Package: limma

Version: 3.7.25

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.7.25.tar.gz

StartedAt: 2011-03-17 16:42:49 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:44:31 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 102.7 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) (2011-03-06 r54683)
* 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 '3.7.25'
* 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 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' ...826,830c826,830
< [1,]  1.025680641  0.04440632
< [2,] -0.008931391 -0.04446419
< [3,]  0.069383171 -0.03407404
< [4,] -0.029375980  0.11198606
< [5,] -0.276173422  0.21529287
---
> [1,]   1.02568064  0.04440632
> [2,]  -0.00893139 -0.04446419
> [3,]   0.06938317 -0.03407404
> [4,]  -0.02937598  0.11198606
> [5,]  -0.27617342  0.21529287
871,872c871,872
<  [1] 0.07551649 0.14100247 0.30870247 0.13909601 0.32893352 0.17192613
<  [7] 0.42951263 0.11976975 0.39067059 0.22671154
---
>  [1] 0.0755165 0.1410025 0.3087025 0.1390960 0.3289335 0.1719261 0.4295126
>  [8] 0.1197697 0.3906706 0.2267115
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	0	0
PrintLayout	0.000	0.000	0.001
TestResults	0.001	0.000	0.001
alias2Symbol	2.637	0.066	2.722
arrayWeights	0.002	0.000	0.003
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.001
avearrays	0.001	0.000	0.002
avereps	0.001	0.000	0.001
backgroundcorrect	0.010	0.001	0.012
blockDiag	0.000	0.000	0.001
cbind	0.007	0.001	0.007
channel2M	0.001	0.000	0.001
classifytests	0.003	0.000	0.003
contrasts.fit	0.027	0.002	0.028
controlStatus	0.018	0.000	0.018
convest	1.803	0.006	1.809
dim	0.002	0.000	0.002
dupcor	0.000	0.000	0.001
ebayes	0.01	0.00	0.01
genas	0.089	0.002	0.092
geneSetTest	0.015	0.001	0.015
getSpacing	0.001	0.000	0.000
getlayout	0.000	0.000	0.001
heatdiagram	0.002	0.000	0.002
helpMethods	0.000	0.000	0.001
imageplot	0.036	0.002	0.038
intraspotCorrelation	0.000	0.001	0.000
isfullrank	0.001	0.000	0.001
isnumeric	0.000	0.001	0.001
kooperberg	0.000	0.000	0.001
limmaUsersGuide	0.002	0.001	0.002
lm.series	0	0	0
lmFit	1.584	0.009	1.593
lmscFit	0.003	0.001	0.004
loessfit	0.333	0.001	0.333
ma3x3	0.001	0.000	0.002
makeContrasts	0.001	0.001	0.001
makeunique	0.001	0.000	0.001
merge	0.008	0.001	0.009
mergeScansRG	0	0	0
modelMatrix	0.002	0.000	0.002
modifyWeights	0.000	0.000	0.001
nec	0	0	0
neqc	0	0	0
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.002	0.000	0.003
normalizeVSN	0.548	0.017	0.564
normalizebetweenarrays	0.003	0.000	0.003
normalizeprintorder	0.000	0.000	0.001
normexpfit	0.001	0.000	0.001
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0.000	0.000	0.001
plotMDS	0.013	0.001	0.014
plotRLDF	0.382	0.008	0.390
plotma	0.014	0.000	0.015
poolvar	0.001	0.000	0.001
printorder	0.014	0.005	0.019
printtipWeights	0.001	0.000	0.000
propexpr	0	0	0
protectMetachar	0.001	0.000	0.001
qqt	0.002	0.000	0.002
qualwt	0	0	0
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0.000	0.000	0.001
readgal	0.001	0.000	0.000
removeext	0.001	0.000	0.000
roast	0.046	0.001	0.047
romer	0.422	0.003	0.425
selectmodel	0.027	0.000	0.027
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.004	0.000	0.005
targetsA2C	0.007	0.000	0.007
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.001	0.001	0.001
unwrapdups	0.001	0.000	0.001
venn	0.041	0.002	0.042
volcanoplot	0	0	0
weightedmedian	0	0	0
zscore	0.000	0.000	0.001