BioC 2.12: CHECK report for limma on petty

Package: limma

Version: 3.16.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.16.8.tar.gz

StartedAt: 2013-10-08 22:55:30 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:58:22 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 171.9 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 3.0.1 (2013-05-16)
* 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 '3.16.8'
* 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 ... [10s/10s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/22s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 8.327  0.224   8.697
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'limma-Tests.R' [3s/3s]
  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 -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
** testing if installed package can be loaded
* DONE (limma)

name	user	system	elapsed
LargeDataObject	0.013	0.001	0.014
PrintLayout	0.012	0.000	0.012
TestResults	0.007	0.000	0.008
alias2Symbol	8.327	0.224	8.697
arrayWeights	0.255	0.004	0.259
arrayWeightsQuick	0.016	0.001	0.016
asMatrixWeights	0.032	0.001	0.033
auROC	0.027	0.002	0.030
avearrays	0.030	0.001	0.031
avereps	0.034	0.001	0.034
backgroundcorrect	0.055	0.002	0.057
barcodeplot	0.038	0.003	0.040
blockDiag	0.031	0.001	0.032
camera	0.107	0.004	0.111
cbind	0.069	0.001	0.070
channel2M	0.039	0.001	0.040
classifytests	0.037	0.002	0.038
contrasts.fit	0.114	0.004	0.119
controlStatus	0.055	0.001	0.056
dim	0.046	0.002	0.048
dupcor	0.044	0.001	0.046
ebayes	0.123	0.003	0.127
fitGammaIntercept	0.043	0.001	0.043
fitfdist	0.030	0.001	0.030
genas	0.184	0.012	0.197
geneSetTest	0.048	0.000	0.048
getSpacing	0.020	0.002	0.022
getlayout	0.016	0.001	0.017
heatdiagram	0.031	0.001	0.032
helpMethods	0.017	0.002	0.017
imageplot	0.092	0.005	0.098
intraspotCorrelation	0.047	0.001	0.050
isfullrank	0.050	0.001	0.051
isnumeric	0.031	0.003	0.034
kooperberg	0.035	0.002	0.037
limmaUsersGuide	0.036	0.002	0.039
lm.series	0.017	0.001	0.019
lmFit	1.209	0.043	1.294
lmscFit	0.040	0.003	0.044
loessfit	0.102	0.004	0.108
ma3x3	0.019	0.001	0.020
makeContrasts	0.034	0.002	0.037
makeunique	0.036	0.003	0.038
merge	0.258	0.005	0.263
mergeScansRG	0.039	0.004	0.043
modelMatrix	0.034	0.005	0.038
modifyWeights	0.019	0.003	0.022
nec	0.035	0.005	0.039
normalizeMedianAbsValues	0.017	0.003	0.019
normalizeRobustSpline	0.143	0.011	0.155
normalizeVSN	0.743	0.054	0.799
normalizebetweenarrays	0.036	0.004	0.040
normalizeprintorder	0.018	0.002	0.021
normexpfit	0.020	0.002	0.022
normexpfitcontrol	0.035	0.003	0.037
normexpfitdetectionp	0.031	0.002	0.033
normexpsignal	0.017	0.001	0.018
plotDensities	0.064	0.005	0.069
plotMDS	0.069	0.004	0.084
plotRLDF	0.719	0.014	0.740
plotma	0.073	0.009	0.086
poolvar	0.029	0.004	0.033
predFCm	0.103	0.011	0.114
printorder	0.028	0.011	0.038
printtipWeights	0.033	0.003	0.036
propTrueNull	0.051	0.003	0.054
propexpr	0.015	0.000	0.016
protectMetachar	0.017	0.001	0.018
qqt	0.021	0.004	0.025
qualwt	0.033	0.003	0.036
rankSumTestwithCorrelation	0.064	0.005	0.069
read.ilmn	0.017	0.002	0.019
read.maimages	0.034	0.003	0.042
readImaGeneHeader	0.032	0.002	0.034
readgal	0.272	0.003	0.285
removeext	0.017	0.002	0.020
roast	0.135	0.007	0.142
romer	0.609	0.059	0.675
selectmodel	0.087	0.006	0.092
squeezeVar	0.018	0.003	0.021
strsplit2	0.032	0.003	0.035
subsetting	0.040	0.003	0.044
targetsA2C	0.042	0.002	0.044
topRomer	0.031	0.001	0.035
toptable	0.030	0.001	0.032
trigammainverse	0.017	0.002	0.020
trimWhiteSpace	0.014	0.003	0.016
uniquegenelist	0.033	0.003	0.036
unwrapdups	0.021	0.003	0.026
venn	0.092	0.007	0.100
volcanoplot	0.017	0.002	0.020
weightedmedian	0.034	0.003	0.039
zscore	0.032	0.003	0.034