Package: limma

Version: 3.9.11

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.9.11.tar.gz

StartedAt: 2011-07-07 04:02:38 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:05:14 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 156.3 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '3.9.11'
* 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 sizes of PDF files under 'inst/doc' ... 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -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-4.2 -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-2.9-bioc/meat/limma.Rcheck/limma/libs/i386
** 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	0.001	0.000	0.000
PrintLayout	0.000	0.000	0.001
TestResults	0.000	0.001	0.001
alias2Symbol	3.917	0.162	4.212
arrayWeights	0.004	0.001	0.005
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.001	0.001
auROC	0.001	0.000	0.001
avearrays	0.002	0.001	0.002
avereps	0.001	0.000	0.001
backgroundcorrect	0.014	0.002	0.015
blockDiag	0.001	0.000	0.001
cbind	0.011	0.002	0.012
channel2M	0.002	0.001	0.002
classifytests	0.004	0.000	0.004
contrasts.fit	0.041	0.003	0.051
controlStatus	0.013	0.001	0.014
convest	2.565	0.023	2.800
dim	0.002	0.000	0.003
dupcor	0.000	0.000	0.001
ebayes	0.015	0.001	0.015
genas	0.125	0.001	0.186
geneSetTest	0.008	0.000	0.009
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
heatdiagram	0.003	0.001	0.004
helpMethods	0.001	0.000	0.000
imageplot	0.052	0.005	0.095
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.002
isnumeric	0.002	0.000	0.002
kooperberg	0	0	0
limmaUsersGuide	0.002	0.001	0.005
lm.series	0	0	0
lmFit	1.521	0.019	1.617
lmscFit	0.004	0.001	0.006
loessfit	0.463	0.004	0.484
ma3x3	0.002	0.000	0.003
makeContrasts	0.001	0.001	0.002
makeunique	0.001	0.000	0.001
merge	0.011	0.001	0.013
mergeScansRG	0.000	0.001	0.000
modelMatrix	0.003	0.000	0.003
modifyWeights	0.000	0.001	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.001	0.001	0.001
normalizeRobustSpline	0.003	0.001	0.004
normalizeVSN	0.672	0.036	0.748
normalizebetweenarrays	0.004	0.000	0.004
normalizeprintorder	0	0	0
normexpfit	0.003	0.000	0.004
normexpfitcontrol	0	0	0
normexpfitdetectionp	0.000	0.001	0.000
normexpsignal	0	0	0
plotDensities	0.000	0.001	0.001
plotMDS	0.019	0.001	0.021
plotRLDF	0.574	0.027	0.604
plotma	0.021	0.001	0.022
poolvar	0.001	0.001	0.001
printorder	0.019	0.009	0.028
printtipWeights	0	0	0
propexpr	0.000	0.001	0.000
protectMetachar	0.001	0.000	0.001
qqt	0.002	0.000	0.003
qualwt	0.000	0.000	0.001
read.ilmn	0.000	0.000	0.001
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0.001	0.000	0.001
readgal	0.000	0.000	0.001
removeext	0.001	0.000	0.000
roast	0.075	0.007	0.083
romer	0.620	0.008	0.654
selectmodel	0.038	0.001	0.040
squeezeVar	0.001	0.000	0.001
strsplit2	0.000	0.000	0.001
subsetting	0.007	0.000	0.007
targetsA2C	0.010	0.000	0.011
topRomer	0.000	0.000	0.001
toptable	0	0	0
trigammainverse	0.001	0.000	0.003
trimWhiteSpace	0	0	0
uniquegenelist	0.001	0.000	0.000
unwrapdups	0.000	0.001	0.001
venn	0.061	0.004	0.078
volcanoplot	0	0	0
weightedmedian	0.000	0.000	0.001
zscore	0.001	0.000	0.001