Package: limma

Version: 3.4.5

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.4.5.tar.gz

StartedAt: 2010-10-04 18:20:14 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:21:30 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 75.3 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/limma.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.4.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'limma' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...896,897c896,897
< 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 -1.821460e-17
> mu+beta    -0.3333333 -1.821460e-17  3.333333e-01
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'limma' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c normexp.c -o normexp.o
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153: warning: floating constant exceeds range of 'double'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (limma)

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0	0	0
TestResults	0.000	0.000	0.001
alias2Symbol	2.852	0.100	3.097
arrayWeights	0.004	0.000	0.003
arrayWeightsQuick	0	0	0
asMatrixWeights	0.000	0.000	0.001
auROC	0.000	0.004	0.000
avereps	0.000	0.000	0.002
backgroundcorrect	0.016	0.000	0.019
blockDiag	0.000	0.000	0.001
cbind	0.008	0.000	0.009
channel2M	0.000	0.000	0.002
classifytests	0.004	0.000	0.003
contrasts.fit	0.048	0.000	0.048
controlStatus	0.008	0.000	0.009
convest	2.356	0.000	2.357
dim	0.000	0.000	0.002
dupcor	0	0	0
ebayes	0.012	0.000	0.013
genas	0.076	0.008	0.082
geneSetTest	0.008	0.000	0.006
getSpacing	0.000	0.000	0.001
getlayout	0	0	0
heatdiagram	0.000	0.000	0.002
helpMethods	0	0	0
imageplot	0.032	0.000	0.034
intraspotCorrelation	0	0	0
isfullrank	0.000	0.000	0.001
isnumeric	0.000	0.000	0.001
kooperberg	0	0	0
limmaUsersGuide	0.000	0.000	0.002
lm.series	0	0	0
lmFit	1.824	0.012	1.836
lmscFit	0.004	0.000	0.004
loessfit	0.596	0.004	0.646
ma3x3	0.000	0.000	0.001
makeContrasts	0.000	0.000	0.001
makeunique	0.000	0.000	0.001
merge	0.008	0.000	0.009
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.000	0.000	0.002
modifyWeights	0.000	0.000	0.001
neqc	0	0	0
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.000	0.000	0.002
normalizeWithinArrays	0	0	0
normalizebetweenarrays	0.000	0.000	0.003
normalizeprintorder	0.000	0.000	0.002
normexpfit	0.004	0.000	0.002
normexpfitcontrol	0	0	0
normexpsignal	0	0	0
plotDensities	0.004	0.004	0.005
plotMDS	0.012	0.000	0.015
plotRLDF	0.668	0.008	0.676
plotma	0.012	0.000	0.014
poolvar	0.000	0.000	0.001
printorder	0.012	0.004	0.017
printtipWeights	0.000	0.000	0.003
propexpr	0.000	0.000	0.001
protectMetachar	0.000	0.000	0.001
qqt	0.004	0.000	0.001
qualwt	0	0	0
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0.000	0.000	0.001
roast	0.092	0.000	0.092
romer	0.492	0.000	0.493
selectmodel	0.028	0.000	0.030
squeezeVar	0.000	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.004	0.000	0.003
targetsA2C	0.008	0.000	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	0	0
venn	0.040	0.004	0.045
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0.000	0.004	0.000