BioC 3.2: CHECK report for limma on linux1.bioconductor.org

Package: limma

Version: 3.26.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.26.0.tar.gz

StartedAt: 2015-10-27 05:05:37 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:07:04 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 87.1 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_3.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘3.26.0’
* 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 ... [3s/3s] 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 ... [7s/9s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 4.241  0.083   5.301
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [6s/7s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...1324a1325
> GO:0051130 positive regulation of cell...  BP 4  1    2 0.553950615 0.023749721
1329d1329
< GO:0031252              cell leading edge  CC 2  2    0 0.030909091 1.000000000
1333a1334
> GO:0051130 positive regulation of cell...  BP  4  1    2 0.5539506 0.023749721
1337a1339
> GO:0010629 negative regulation of gene...  BP  5  0    2 1.0000000 0.038228009
1339,1341c1341
< GO:0043230        extracellular organelle  CC 14  1    3 0.9502416 0.055161144
< GO:0065010 extracellular membrane-boun...  CC 14  1    3 0.9502416 0.055161144
< GO:0070062          extracellular exosome  CC 14  1    3 0.9502416 0.055161144
---
> GO:0048519 negative regulation of biol...  BP 14  2    3 0.7685153 0.055161144
 [6s/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

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	0.000	0.004	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	4.241	0.083	5.301
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.001	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.002	0.000	0.002
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.007	0.000	0.007
barcodeplot	0.037	0.000	0.037
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.001
camera	0.030	0.004	0.035
cbind	0.006	0.000	0.006
changelog	0.002	0.000	0.002
channel2M	0.002	0.000	0.002
classifytests	0.002	0.000	0.002
contrastAsCoef	0.007	0.000	0.007
contrasts.fit	0.017	0.000	0.017
controlStatus	0.008	0.000	0.008
diffSplice	0.001	0.000	0.001
dim	0.002	0.000	0.002
dupcor	0	0	0
ebayes	0.014	0.000	0.014
fitGammaIntercept	0.000	0.000	0.001
fitfdist	0.000	0.000	0.001
genas	0.109	0.003	0.113
geneSetTest	0.001	0.000	0.001
getSpacing	0.000	0.000	0.001
getlayout	0.000	0.004	0.001
goana	0.000	0.000	0.001
heatdiagram	0	0	0
helpMethods	0	0	0
ids2indices	0	0	0
imageplot	0.048	0.000	0.096
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	0.001	0.000	0.001
lm.series	0	0	0
lmFit	0.464	0.031	0.715
lmscFit	0.001	0.000	0.001
loessfit	0.009	0.000	0.009
ma3x3	0.002	0.000	0.002
makeContrasts	0.002	0.000	0.002
makeunique	0.001	0.000	0.001
mdplot	0.004	0.000	0.004
merge	0.003	0.000	0.006
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.003	0.000	0.003
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.001
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.023	0.004	0.027
normalizeVSN	0.529	0.012	0.679
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.001	0.000	0.001
plotExons	0.001	0.000	0.000
plotMD	0.029	0.000	0.029
plotMDS	0.028	0.000	0.028
plotRLDF	0.272	0.004	0.404
plotSplice	0	0	0
plotWithHighlights	0.009	0.000	0.009
plotma	0.029	0.000	0.029
poolvar	0.000	0.004	0.002
predFCm	0.024	0.000	0.025
printorder	0.019	0.000	0.019
printtipWeights	0.001	0.000	0.001
propTrueNull	0.003	0.000	0.002
propexpr	0.001	0.000	0.000
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.000	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.008	0.000	0.008
read.idat	0.001	0.000	0.001
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.000	0.001
readImaGeneHeader	0.001	0.000	0.001
readgal	0.000	0.000	0.001
removeBatchEffect	0.004	0.000	0.004
removeext	0.001	0.000	0.001
roast	0.036	0.000	0.036
romer	0.042	0.000	0.059
selectmodel	0.014	0.000	0.015
squeezeVar	0.002	0.000	0.001
strsplit2	0.001	0.000	0.002
subsetting	0.005	0.000	0.004
targetsA2C	0.006	0.000	0.005
topGO	0.000	0.000	0.001
topRomer	0.000	0.000	0.001
topSplice	0.001	0.000	0.000
toptable	0.000	0.000	0.001
tricubeMovingAverage	0.003	0.000	0.003
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.002
venn	0.027	0.000	0.026
volcanoplot	0.001	0.000	0.000
weightedLowess	0.011	0.000	0.012
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.002