Package: limma

Version: 3.8.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.8.3.tar.gz

StartedAt: 2011-10-20 15:39:51 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:42:22 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 150.1 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 2.13.2 (2011-09-30)
* 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 '3.8.3'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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' ...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 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/2.13/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-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-2.8-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	0.000	0.001
TestResults	0	0	0
alias2Symbol	3.852	0.166	4.517
arrayWeights	0.004	0.002	0.006
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.000	0.009
auROC	0.001	0.001	0.011
avearrays	0.002	0.000	0.002
avereps	0.002	0.000	0.002
backgroundcorrect	0.014	0.003	0.017
blockDiag	0.001	0.001	0.002
cbind	0.024	0.002	0.026
channel2M	0.002	0.000	0.002
classifytests	0.003	0.001	0.004
contrasts.fit	0.036	0.002	0.038
controlStatus	0.012	0.001	0.012
convest	2.782	0.019	2.952
dim	0.002	0.000	0.002
dupcor	0.000	0.000	0.001
ebayes	0.014	0.000	0.015
genas	0.127	0.002	0.133
geneSetTest	0.008	0.000	0.009
getSpacing	0.000	0.000	0.001
getlayout	0	0	0
heatdiagram	0.003	0.001	0.004
helpMethods	0.000	0.001	0.000
imageplot	0.046	0.004	0.051
intraspotCorrelation	0.001	0.000	0.001
isfullrank	0.002	0.000	0.001
isnumeric	0.002	0.001	0.002
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.002	0.001	0.004
lm.series	0	0	0
lmFit	1.446	0.017	1.633
lmscFit	0.004	0.001	0.005
loessfit	0.474	0.005	0.511
ma3x3	0.002	0.000	0.002
makeContrasts	0.001	0.001	0.002
makeunique	0.001	0.000	0.001
merge	0.010	0.001	0.011
mergeScansRG	0.000	0.000	0.001
modelMatrix	0.003	0.001	0.003
modifyWeights	0.000	0.000	0.001
nec	0.000	0.001	0.000
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.003	0.001	0.004
normalizeVSN	0.637	0.035	0.695
normalizebetweenarrays	0.003	0.001	0.004
normalizeprintorder	0.001	0.000	0.000
normexpfit	0.002	0.001	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	0.018	0.003	0.024
plotRLDF	0.573	0.024	0.614
plotma	0.018	0.000	0.019
poolvar	0.001	0.000	0.001
printorder	0.017	0.008	0.026
printtipWeights	0.001	0.000	0.001
propexpr	0	0	0
protectMetachar	0.000	0.000	0.001
qqt	0.002	0.000	0.002
qualwt	0.000	0.001	0.001
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0.001	0.000	0.001
roast	0.069	0.008	0.076
romer	0.600	0.006	0.615
selectmodel	0.036	0.000	0.037
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.001
subsetting	0.006	0.000	0.007
targetsA2C	0.009	0.000	0.009
topRomer	0	0	0
toptable	0	0	0
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.000	0.001	0.001
unwrapdups	0.001	0.000	0.001
venn	0.059	0.003	0.062
volcanoplot	0.000	0.000	0.001
weightedmedian	0	0	0
zscore	0.001	0.000	0.000