Package: limma

Version: 3.12.3

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.12.3.tar.gz

StartedAt: 2012-09-24 00:44:01 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:46:02 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 120.9 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/limma.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '3.12.3'
* 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 whether package 'limma' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'limma-Tests.R'
  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.   :-5.82498   Min.   :-5.69877  
>  1st Qu.:-1.19140   1st Qu.:-1.55421  
>  Median :-0.19318   Median : 0.06267  
>  Mean   : 0.08691   Mean   :-0.05369  
>  3rd Qu.: 1.48646   3rd Qu.: 1.41900  
>  Max.   : 7.16195   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,] -1.0618269  4.5343276
> [2,]  0.8507603  0.3495635
> [3,]  2.7703696  1.4459533
> [4,] -1.8511286  0.4894799
> [5,]  1.9180276 -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,] -1.0618269  4.5343276
> [2,]  0.8507603  0.3495635
> [3,]  2.7703696  1.4459533
> [4,] -1.8511286  0.4894799
> [5,]  1.9180276 -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
 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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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-2.10-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	0.000	0.000	0.001
PrintLayout	0.000	0.000	0.001
TestResults	0.000	0.000	0.001
alias2Symbol	5.665	0.193	5.874
arrayWeights	0.000	0.000	0.001
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.001	0.001
auROC	0.009	0.001	0.011
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.009	0.001	0.009
barcodeplot	0.005	0.001	0.006
blockDiag	0.001	0.000	0.001
camera	0.026	0.003	0.029
cbind	0.007	0.001	0.007
channel2M	0.002	0.000	0.002
classifytests	0.002	0.000	0.002
contrasts.fit	0.024	0.001	0.026
controlStatus	0.009	0.001	0.009
dim	0.001	0.001	0.002
dupcor	0	0	0
ebayes	0.019	0.002	0.022
genas	0.084	0.001	0.086
geneSetTest	0.001	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
heatdiagram	0	0	0
helpMethods	0	0	0
imageplot	0.035	0.004	0.039
intraspotCorrelation	0.000	0.001	0.001
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0.000	0.001	0.000
limmaUsersGuide	0.002	0.002	0.004
lm.series	0	0	0
lmFit	0.948	0.020	0.968
lmscFit	0	0	0
loessfit	0.041	0.003	0.044
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.001	0.001
makeunique	0.000	0.000	0.001
merge	0.007	0.001	0.007
mergeScansRG	0.001	0.000	0.000
modelMatrix	0.002	0.001	0.003
modifyWeights	0	0	0
nec	0.000	0.001	0.000
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0	0	0
normalizeVSN	0.470	0.053	0.526
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0	0	0
normexpfit	0.002	0.001	0.002
normexpfitcontrol	0	0	0
normexpfitdetectionp	0	0	0
normexpsignal	0.000	0.000	0.001
plotDensities	0.001	0.000	0.000
plotMDS	0.015	0.002	0.016
plotRLDF	0.635	0.019	0.654
plotma	0.016	0.003	0.018
poolvar	0.001	0.000	0.001
printorder	0.013	0.007	0.020
printtipWeights	0	0	0
propTrueNull	0.533	0.015	0.549
propexpr	0.000	0.000	0.001
protectMetachar	0	0	0
qqt	0.002	0.001	0.003
qualwt	0.000	0.001	0.001
rankSumTestwithCorrelation	0.007	0.000	0.008
read.ilmn	0	0	0
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0.001	0.000	0.001
readgal	0	0	0
removeext	0.000	0.000	0.001
roast	0.040	0.004	0.045
romer	0.323	0.003	0.327
selectmodel	0.019	0.001	0.018
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.000
subsetting	0.004	0.000	0.005
targetsA2C	0.006	0.001	0.007
topRomer	0	0	0
toptable	0.000	0.000	0.001
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0	0	0
unwrapdups	0.000	0.000	0.001
venn	0.028	0.002	0.031
volcanoplot	0	0	0
weightedmedian	0.001	0.000	0.000
zscore	0.002	0.000	0.001