BioC 3.2: CHECK report for limma on perceval

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 09:20:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:22:42 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 143.0 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 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [6s/7s] 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 ... [10s/11s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.417   0.14   5.568
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [9s/9s]
  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
 [9s/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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c normexp.c -o normexp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c weighted_lowess.c -o weighted_lowess.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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	0.000	0.001	0.001
PrintLayout	0.003	0.000	0.003
TestResults	0.001	0.001	0.001
alias2Symbol	5.417	0.140	5.568
arrayWeights	0.001	0.001	0.001
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.000	0.002
auROC	0.001	0.000	0.001
avearrays	0.002	0.001	0.003
avereps	0.002	0.000	0.001
backgroundcorrect	0.008	0.001	0.008
barcodeplot	0.039	0.004	0.053
beadCountWeights	0.001	0.000	0.001
blockDiag	0.001	0.000	0.002
camera	0.032	0.002	0.035
cbind	0.006	0.000	0.007
changelog	0.001	0.000	0.002
channel2M	0.002	0.000	0.003
classifytests	0.002	0.000	0.003
contrastAsCoef	0.008	0.000	0.008
contrasts.fit	0.018	0.001	0.018
controlStatus	0.008	0.000	0.008
diffSplice	0.001	0.000	0.001
dim	0.002	0.000	0.002
dupcor	0.000	0.000	0.001
ebayes	0.014	0.001	0.016
fitGammaIntercept	0.001	0.000	0.002
fitfdist	0.001	0.000	0.001
genas	0.135	0.007	0.141
geneSetTest	0.002	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0.001	0.000	0.000
goana	0.002	0.001	0.001
heatdiagram	0.001	0.000	0.001
helpMethods	0.000	0.000	0.001
ids2indices	0.001	0.001	0.001
imageplot	0.037	0.002	0.041
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.002	0.001	0.002
isnumeric	0.002	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.002	0.001	0.002
lm.series	0.000	0.000	0.001
lmFit	0.615	0.023	0.681
lmscFit	0.002	0.000	0.004
loessfit	0.011	0.003	0.026
ma3x3	0.003	0.000	0.003
makeContrasts	0.003	0.000	0.004
makeunique	0.002	0.000	0.002
mdplot	0.006	0.001	0.009
merge	0.010	0.000	0.011
mergeScansRG	0.002	0.000	0.001
modelMatrix	0.004	0.001	0.006
modifyWeights	0.002	0.000	0.002
nec	0.002	0.000	0.002
normalizeMedianAbsValues	0.002	0.001	0.003
normalizeRobustSpline	0.048	0.003	0.065
normalizeVSN	1.072	0.035	1.379
normalizebetweenarrays	0.005	0.001	0.008
normalizeprintorder	0.002	0.000	0.001
normexpfit	0.003	0.000	0.004
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0.001	0.000	0.002
normexpsignal	0.000	0.000	0.001
plotDensities	0.002	0.000	0.001
plotExons	0.002	0.001	0.002
plotMD	0.046	0.005	0.056
plotMDS	0.043	0.001	0.072
plotRLDF	0.403	0.009	0.538
plotSplice	0.001	0.000	0.001
plotWithHighlights	0.015	0.002	0.020
plotma	0.053	0.008	0.089
poolvar	0.003	0.000	0.002
predFCm	0.061	0.000	0.087
printorder	0.012	0.008	0.028
printtipWeights	0.001	0.000	0.002
propTrueNull	0.007	0.001	0.008
propexpr	0.001	0.000	0.001
protectMetachar	0.002	0.000	0.002
qqt	0.007	0.002	0.011
qualwt	0.001	0.000	0.001
rankSumTestwithCorrelation	0.015	0.001	0.016
read.idat	0.002	0.000	0.001
read.ilmn	0.001	0.000	0.001
read.maimages	0.001	0.001	0.002
readImaGeneHeader	0.001	0.000	0.001
readgal	0.001	0.000	0.005
removeBatchEffect	0.010	0.001	0.012
removeext	0.002	0.000	0.003
roast	0.081	0.003	0.107
romer	0.050	0.002	0.066
selectmodel	0.026	0.000	0.029
squeezeVar	0.002	0.000	0.007
strsplit2	0.001	0.001	0.002
subsetting	0.009	0.001	0.010
targetsA2C	0.010	0.000	0.016
topGO	0.001	0.000	0.001
topRomer	0.001	0.000	0.001
topSplice	0.001	0.000	0.000
toptable	0.001	0.000	0.001
tricubeMovingAverage	0.004	0.001	0.008
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.008
uniquegenelist	0.002	0.000	0.002
unwrapdups	0.002	0.001	0.004
venn	0.061	0.002	0.074
volcanoplot	0.001	0.000	0.001
weightedLowess	0.011	0.001	0.016
weightedmedian	0.002	0.000	0.005
zscore	0.003	0.000	0.004