BioC 2.12: CHECK report for limma on pelham

Package: limma

Version: 3.15.18

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.15.18.tar.gz

StartedAt: 2013-03-24 07:08:13 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 07:10:34 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 140.7 seconds

RetCode: 0

Status: OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.15.18'
* 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 ... [8s/8s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 6.696  0.208    6.99
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'limma-Tests.R' [2s/2s]
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...588,592c588,592
< 0%   -0.78835384 -0.788312144 -0.79410956 -2.04434053 -2.0438088 -10.9766130
< 25%  -0.18340154 -0.183595325 -0.17340349 -0.59321065 -0.5863777  -0.7816385
< 50%  -0.11492924 -0.123303508 -0.04476096  0.05874864  0.0827054  -0.2577724
< 75%   0.01507921 -0.006825877  0.14015263  0.56010750  0.5606874   0.4406875
< 100%  0.21653837  0.193234186 11.47140874  2.57936026  2.5816432   2.5397022
---
> 0%   -0.78835384 -0.78097895 -0.78367166 -2.04434053 -2.04315267 -11.5610680
> 25%  -0.18340154 -0.18907787 -0.15525721 -0.59321065 -0.59309327  -0.8249477
> 50%  -0.11492924 -0.12136183 -0.03316003  0.05874864  0.08898459  -0.2466309
> 75%   0.01507921 -0.01000344  0.13229151  0.56010750  0.56606786   0.4502908
> 100%  0.21653837  0.21604173 11.69912073  2.57936026  2.56259812   2.5149556
630,635c630,635
<  Min.   :-5.88044   Min.   :-5.66985  
<  1st Qu.:-1.18483   1st Qu.:-1.57014  
<  Median :-0.21632   Median : 0.04823  
<  Mean   : 0.03487   Mean   :-0.05481  
<  3rd Qu.: 1.49669   3rd Qu.: 1.45113  
<  Max.   : 7.07324   Max.   : 6.19744  
---
>  Min.   :-5.85163   Min.   :-5.69877  
>  1st Qu.:-1.18482   1st Qu.:-1.55421  
>  Median :-0.21631   Median : 0.06267  
>  Mean   : 0.03613   Mean   :-0.05369  
>  3rd Qu.: 1.49673   3rd Qu.: 1.41900  
>  Max.   : 7.07528   Max.   : 6.28902  
646,650c646,650
< [1,] -1.1689588  4.5558123
< [2,]  0.8971363  0.3296544
< [3,]  2.8247439  1.4249960
< [4,] -1.8533240  0.4804851
< [5,]  1.9158459 -5.5087631
---
> [1,] -1.1623390  4.5343276
> [2,]  0.8971391  0.3495635
> [3,]  2.8247455  1.4459533
> [4,] -1.8533288  0.4894799
> [5,]  1.9158416 -5.5363732
661,665c661,665
< [1,] -1.1689588  4.5558123
< [2,]  0.8971363  0.3296544
< [3,]  2.8247439  1.4249960
< [4,] -1.8533240  0.4804851
< [5,]  1.9158459 -5.5087631
---
> [1,] -1.1623390  4.5343276
> [2,]  0.8971391  0.3495635
> [3,]  2.8247455  1.4459533
> [4,] -1.8533288  0.4894799
> [5,]  1.9158416 -5.5363732
981,982c981,982
< mu+alpha    0.3333333 3.333333e-01  5.551115e-17
< mu+beta    -0.3333333 5.551115e-17  3.333333e-01
---
> mu+alpha    0.3333333 3.333333e-01  9.280771e-17
> mu+beta    -0.3333333 9.280771e-17  3.333333e-01
 [3s/3s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* 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  -c normexp.c -o normexp.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/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'limma.Rnw' 
** testing if installed package can be loaded
* DONE (limma)

name	user	system	elapsed
LargeDataObject	0.008	0.001	0.009
PrintLayout	0.011	0.002	0.013
TestResults	0.007	0.001	0.008
alias2Symbol	6.696	0.208	6.990
arrayWeights	0.250	0.003	0.253
arrayWeightsQuick	0.029	0.002	0.031
asMatrixWeights	0.027	0.003	0.030
auROC	0.045	0.001	0.046
avearrays	0.046	0.001	0.047
avereps	0.045	0.004	0.048
backgroundcorrect	0.040	0.003	0.043
barcodeplot	0.047	0.004	0.051
blockDiag	0.030	0.001	0.031
camera	0.131	0.003	0.134
cbind	0.066	0.003	0.068
channel2M	0.030	0.002	0.031
classifytests	0.042	0.000	0.043
contrasts.fit	0.069	0.007	0.074
controlStatus	0.038	0.002	0.041
dim	0.045	0.004	0.048
dupcor	0.030	0.003	0.033
ebayes	0.086	0.010	0.095
fitGammaIntercept	0.044	0.003	0.046
fitfdist	0.016	0.001	0.016
genas	0.185	0.011	0.197
geneSetTest	0.041	0.002	0.042
getSpacing	0.043	0.002	0.045
getlayout	0.029	0.001	0.031
heatdiagram	0.029	0.001	0.030
helpMethods	0.015	0.002	0.017
imageplot	0.074	0.005	0.079
intraspotCorrelation	0.034	0.003	0.037
isfullrank	0.049	0.000	0.049
isnumeric	0.037	0.004	0.041
kooperberg	0.046	0.003	0.050
limmaUsersGuide	0.018	0.002	0.021
lm.series	0.015	0.001	0.016
lmFit	1.231	0.044	1.278
lmscFit	0.044	0.004	0.047
loessfit	0.113	0.005	0.118
ma3x3	0.032	0.002	0.034
makeContrasts	0.051	0.002	0.052
makeunique	0.032	0.002	0.033
merge	0.054	0.004	0.058
mergeScansRG	0.044	0.002	0.046
modelMatrix	0.048	0.001	0.049
modifyWeights	0.032	0.003	0.035
nec	0.043	0.003	0.046
normalizeMedianAbsValues	0.017	0.003	0.020
normalizeRobustSpline	0.135	0.008	0.143
normalizeVSN	0.621	0.038	0.659
normalizebetweenarrays	0.052	0.001	0.052
normalizeprintorder	0.022	0.004	0.025
normexpfit	0.034	0.003	0.037
normexpfitcontrol	0.031	0.003	0.034
normexpfitdetectionp	0.032	0.003	0.036
normexpsignal	0.018	0.001	0.019
plotDensities	0.070	0.007	0.078
plotMDS	0.055	0.006	0.061
plotRLDF	0.441	0.018	0.466
plotma	0.076	0.016	0.096
poolvar	0.036	0.006	0.043
predFCm	0.103	0.009	0.115
printorder	0.025	0.012	0.041
printtipWeights	0.035	0.008	0.043
propTrueNull	0.034	0.007	0.041
propexpr	0.032	0.004	0.037
protectMetachar	0.017	0.003	0.019
qqt	0.021	0.004	0.026
qualwt	0.035	0.004	0.040
rankSumTestwithCorrelation	0.315	0.006	0.326
read.ilmn	0.016	0.003	0.020
read.maimages	0.034	0.006	0.043
readImaGeneHeader	0.017	0.004	0.020
readgal	0.016	0.003	0.020
removeext	0.019	0.004	0.022
roast	0.157	0.011	0.179
romer	0.538	0.065	0.635
selectmodel	0.057	0.008	0.065
squeezeVar	0.031	0.003	0.036
strsplit2	0.033	0.005	0.038
subsetting	0.039	0.005	0.051
targetsA2C	0.040	0.003	0.042
topRomer	0.017	0.003	0.020
toptable	0.017	0.004	0.020
trigammainverse	0.018	0.004	0.021
trimWhiteSpace	0.018	0.003	0.021
uniquegenelist	0.019	0.005	0.024
unwrapdups	0.035	0.006	0.043
venn	0.087	0.009	0.096
volcanoplot	0.019	0.004	0.023
weightedmedian	0.018	0.003	0.021
zscore	0.034	0.006	0.039

Summary

Command output