BioC 3.2: CHECK report for limma on zin1

Package: limma

Version: 3.26.9

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.26.9.tar.gz

StartedAt: 2016-04-23 02:18:01 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:19:14 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 73.5 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.26.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/limma.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘3.26.9’
* 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 ... [4s/4s] 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 ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [4s/4s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK
 [5s/5s] 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-3.2-bioc/meat/limma.Rcheck/00check.log’
for details.

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o limma.so normexp.o weighted_lowess.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.001	0.000	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	3.369	0.048	4.190
arrayWeights	0.001	0.000	0.000
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.001	0.000	0.000
auROC	0.001	0.000	0.001
avearrays	0.002	0.000	0.002
avereps	0.001	0.000	0.002
backgroundcorrect	0.005	0.000	0.006
barcodeplot	0.026	0.004	0.030
beadCountWeights	0	0	0
blockDiag	0.001	0.000	0.001
camera	0.036	0.000	0.036
cbind	0.005	0.000	0.004
changelog	0.001	0.000	0.002
channel2M	0.001	0.000	0.002
classifytests	0.002	0.000	0.002
contrastAsCoef	0.006	0.000	0.005
contrasts.fit	0.014	0.000	0.014
controlStatus	0.006	0.000	0.005
diffSplice	0.000	0.000	0.001
dim	0.001	0.000	0.001
dupcor	0.001	0.000	0.001
ebayes	0.011	0.000	0.012
fitGammaIntercept	0.001	0.000	0.001
fitfdist	0.001	0.000	0.000
genas	0.084	0.004	0.088
geneSetTest	0.001	0.000	0.001
getSpacing	0.000	0.000	0.001
getlayout	0.001	0.000	0.000
goana	0.001	0.000	0.001
heatdiagram	0.000	0.000	0.001
helpMethods	0	0	0
ids2indices	0.001	0.000	0.000
imageplot	0.032	0.000	0.033
intraspotCorrelation	0.001	0.000	0.000
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.000	0.002
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.000	0.000	0.001
lm.series	0.000	0.000	0.001
lmFit	0.367	0.015	0.413
lmscFit	0.001	0.000	0.001
loessfit	0.006	0.000	0.006
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.000	0.001
makeunique	0.001	0.000	0.001
mdplot	0.003	0.000	0.003
merge	0.000	0.004	0.005
mergeScansRG	0	0	0
modelMatrix	0.000	0.004	0.002
modifyWeights	0.000	0.000	0.001
nec	0	0	0
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.021	0.000	0.033
normalizeVSN	0.372	0.000	0.395
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0	0	0
normexpfit	0.002	0.000	0.001
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0.001	0.000	0.001
plotExons	0	0	0
plotMD	0.023	0.000	0.023
plotMDS	0.022	0.000	0.022
plotRLDF	0.010	0.000	0.022
plotSplice	0.001	0.000	0.000
plotWithHighlights	0.008	0.000	0.019
plotma	0.022	0.000	0.023
poolvar	0.001	0.000	0.001
predFCm	0.03	0.00	0.03
printorder	0.004	0.003	0.007
printtipWeights	0.000	0.000	0.001
propTrueNull	0.002	0.000	0.002
propexpr	0.000	0.000	0.001
protectMetachar	0.000	0.000	0.001
qqt	0.001	0.000	0.002
qualwt	0.001	0.000	0.000
rankSumTestwithCorrelation	0.006	0.000	0.006
read.idat	0.001	0.000	0.001
read.ilmn	0.000	0.000	0.001
read.maimages	0.001	0.000	0.000
readImaGeneHeader	0.001	0.000	0.001
readgal	0	0	0
removeBatchEffect	0.003	0.000	0.003
removeext	0.001	0.000	0.001
roast	0.191	0.000	0.203
romer	0.024	0.000	0.024
selectmodel	0.01	0.00	0.01
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.003	0.000	0.004
targetsA2C	0.001	0.004	0.005
topGO	0	0	0
topRomer	0	0	0
topSplice	0	0	0
toptable	0	0	0
tricubeMovingAverage	0.002	0.000	0.002
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0	0	0
uniquegenelist	0.001	0.000	0.001
unwrapdups	0	0	0
venn	0.021	0.000	0.021
volcanoplot	0	0	0
weightedLowess	0.006	0.004	0.009
weightedmedian	0.000	0.000	0.001
zscore	0.001	0.000	0.001