.000	0.001
normexpfit	0.002	0.000	0.001
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.000
normexpsignal	0	0	0
plotDensities	0.000	0.000	0.001
plotExons	0.001	0.000	0.001
plotMD	0.023	0.000	0.023
plotMDS	0.012	0.000	0.011
plotRLDF	0.195	0.003	0.217
plotSplice	0	0	0
plotWithHighlights	0.006	0.000	0.007
plotma	0.022	0.000	0.022
poolvar	0.001	0.000	0.001
predFCm	0.03	0.00	0.03
printorder	0.004	0.003	0.008
printtipWeights	0.001	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0	0	0
protectMetachar	0.001	0.000	0.001
qqt	0.002	0.000	0.003
qualwt	0	0	0
rankSumTestwithCorrelation	0.006	0.000	0.034
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	0	0
removeBatchEffect	0.003	0.000	0.004
removeext	0.001	0.000	0.001
roast	0.028	0.000	0.060
romer	0.034	0.000	0.073
selectmodel	0.011	0.000	0.023
squeezeVar	0.001	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.004	0.000	0.015
targetsA2C	0.004	0.000	0.005
topGO	0.001	0.000	0.000
topRomer	0.001	0.000	0.000
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.002	0.000	0.014
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.022	0.000	0.046
volcanoplot	0	0	0
weightedLowess	0.009	0.000	0.010
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.001