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 19:56:47 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:58:56 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 128.3 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: UTF-8
* 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	0.001	0.000	0.001
TestResults	0	0	0
alias2Symbol	3.265	0.141	3.467
arrayWeights	0.009	0.001	0.010
arrayWeightsQuick	0.001	0.000	0.000
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.001
avearrays	0.002	0.000	0.002
avereps	0.001	0.000	0.002
backgroundcorrect	0.013	0.001	0.014
blockDiag	0.001	0.000	0.002
cbind	0.011	0.001	0.013
channel2M	0.002	0.001	0.003
classifytests	0.004	0.001	0.005
contrasts.fit	0.036	0.002	0.038
controlStatus	0.012	0.001	0.013
convest	2.711	0.012	2.728
dim	0.002	0.001	0.003
dupcor	0.001	0.000	0.001
ebayes	0.016	0.001	0.018
genas	0.126	0.002	0.130
geneSetTest	0.008	0.000	0.009
getSpacing	0.001	0.001	0.002
getlayout	0.000	0.000	0.001
heatdiagram	0.006	0.001	0.008
helpMethods	0.000	0.001	0.001
imageplot	0.047	0.004	0.051
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.002
isnumeric	0.002	0.000	0.002
kooperberg	0.001	0.000	0.001
limmaUsersGuide	0.003	0.001	0.005
lm.series	0	0	0
lmFit	2.207	0.020	2.229
lmscFit	0.012	0.001	0.014
loessfit	0.445	0.003	0.448
ma3x3	0.002	0.000	0.002
makeContrasts	0.002	0.001	0.002
makeunique	0.002	0.000	0.002
merge	0.011	0.001	0.012
mergeScansRG	0.001	0.000	0.000
modelMatrix	0.003	0.000	0.004
modifyWeights	0.001	0.001	0.001
nec	0.001	0.000	0.000
neqc	0	0	0
normalizeMedianAbsValues	0.001	0.000	0.002
normalizeRobustSpline	0.004	0.001	0.005
normalizeVSN	0.655	0.031	0.705
normalizebetweenarrays	0.004	0.000	0.004
normalizeprintorder	0	0	0
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0.001	0.000	0.000
normexpfitdetectionp	0	0	0
normexpsignal	0.001	0.000	0.001
plotDensities	0.000	0.001	0.001
plotMDS	0.030	0.003	0.033
plotRLDF	0.539	0.024	0.563
plotma	0.019	0.000	0.020
poolvar	0.002	0.000	0.002
printorder	0.023	0.009	0.032
printtipWeights	0.001	0.000	0.000
propexpr	0.000	0.001	0.000
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.000	0.002
qualwt	0	0	0
read.ilmn	0	0	0
read.maimages	0.000	0.000	0.001
readImaGeneHeader	0.001	0.000	0.000
readgal	0.000	0.001	0.001
removeext	0.000	0.000	0.001
roast	0.070	0.007	0.077
romer	0.625	0.005	0.630
selectmodel	0.039	0.000	0.039
squeezeVar	0.001	0.001	0.002
strsplit2	0.001	0.000	0.002
subsetting	0.006	0.001	0.007
targetsA2C	0.010	0.000	0.009
topRomer	0	0	0
toptable	0.001	0.000	0.000
trigammainverse	0.000	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.000	0.001
venn	0.044	0.001	0.045
volcanoplot	0.000	0.001	0.000
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.000	0.001