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: 2013-03-25 03:19:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:21:36 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 145.1 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 7.618  0.304   7.954
* 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c normexp.c -o normexp.o
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153: warning: floating constant exceeds range of 'double'
normexp.c:167: warning: ISO C forbids passing argument 9 of 'nmmin' between function pointer and 'void *'
gcc -arch i386 -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/i386
** 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	0.006	0.004	0.010
PrintLayout	0.010	0.008	0.019
TestResults	0.007	0.006	0.014
alias2Symbol	7.618	0.304	7.954
arrayWeights	0.061	0.012	0.073
arrayWeightsQuick	0.029	0.006	0.036
asMatrixWeights	0.048	0.007	0.055
auROC	0.183	0.011	0.196
avearrays	0.034	0.009	0.042
avereps	0.032	0.011	0.043
backgroundcorrect	0.045	0.011	0.056
barcodeplot	0.048	0.015	0.068
blockDiag	0.033	0.010	0.043
camera	0.098	0.023	0.128
cbind	0.083	0.015	0.100
channel2M	0.030	0.006	0.036
classifytests	0.026	0.008	0.035
contrasts.fit	0.088	0.016	0.105
controlStatus	0.042	0.008	0.050
dim	0.060	0.014	0.075
dupcor	0.031	0.007	0.039
ebayes	0.077	0.022	0.100
fitGammaIntercept	0.028	0.009	0.037
fitfdist	0.022	0.006	0.029
genas	0.195	0.050	0.253
geneSetTest	0.048	0.010	0.058
getSpacing	0.040	0.007	0.048
getlayout	0.020	0.006	0.026
heatdiagram	0.020	0.009	0.033
helpMethods	0.019	0.005	0.024
imageplot	0.063	0.011	0.075
intraspotCorrelation	0.043	0.008	0.049
isfullrank	0.162	0.012	0.176
isnumeric	0.041	0.011	0.053
kooperberg	0.029	0.009	0.040
limmaUsersGuide	0.019	0.010	0.030
lm.series	0.011	0.004	0.016
lmFit	1.074	0.078	1.162
lmscFit	0.057	0.016	0.075
loessfit	0.112	0.016	0.130
ma3x3	0.020	0.007	0.028
makeContrasts	0.028	0.009	0.037
makeunique	0.017	0.006	0.023
merge	0.047	0.014	0.064
mergeScansRG	0.030	0.009	0.039
modelMatrix	0.039	0.011	0.054
modifyWeights	0.028	0.008	0.041
nec	0.032	0.008	0.041
normalizeMedianAbsValues	0.019	0.005	0.026
normalizeRobustSpline	0.097	0.021	0.123
normalizeVSN	0.768	0.112	0.896
normalizebetweenarrays	0.044	0.008	0.053
normalizeprintorder	0.028	0.006	0.034
normexpfit	0.034	0.007	0.041
normexpfitcontrol	0.035	0.007	0.043
normexpfitdetectionp	0.037	0.008	0.047
normexpsignal	0.019	0.004	0.023
plotDensities	0.204	0.017	0.221
plotMDS	0.046	0.011	0.060
plotRLDF	0.529	0.033	0.563
plotma	0.080	0.029	0.114
poolvar	0.035	0.014	0.050
predFCm	0.081	0.025	0.109
printorder	0.027	0.016	0.042
printtipWeights	0.047	0.016	0.065
propTrueNull	0.050	0.016	0.067
propexpr	0.018	0.007	0.025
protectMetachar	0.015	0.006	0.022
qqt	0.015	0.008	0.024
qualwt	0.012	0.007	0.019
rankSumTestwithCorrelation	0.052	0.017	0.072
read.ilmn	0.021	0.007	0.027
read.maimages	0.031	0.012	0.043
readImaGeneHeader	0.017	0.007	0.024
readgal	0.016	0.007	0.023
removeext	0.030	0.008	0.040
roast	0.123	0.023	0.145
romer	0.542	0.022	0.564
selectmodel	0.053	0.014	0.068
squeezeVar	0.012	0.006	0.018
strsplit2	0.022	0.009	0.034
subsetting	0.027	0.010	0.038
targetsA2C	0.029	0.007	0.038
topRomer	0.002	0.004	0.007
toptable	0.011	0.005	0.015
trigammainverse	0.011	0.006	0.018
trimWhiteSpace	0.021	0.007	0.028
uniquegenelist	0.022	0.008	0.033
unwrapdups	0.021	0.009	0.030
venn	0.060	0.015	0.077
volcanoplot	0.011	0.005	0.017
weightedmedian	0.026	0.008	0.035
zscore	0.022	0.010	0.032