Package: limma

Version: 3.14.4

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.14.4.tar.gz

StartedAt: 2013-03-25 00:12:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:14:27 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 108.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: limma.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/limma.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '3.14.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 for left-over 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 ... WARNING
Foreign function calls with 'PACKAGE' argument in a base package:
  .C("loess_raw", ..., PACKAGE = "stats")
  .C("lowess", ..., PACKAGE = "stats")
  .Fortran("lowesw", ..., PACKAGE = "stats")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* 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 ... OK
* 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.908  0.281   6.336
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...588,592c588,592
< 0%   -0.78835384 -0.788312144 -0.79410956 -2.04434053 -2.0438088 -10.9766130
< 25%  -0.18340154 -0.183595325 -0.17340349 -0.59321065 -0.5863777  -0.7816385
< 50%  -0.11492924 -0.123303508 -0.04476096  0.05874864  0.0827054  -0.2577724
< 75%   0.01507921 -0.006825877  0.14015263  0.56010750  0.5606874   0.4406875
< 100%  0.21653837  0.193234186 11.47140874  2.57936026  2.5816432   2.5397022
---
> 0%   -0.78835384 -0.78097895 -0.78367166 -2.04434053 -2.04315267 -11.5610680
> 25%  -0.18340154 -0.18907787 -0.15525721 -0.59321065 -0.59309327  -0.8249477
> 50%  -0.11492924 -0.12136183 -0.03316003  0.05874864  0.08898459  -0.2466309
> 75%   0.01507921 -0.01000344  0.13229151  0.56010750  0.56606786   0.4502908
> 100%  0.21653837  0.21604173 11.69912073  2.57936026  2.56259812   2.5149556
630,635c630,635
<  Min.   :-5.88044   Min.   :-5.66985  
<  1st Qu.:-1.18483   1st Qu.:-1.57014  
<  Median :-0.21632   Median : 0.04823  
<  Mean   : 0.03487   Mean   :-0.05481  
<  3rd Qu.: 1.49669   3rd Qu.: 1.45113  
<  Max.   : 7.07324   Max.   : 6.19744  
---
>  Min.   :-5.85163   Min.   :-5.69877  
>  1st Qu.:-1.18482   1st Qu.:-1.55421  
>  Median :-0.21631   Median : 0.06267  
>  Mean   : 0.03613   Mean   :-0.05369  
>  3rd Qu.: 1.49673   3rd Qu.: 1.41900  
>  Max.   : 7.07528   Max.   : 6.28902  
646,650c646,650
< [1,] -1.1689588  4.5558123
< [2,]  0.8971363  0.3296544
< [3,]  2.8247439  1.4249960
< [4,] -1.8533240  0.4804851
< [5,]  1.9158459 -5.5087631
---
> [1,] -1.1623390  4.5343276
> [2,]  0.8971391  0.3495635
> [3,]  2.8247455  1.4459533
> [4,] -1.8533288  0.4894799
> [5,]  1.9158416 -5.5363732
661,665c661,665
< [1,] -1.1689588  4.5558123
< [2,]  0.8971363  0.3296544
< [3,]  2.8247439  1.4249960
< [4,] -1.8533240  0.4804851
< [5,]  1.9158459 -5.5087631
---
> [1,] -1.1623390  4.5343276
> [2,]  0.8971391  0.3495635
> [3,]  2.8247455  1.4459533
> [4,] -1.8533288  0.4894799
> [5,]  1.9158416 -5.5363732
906c906
<   'rlm' failed to converge in 20 steps
---
>   rlm failed to converge in 20 steps
981,982c981,982
< 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/limma.Rcheck/00check.log'
for details.

* installing *source* package 'limma' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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-2.11-bioc/meat/limma.Rcheck/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'limma.Rnw' 
** 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	0.000	0.000	0.001
alias2Symbol	5.908	0.281	6.336
arrayWeights	0.001	0.000	0.001
arrayWeightsQuick	0	0	0
asMatrixWeights	0.001	0.000	0.002
auROC	0.001	0.001	0.001
avearrays	0.001	0.000	0.001
avereps	0.001	0.000	0.001
backgroundcorrect	0.008	0.001	0.010
barcodeplot	0.006	0.003	0.011
blockDiag	0.001	0.000	0.002
camera	0.028	0.006	0.036
cbind	0.006	0.000	0.007
channel2M	0.001	0.000	0.002
classifytests	0.002	0.000	0.003
contrasts.fit	0.024	0.002	0.028
controlStatus	0.009	0.001	0.010
dim	0.001	0.000	0.002
dupcor	0.000	0.001	0.000
ebayes	0.011	0.002	0.013
genas	0.088	0.008	0.100
geneSetTest	0.001	0.000	0.001
getSpacing	0.001	0.000	0.001
getlayout	0	0	0
heatdiagram	0	0	0
helpMethods	0	0	0
imageplot	0.034	0.007	0.043
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.001	0.000	0.001
isnumeric	0.001	0.000	0.001
kooperberg	0.001	0.000	0.000
limmaUsersGuide	0.002	0.002	0.003
lm.series	0	0	0
lmFit	0.846	0.026	0.879
lmscFit	0	0	0
loessfit	0.042	0.005	0.047
ma3x3	0.001	0.000	0.001
makeContrasts	0.001	0.000	0.001
makeunique	0.000	0.000	0.001
merge	0.007	0.001	0.007
mergeScansRG	0.001	0.001	0.001
modelMatrix	0.002	0.000	0.003
modifyWeights	0.000	0.001	0.001
nec	0.000	0.000	0.001
normalizeMedianAbsValues	0.000	0.000	0.001
normalizeRobustSpline	0.089	0.011	0.104
normalizeVSN	0.532	0.070	0.614
normalizebetweenarrays	0.002	0.001	0.003
normalizeprintorder	0	0	0
normexpfit	0.001	0.000	0.002
normexpfitcontrol	0	0	0
normexpfitdetectionp	0	0	0
normexpsignal	0	0	0
plotDensities	0.001	0.001	0.000
plotMDS	0.232	0.006	0.239
plotRLDF	0.758	0.025	0.785
plotma	0.017	0.005	0.022
poolvar	0.001	0.001	0.001
printorder	0.014	0.006	0.021
printtipWeights	0	0	0
propTrueNull	0.643	0.012	0.658
propexpr	0.001	0.000	0.001
protectMetachar	0.001	0.000	0.001
qqt	0.004	0.003	0.009
qualwt	0	0	0
rankSumTestwithCorrelation	0.009	0.001	0.010
read.ilmn	0	0	0
read.maimages	0	0	0
readImaGeneHeader	0	0	0
readgal	0	0	0
removeext	0.001	0.000	0.000
roast	0.063	0.009	0.073
romer	0.469	0.003	0.473
selectmodel	0.020	0.000	0.022
squeezeVar	0.001	0.000	0.001
strsplit2	0.001	0.000	0.000
subsetting	0.005	0.001	0.005
targetsA2C	0.007	0.001	0.008
topRomer	0	0	0
toptable	0.000	0.001	0.000
trigammainverse	0.001	0.000	0.000
trimWhiteSpace	0.001	0.000	0.000
uniquegenelist	0.000	0.001	0.000
unwrapdups	0.001	0.000	0.001
venn	0.051	0.004	0.059
volcanoplot	0	0	0
weightedmedian	0.000	0.000	0.001
zscore	0.001	0.000	0.001