Package: limma

Version: 3.7.24

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.7.24.tar.gz

StartedAt: 2011-02-24 16:03:58 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:05:32 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 93.4 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/limma.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 '3.7.24'
* 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 ... 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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 -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-2.8-bioc/meat/limma.Rcheck/limma/libs/i386
** 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	0.000	0.000	0.001
PrintLayout	0.000	0.001	0.000
TestResults	0.000	0.000	0.001
alias2Symbol	2.310	0.067	2.389
arrayWeights	0.003	0.001	0.003
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.000	0.001	0.000
auROC	0.001	0.000	0.001
avearrays	0.001	0.000	0.002
avereps	0.000	0.000	0.001
backgroundcorrect	0.010	0.001	0.010
blockDiag	0.001	0.000	0.001
cbind	0.008	0.001	0.009
channel2M	0.001	0.000	0.002
classifytests	0.003	0.001	0.004
contrasts.fit	0.027	0.002	0.028
controlStatus	0.008	0.000	0.009
convest	2.038	0.008	2.047
dim	0.002	0.000	0.002
dupcor	0	0	0
ebayes	0.010	0.000	0.011
genas	0.090	0.002	0.091
geneSetTest	0.006	0.001	0.006
getSpacing	0.000	0.000	0.001
getlayout	0	0	0
heatdiagram	0.002	0.000	0.003
helpMethods	0	0	0
imageplot	0.036	0.001	0.038
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.002	0.001	0.003
lm.series	0.000	0.001	0.000
lmFit	1.630	0.014	1.645
lmscFit	0.002	0.001	0.003
loessfit	0.324	0.001	0.325
ma3x3	0.001	0.000	0.002
makeContrasts	0.001	0.001	0.001
makeunique	0.000	0.000	0.001
merge	0.008	0.001	0.009
mergeScansRG	0	0	0
modelMatrix	0.002	0.001	0.002
modifyWeights	0.000	0.000	0.001
nec	0.000	0.001	0.000
neqc	0.000	0.000	0.001
normalizeMedianAbsValues	0	0	0
normalizeRobustSpline	0.002	0.000	0.003
normalizeVSN	0.459	0.018	0.476
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0	0	0
normexpfit	0.002	0.000	0.002
normexpfitcontrol	0.001	0.000	0.001
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0.000	0.001	0.001
plotMDS	0.021	0.001	0.023
plotRLDF	0.395	0.007	0.402
plotma	0.014	0.001	0.015
poolvar	0.001	0.000	0.001
printorder	0.015	0.006	0.020
printtipWeights	0.000	0.001	0.001
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0.002	0.000	0.002
qualwt	0	0	0
read.ilmn	0	0	0
read.maimages	0.001	0.000	0.000
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0	0	0
roast	0.046	0.001	0.047
romer	0.452	0.003	0.455
selectmodel	0.027	0.000	0.028
squeezeVar	0.000	0.001	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.005	0.001	0.005
targetsA2C	0.007	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	0.001	0.000	0.000
venn	0.032	0.001	0.034
volcanoplot	0	0	0
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.000	0.001