Package: limma

Version: 3.13.7

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.13.7.tar.gz

StartedAt: 2012-06-21 01:14:53 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:17:10 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 137.2 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/limma.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '3.13.7'
* 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' ...898,899c898,899
< 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-2.11-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	0	0
PrintLayout	0.000	0.000	0.001
TestResults	0	0	0
alias2Symbol	7.027	0.241	7.571
arrayWeights	0	0	0
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.002
avearrays	0.002	0.001	0.002
avereps	0.001	0.000	0.001
backgroundcorrect	0.012	0.002	0.013
barcodeplot	0.007	0.002	0.009
blockDiag	0.013	0.002	0.015
camera	0.022	0.003	0.025
cbind	0.009	0.001	0.009
channel2M	0.002	0.001	0.003
classifytests	0.003	0.000	0.003
contrasts.fit	0.033	0.002	0.036
controlStatus	0.025	0.001	0.026
convest	2.829	0.015	2.858
dim	0.002	0.000	0.002
dupcor	0.001	0.000	0.001
ebayes	0.013	0.001	0.016
genas	0.105	0.001	0.107
geneSetTest	0.001	0.000	0.002
getSpacing	0	0	0
getlayout	0.000	0.000	0.001
heatdiagram	0.000	0.000	0.001
helpMethods	0	0	0
imageplot	0.050	0.006	0.057
intraspotCorrelation	0.000	0.001	0.000
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.001	0.001
kooperberg	0	0	0
limmaUsersGuide	0.002	0.001	0.004
lm.series	0	0	0
lmFit	1.098	0.019	1.152
lmscFit	0.001	0.000	0.001
loessfit	0.791	0.005	0.826
ma3x3	0.002	0.001	0.002
makeContrasts	0.001	0.000	0.002
makeunique	0.001	0.001	0.001
merge	0.009	0.001	0.009
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.002	0.001	0.004
modifyWeights	0.001	0.000	0.001
nec	0.000	0.001	0.000
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.001	0.000	0.001
normalizeVSN	0.648	0.058	0.715
normalizebetweenarrays	0.004	0.000	0.004
normalizeprintorder	0.000	0.000	0.001
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.001	0.000	0.000
normexpsignal	0	0	0
plotDensities	0.000	0.000	0.001
plotMDS	0.019	0.003	0.021
plotRLDF	0.534	0.027	0.576
plotma	0.023	0.005	0.028
poolvar	0.001	0.000	0.001
printorder	0.019	0.008	0.028
printtipWeights	0	0	0
propexpr	0.000	0.000	0.001
protectMetachar	0.000	0.001	0.000
qqt	0.003	0.001	0.004
qualwt	0.001	0.000	0.000
rankSumTestwithCorrelation	0.011	0.000	0.015
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0.001	0.000	0.002
roast	0.070	0.006	0.077
romer	0.650	0.006	0.664
selectmodel	0.027	0.000	0.027
squeezeVar	0.001	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.005	0.000	0.006
targetsA2C	0.009	0.000	0.009
topRomer	0	0	0
toptable	0.000	0.000	0.001
trigammainverse	0	0	0
trimWhiteSpace	0.000	0.001	0.001
uniquegenelist	0.001	0.000	0.003
unwrapdups	0.000	0.001	0.001
venn	0.037	0.003	0.041
volcanoplot	0	0	0
weightedmedian	0.001	0.000	0.001
zscore	0.002	0.000	0.001