Package: limma

Version: 3.9.11

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.9.11.tar.gz

StartedAt: 2011-07-07 01:10:49 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:12:31 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 101.8 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.9.11’
* 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 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 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 for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ call not declared from: ‘sma’
* 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
‘library’ or ‘require’ call not declared from: ‘marray’
* checking tests ...
  Running ‘limma-Tests.R’
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...920,921c920,921
< 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/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘limma.Rnw’ 
** testing if installed package can be loaded

* DONE (limma)

name	user	system	elapsed
LargeDataObject	0	0	0
PrintLayout	0	0	0
TestResults	0	0	0
alias2Symbol	2.672	0.068	2.775
arrayWeights	0.008	0.000	0.005
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.000	0.000	0.001
auROC	0.000	0.000	0.001
avearrays	0.000	0.000	0.001
avereps	0	0	0
backgroundcorrect	0.012	0.000	0.009
blockDiag	0.000	0.000	0.001
cbind	0.008	0.000	0.007
channel2M	0.000	0.000	0.001
classifytests	0.000	0.000	0.002
contrasts.fit	0.040	0.004	0.042
controlStatus	0.008	0.000	0.007
convest	2.984	0.004	3.021
dim	0.000	0.000	0.002
dupcor	0	0	0
ebayes	0.008	0.000	0.011
genas	0.088	0.000	0.088
geneSetTest	0.004	0.000	0.006
getSpacing	0.000	0.000	0.001
getlayout	0	0	0
heatdiagram	0.004	0.000	0.004
helpMethods	0	0	0
imageplot	0.032	0.000	0.033
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.000	0.004	0.001
isnumeric	0.000	0.000	0.002
kooperberg	0	0	0
limmaUsersGuide	0.004	0.000	0.003
lm.series	0	0	0
lmFit	1.120	0.004	1.133
lmscFit	0.004	0.000	0.005
loessfit	0.628	0.000	0.651
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	0.007
mergeScansRG	0	0	0
modelMatrix	0.000	0.000	0.002
modifyWeights	0	0	0
nec	0	0	0
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.004	0.000	0.003
normalizeVSN	0.428	0.016	0.447
normalizebetweenarrays	0.000	0.000	0.002
normalizeprintorder	0	0	0
normexpfit	0.000	0.000	0.002
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0	0	0
plotMDS	0.016	0.000	0.014
plotRLDF	0.792	0.012	0.804
plotma	0.016	0.000	0.014
poolvar	0	0	0
printorder	0.008	0.008	0.016
printtipWeights	0	0	0
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0.004	0.000	0.002
qualwt	0	0	0
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0.004	0.000	0.000
removeext	0	0	0
roast	0.064	0.000	0.065
romer	0.600	0.004	0.603
selectmodel	0.028	0.000	0.028
squeezeVar	0	0	0
strsplit2	0.000	0.000	0.001
subsetting	0.004	0.000	0.005
targetsA2C	0.004	0.000	0.006
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0	0	0
unwrapdups	0	0	0
venn	0.040	0.000	0.042
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0	0	0