BioC 3.2: CHECK report for limma on oaxaca

Package: limma

Version: 3.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.26.0.tar.gz

StartedAt: 2015-10-27 05:02:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:05:03 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 136.7 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limma_3.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/limma.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘3.26.0’
* 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 ... [5s/6s] 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 ... [8s/12s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 4.858  0.105   7.749
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [7s/10s]
  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
 [7s/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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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-3.2-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	0.001	0.001	0.001
PrintLayout	0.001	0.000	0.004
TestResults	0.001	0.000	0.001
alias2Symbol	4.858	0.105	7.749
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.000	0.007
auROC	0.002	0.000	0.002
avearrays	0.001	0.000	0.002
avereps	0.001	0.000	0.006
backgroundcorrect	0.008	0.001	0.015
barcodeplot	0.035	0.004	0.046
beadCountWeights	0.001	0.000	0.001
blockDiag	0.002	0.000	0.001
camera	0.035	0.002	0.051
cbind	0.007	0.001	0.012
changelog	0.002	0.000	0.002
channel2M	0.002	0.000	0.002
classifytests	0.002	0.000	0.003
contrastAsCoef	0.009	0.000	0.017
contrasts.fit	0.020	0.000	0.027
controlStatus	0.009	0.000	0.016
diffSplice	0.000	0.000	0.001
dim	0.002	0.000	0.003
dupcor	0.001	0.000	0.006
ebayes	0.017	0.002	0.022
fitGammaIntercept	0.002	0.000	0.001
fitfdist	0.001	0.000	0.001
genas	0.108	0.005	0.163
geneSetTest	0.001	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0.001	0.000	0.001
goana	0.002	0.000	0.002
heatdiagram	0.001	0.000	0.001
helpMethods	0	0	0
ids2indices	0.001	0.000	0.001
imageplot	0.036	0.003	0.051
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.002
isnumeric	0.001	0.000	0.002
kooperberg	0.001	0.000	0.002
limmaUsersGuide	0.001	0.001	0.003
lm.series	0.000	0.000	0.001
lmFit	0.602	0.019	0.961
lmscFit	0.001	0.000	0.001
loessfit	0.007	0.001	0.012
ma3x3	0.002	0.001	0.002
makeContrasts	0.002	0.000	0.006
makeunique	0.001	0.000	0.001
mdplot	0.004	0.001	0.006
merge	0.008	0.001	0.011
mergeScansRG	0.001	0.000	0.001
modelMatrix	0.003	0.001	0.009
modifyWeights	0.001	0.000	0.001
nec	0.001	0.001	0.002
normalizeMedianAbsValues	0.001	0.000	0.002
normalizeRobustSpline	0.029	0.002	0.045
normalizeVSN	0.633	0.018	0.960
normalizebetweenarrays	0.003	0.001	0.004
normalizeprintorder	0.001	0.000	0.001
normexpfit	0.002	0.000	0.003
normexpfitcontrol	0.000	0.001	0.002
normexpfitdetectionp	0.001	0.000	0.005
normexpsignal	0.000	0.000	0.001
plotDensities	0.001	0.000	0.001
plotExons	0.001	0.000	0.001
plotMD	0.028	0.003	0.040
plotMDS	0.028	0.002	0.051
plotRLDF	0.255	0.005	0.386
plotSplice	0.000	0.000	0.001
plotWithHighlights	0.008	0.001	0.010
plotma	0.027	0.003	0.036
poolvar	0.001	0.000	0.002
predFCm	0.019	0.001	0.038
printorder	0.019	0.006	0.033
printtipWeights	0.001	0.000	0.001
propTrueNull	0.004	0.000	0.011
propexpr	0	0	0
protectMetachar	0.001	0.000	0.001
qqt	0.003	0.001	0.003
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.009	0.000	0.019
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	0.001	0.000	0.000
removeBatchEffect	0.005	0.001	0.010
removeext	0.001	0.000	0.001
roast	0.037	0.001	0.058
romer	0.043	0.002	0.067
selectmodel	0.016	0.000	0.020
squeezeVar	0.001	0.001	0.001
strsplit2	0.001	0.000	0.002
subsetting	0.006	0.001	0.013
targetsA2C	0.007	0.000	0.009
topGO	0	0	0
topRomer	0	0	0
topSplice	0.001	0.000	0.000
toptable	0.001	0.000	0.006
tricubeMovingAverage	0.003	0.001	0.004
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.002
venn	0.026	0.001	0.039
volcanoplot	0.000	0.000	0.001
weightedLowess	0.009	0.001	0.013
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.006