BioC 2.13: CHECK report for limma on perceval

Package: limma

Version: 3.18.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.18.13.tar.gz

StartedAt: 2014-04-05 02:18:33 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:20:49 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 135.2 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/limma.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘3.18.13’
* 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 ‘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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 6.579  0.207   6.823
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [3s/3s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...631,636c631,636
<  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  
647,651c647,651
< [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
662,666c662,666
< [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
994,995c994,995
< 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 vignette outputs ... 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 -Wall  -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-2.13-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	0.003	0.000	0.003
PrintLayout	0.005	0.001	0.005
TestResults	0.005	0.000	0.006
alias2Symbol	6.579	0.207	6.823
arrayWeights	0.085	0.002	0.087
arrayWeightsQuick	0.052	0.000	0.052
asMatrixWeights	0.031	0.001	0.031
auROC	0.038	0.003	0.041
avearrays	0.038	0.002	0.040
avereps	0.038	0.002	0.041
backgroundcorrect	0.049	0.003	0.052
barcodeplot	0.035	0.003	0.038
beadCountWeights	0.037	0.001	0.039
blockDiag	0.036	0.002	0.038
camera	0.092	0.006	0.098
cbind	0.103	0.002	0.106
channel2M	0.054	0.001	0.055
classifytests	0.032	0.001	0.033
contrastAsCoef	0.057	0.003	0.060
contrasts.fit	0.104	0.003	0.106
controlStatus	0.061	0.001	0.062
dim	0.060	0.002	0.062
dupcor	0.030	0.001	0.031
ebayes	0.110	0.002	0.113
fitGammaIntercept	0.041	0.000	0.041
fitfdist	0.039	0.001	0.039
genas	0.364	0.023	0.386
geneSetTest	0.068	0.001	0.069
getSpacing	0.046	0.002	0.049
getlayout	0.014	0.001	0.015
heatdiagram	0.039	0.003	0.042
helpMethods	0.018	0.001	0.019
imageplot	0.077	0.005	0.083
intraspotCorrelation	0.034	0.002	0.036
isfullrank	0.053	0.002	0.054
isnumeric	0.034	0.001	0.036
kooperberg	0.023	0.002	0.026
limmaUsersGuide	0.025	0.002	0.027
lm.series	0.021	0.001	0.022
lmFit	0.986	0.038	1.029
lmscFit	0.046	0.002	0.048
loessfit	0.257	0.017	0.275
ma3x3	0.339	0.004	0.343
makeContrasts	0.052	0.005	0.057
makeunique	0.026	0.004	0.030
merge	0.084	0.008	0.094
mergeScansRG	0.027	0.003	0.030
modelMatrix	0.043	0.005	0.047
modifyWeights	0.028	0.003	0.031
nec	0.065	0.007	0.072
normalizeMedianAbsValues	0.046	0.003	0.049
normalizeRobustSpline	0.170	0.014	0.183
normalizeVSN	0.609	0.041	0.653
normalizebetweenarrays	0.043	0.002	0.046
normalizeprintorder	0.048	0.001	0.050
normexpfit	0.060	0.003	0.063
normexpfitcontrol	0.043	0.004	0.047
normexpfitdetectionp	0.033	0.003	0.037
normexpsignal	0.018	0.002	0.019
plotDensities	0.047	0.003	0.049
plotMDS	0.087	0.005	0.093
plotRLDF	0.532	0.017	0.550
plotma	0.110	0.015	0.125
poolvar	0.046	0.005	0.052
predFCm	0.116	0.008	0.123
printorder	0.029	0.010	0.040
printtipWeights	0.068	0.004	0.072
propTrueNull	0.074	0.005	0.079
propexpr	0.020	0.003	0.023
protectMetachar	0.019	0.003	0.022
qqt	0.041	0.005	0.046
qualwt	0.045	0.003	0.049
rankSumTestwithCorrelation	0.097	0.004	0.100
read.ilmn	0.027	0.002	0.030
read.maimages	0.040	0.005	0.046
readImaGeneHeader	0.018	0.004	0.021
readgal	0.020	0.002	0.023
removeext	0.017	0.003	0.021
roast	0.139	0.009	0.147
romer	0.522	0.059	0.582
selectmodel	0.070	0.008	0.077
squeezeVar	0.047	0.004	0.052
strsplit2	0.033	0.004	0.037
subsetting	0.045	0.004	0.050
targetsA2C	0.049	0.003	0.052
topRomer	0.023	0.001	0.024
toptable	0.027	0.003	0.029
trigammainverse	0.021	0.003	0.024
trimWhiteSpace	0.022	0.003	0.026
uniquegenelist	0.025	0.003	0.029
unwrapdups	0.018	0.003	0.020
venn	0.105	0.008	0.113
volcanoplot	0.024	0.002	0.027
weightedmedian	0.043	0.003	0.047
zscore	0.040	0.005	0.045