Package: limma

Version: 3.6.9

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.6.9.tar.gz

StartedAt: 2011-03-31 06:28:06 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:30:36 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 150.5 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/limma.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘3.6.9’
* 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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-2.7-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	0	0
PrintLayout	0.001	0.000	0.001
TestResults	0	0	0
alias2Symbol	3.678	0.173	3.954
arrayWeights	0.010	0.001	0.011
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.002
avearrays	0.002	0.000	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.014	0.001	0.015
blockDiag	0.001	0.000	0.001
cbind	0.012	0.002	0.014
channel2M	0.002	0.000	0.003
classifytests	0.016	0.001	0.016
contrasts.fit	0.038	0.003	0.041
controlStatus	0.012	0.000	0.014
convest	2.593	0.017	2.653
dim	0.003	0.000	0.003
dupcor	0.001	0.000	0.001
ebayes	0.016	0.001	0.017
genas	0.130	0.006	0.156
geneSetTest	0.009	0.001	0.009
getSpacing	0.001	0.000	0.002
getlayout	0.000	0.000	0.001
heatdiagram	0.008	0.001	0.009
helpMethods	0.000	0.000	0.001
imageplot	0.047	0.005	0.052
intraspotCorrelation	0.000	0.001	0.000
isfullrank	0.001	0.000	0.001
isnumeric	0.002	0.001	0.002
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.003	0.001	0.005
lm.series	0.001	0.000	0.000
lmFit	2.319	0.023	2.401
lmscFit	0.013	0.001	0.015
loessfit	0.486	0.005	0.508
ma3x3	0.002	0.001	0.003
makeContrasts	0.002	0.000	0.002
makeunique	0.002	0.000	0.002
merge	0.011	0.001	0.012
mergeScansRG	0.000	0.001	0.001
modelMatrix	0.004	0.000	0.004
modifyWeights	0.001	0.001	0.002
nec	0	0	0
neqc	0	0	0
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.004	0.001	0.004
normalizeVSN	0.663	0.035	0.725
normalizeWithinArrays	0.000	0.000	0.001
normalizebetweenarrays	0.004	0.000	0.005
normalizeprintorder	0.004	0.001	0.005
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0.000	0.000	0.001
normexpsignal	0	0	0
plotDensities	0.019	0.001	0.021
plotMDS	0.020	0.004	0.023
plotRLDF	0.597	0.031	0.655
plotma	0.019	0.001	0.020
poolvar	0.002	0.001	0.002
printorder	0.023	0.009	0.032
printtipWeights	0.013	0.001	0.014
propexpr	0	0	0
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.000	0.003
qualwt	0.001	0.001	0.001
read.ilmn	0	0	0
read.maimages	0.001	0.000	0.000
readImaGeneHeader	0.000	0.001	0.000
readgal	0	0	0
removeext	0.000	0.000	0.001
roast	0.114	0.013	0.129
romer	0.631	0.009	0.658
selectmodel	0.038	0.001	0.038
squeezeVar	0.002	0.000	0.002
strsplit2	0.001	0.001	0.002
subsetting	0.007	0.001	0.007
targetsA2C	0.01	0.00	0.01
topRomer	0.001	0.000	0.000
toptable	0	0	0
trigammainverse	0.001	0.000	0.000
trimWhiteSpace	0.001	0.001	0.000
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.001	0.002
venn	0.048	0.001	0.049
volcanoplot	0.001	0.000	0.000
weightedmedian	0.001	0.000	0.001
zscore	0.001	0.001	0.001