Package: limma

Version: 3.9.5

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.9.5.tar.gz

StartedAt: 2011-06-22 03:46:47 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 03:49:17 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 149.7 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) (2011-06-03 r56037)
* 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 ‘3.9.5’
* 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/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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	0.000	0.000	0.001
PrintLayout	0.001	0.000	0.001
TestResults	0	0	0
alias2Symbol	3.729	0.161	4.109
arrayWeights	0.009	0.001	0.011
arrayWeightsQuick	0.000	0.000	0.001
asMatrixWeights	0.001	0.000	0.001
auROC	0.001	0.000	0.001
avearrays	0.002	0.000	0.002
avereps	0.002	0.001	0.002
backgroundcorrect	0.013	0.001	0.014
blockDiag	0.002	0.001	0.002
cbind	0.010	0.001	0.011
channel2M	0.002	0.000	0.002
classifytests	0.004	0.000	0.004
contrasts.fit	0.036	0.002	0.038
controlStatus	0.024	0.001	0.025
convest	2.636	0.019	2.782
dim	0.003	0.000	0.003
dupcor	0.001	0.000	0.001
ebayes	0.016	0.001	0.018
genas	0.123	0.001	0.134
geneSetTest	0.010	0.000	0.011
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
heatdiagram	0.007	0.001	0.008
helpMethods	0	0	0
imageplot	0.058	0.005	0.064
intraspotCorrelation	0	0	0
isfullrank	0.001	0.000	0.002
isnumeric	0.001	0.000	0.002
kooperberg	0	0	0
limmaUsersGuide	0.003	0.001	0.004
lm.series	0.000	0.000	0.001
lmFit	1.495	0.019	1.596
lmscFit	0.013	0.001	0.015
loessfit	0.463	0.005	0.497
ma3x3	0.002	0.000	0.003
makeContrasts	0.002	0.001	0.002
makeunique	0.002	0.000	0.001
merge	0.012	0.001	0.014
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.004	0.000	0.004
modifyWeights	0.001	0.000	0.001
nec	0.001	0.000	0.000
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.004	0.001	0.008
normalizeVSN	0.655	0.037	0.705
normalizebetweenarrays	0.004	0.000	0.004
normalizeprintorder	0.000	0.000	0.001
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0	0	0
normexpfitdetectionp	0	0	0
normexpsignal	0.000	0.000	0.001
plotDensities	0.001	0.000	0.001
plotMDS	0.019	0.001	0.021
plotRLDF	0.537	0.024	0.564
plotma	0.021	0.001	0.022
poolvar	0.001	0.000	0.002
printorder	0.023	0.009	0.032
printtipWeights	0.001	0.001	0.001
propexpr	0.000	0.000	0.001
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.000	0.003
qualwt	0.001	0.000	0.001
read.ilmn	0	0	0
read.maimages	0.001	0.000	0.000
readImaGeneHeader	0	0	0
readgal	0.001	0.000	0.001
removeext	0.000	0.000	0.001
roast	0.067	0.007	0.074
romer	0.655	0.017	0.777
selectmodel	0.056	0.002	0.071
squeezeVar	0.002	0.000	0.002
strsplit2	0.001	0.001	0.002
subsetting	0.007	0.001	0.008
targetsA2C	0.010	0.000	0.011
topRomer	0.001	0.000	0.000
toptable	0	0	0
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.000	0.000	0.001
uniquegenelist	0.002	0.001	0.002
unwrapdups	0.001	0.000	0.001
venn	0.045	0.001	0.050
volcanoplot	0.000	0.000	0.001
weightedmedian	0.001	0.001	0.001
zscore	0.001	0.000	0.001