Package: limma

Version: 3.12.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.12.0.tar.gz

StartedAt: 2012-04-01 01:52:42 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:54:01 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 79.4 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/limma.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.12.0'
* 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 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
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c normexp.c -o normexp.o
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153:3: warning: floating constant exceeds range of 'double' [-Woverflow]
gcc -std=gnu99 -shared -L/usr/local/lib -o limma.so normexp.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/limma.Rcheck/limma/libs
** 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	0.004	0.000	0.001
TestResults	0	0	0
alias2Symbol	4.308	0.084	4.513
arrayWeights	0	0	0
arrayWeightsQuick	0	0	0
asMatrixWeights	0	0	0
auROC	0.000	0.000	0.001
avearrays	0.000	0.000	0.001
avereps	0	0	0
backgroundcorrect	0.008	0.000	0.007
barcodeplot	0.004	0.000	0.004
blockDiag	0	0	0
camera	0.144	0.000	0.143
cbind	0.008	0.000	0.005
channel2M	0.000	0.000	0.001
classifytests	0.004	0.000	0.001
contrasts.fit	0.020	0.000	0.019
controlStatus	0.004	0.000	0.007
convest	1.160	0.008	1.171
dim	0.004	0.000	0.001
dupcor	0	0	0
ebayes	0.012	0.000	0.012
genas	0.064	0.000	0.070
geneSetTest	0.000	0.000	0.001
getSpacing	0.000	0.000	0.001
getlayout	0.000	0.000	0.001
heatdiagram	0	0	0
helpMethods	0	0	0
imageplot	0.032	0.000	0.033
intraspotCorrelation	0	0	0
isfullrank	0.000	0.000	0.001
isnumeric	0.000	0.000	0.001
kooperberg	0	0	0
limmaUsersGuide	0.004	0.000	0.007
lm.series	0	0	0
lmFit	0.700	0.012	0.721
lmscFit	0	0	0
loessfit	0.604	0.000	0.600
ma3x3	0.000	0.000	0.001
makeContrasts	0	0	0
makeunique	0.000	0.004	0.001
merge	0.004	0.000	0.006
mergeScansRG	0	0	0
modelMatrix	0.004	0.000	0.002
modifyWeights	0.000	0.000	0.001
nec	0	0	0
normalizeMedianAbsValues	0.004	0.000	0.000
normalizeRobustSpline	0	0	0
normalizeVSN	0.368	0.044	0.498
normalizebetweenarrays	0.012	0.000	0.012
normalizeprintorder	0	0	0
normexpfit	0.000	0.004	0.001
normexpfitcontrol	0	0	0
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0	0	0
plotMDS	0.008	0.000	0.011
plotRLDF	0.516	0.004	0.521
plotma	0.012	0.000	0.013
poolvar	0	0	0
printorder	0.008	0.004	0.012
printtipWeights	0	0	0
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0.000	0.004	0.002
qualwt	0	0	0
rankSumTestwithCorrelation	0.004	0.000	0.006
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0	0	0
roast	0.044	0.000	0.041
romer	0.284	0.000	0.283
selectmodel	0.016	0.000	0.016
squeezeVar	0	0	0
strsplit2	0	0	0
subsetting	0.004	0.000	0.003
targetsA2C	0.008	0.000	0.005
topRomer	0.000	0.000	0.001
toptable	0	0	0
trigammainverse	0	0	0
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.000	0.000	0.001
unwrapdups	0.000	0.000	0.001
venn	0.024	0.000	0.024
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0	0	0