Package: limma

Version: 3.6.9

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.6.9.tar.gz

StartedAt: 2011-04-07 07:18:42 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 07:20:16 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 93.6 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/limma.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘3.6.9’
* 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 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 package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-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	0	0
alias2Symbol	2.612	0.068	2.786
arrayWeights	0.004	0.000	0.004
arrayWeightsQuick	0	0	0
asMatrixWeights	0.000	0.000	0.001
auROC	0.004	0.000	0.001
avearrays	0.000	0.000	0.001
avereps	0.004	0.000	0.001
backgroundcorrect	0.004	0.004	0.010
blockDiag	0.000	0.000	0.001
cbind	0.004	0.000	0.007
channel2M	0.000	0.000	0.001
classifytests	0.004	0.000	0.002
contrasts.fit	0.024	0.004	0.027
controlStatus	0.004	0.004	0.008
convest	2.620	0.000	2.619
dim	0.000	0.004	0.002
dupcor	0.000	0.000	0.001
ebayes	0.008	0.000	0.010
genas	0.084	0.000	0.085
geneSetTest	0.004	0.000	0.006
getSpacing	0	0	0
getlayout	0	0	0
heatdiagram	0.000	0.004	0.003
helpMethods	0	0	0
imageplot	0.032	0.000	0.031
intraspotCorrelation	0	0	0
isfullrank	0.000	0.000	0.001
isnumeric	0	0	0
kooperberg	0	0	0
limmaUsersGuide	0.000	0.000	0.003
lm.series	0	0	0
lmFit	1.528	0.016	1.555
lmscFit	0.004	0.000	0.005
loessfit	0.532	0.000	0.530
ma3x3	0.000	0.000	0.002
makeContrasts	0.000	0.000	0.001
makeunique	0.000	0.000	0.001
merge	0.008	0.000	0.008
mergeScansRG	0.000	0.004	0.001
modelMatrix	0.000	0.000	0.002
modifyWeights	0	0	0
nec	0	0	0
neqc	0	0	0
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0.000	0.004	0.003
normalizeVSN	0.400	0.040	0.438
normalizeWithinArrays	0	0	0
normalizebetweenarrays	0.004	0.000	0.003
normalizeprintorder	0.000	0.004	0.003
normexpfit	0.000	0.000	0.002
normexpfitcontrol	0	0	0
normexpsignal	0	0	0
plotDensities	0.008	0.000	0.006
plotMDS	0.012	0.000	0.015
plotRLDF	0.696	0.000	0.698
plotma	0.012	0.000	0.012
poolvar	0.000	0.000	0.001
printorder	0.012	0.004	0.017
printtipWeights	0.004	0.000	0.004
propexpr	0	0	0
protectMetachar	0.000	0.000	0.001
qqt	0.004	0.000	0.002
qualwt	0.000	0.000	0.001
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0.000	0.004	0.000
removeext	0.000	0.000	0.001
roast	0.080	0.000	0.082
romer	0.444	0.000	0.444
selectmodel	0.024	0.000	0.024
squeezeVar	0.000	0.000	0.001
strsplit2	0	0	0
subsetting	0.004	0.000	0.005
targetsA2C	0.008	0.000	0.007
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0	0	0
trimWhiteSpace	0	0	0
uniquegenelist	0	0	0
unwrapdups	0.000	0.000	0.001
venn	0.040	0.008	0.048
volcanoplot	0.004	0.000	0.000
weightedmedian	0.000	0.000	0.001
zscore	0.000	0.000	0.001