Package: limma

Version: 3.16.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.16.2.tar.gz

StartedAt: 2013-05-01 07:27:04 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:29:40 -0700 (Wed, 01 May 2013)

EllapsedTime: 155.4 seconds

RetCode: 0

Status:  OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.16.2'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'limma' can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... 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 ... 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 installed files from 'inst/doc' ... OK
* checking examples ... [22s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 8.615  0.264   9.194
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'limma-Tests.R' [3s/3s]
  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
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
 [3s/3s] 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c normexp.c -o normexp.o
normexp.c:153:20: warning: magnitude of floating-point constant too large for type 'double'; maximum is 1.797693134862316E+308 [-Wliteral-range]
  double abstol = -1e500; // infinity
                   ^
normexp.c:167:78: warning: passing 'void (*)()' to parameter of type 'void *' converts between void pointer and function pointer [-Wpedantic]
  nmmin(3, par, parsOut, Fmin, normexp_m2loglik_saddle, fail, abstol, intol, &ex, alpha, beta, gamma, trace, fncount, maxit);
                                                                             ^˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Applic.h:69:51: note: passing argument to parameter 'ex' here
           int *fail, double abstol, double intol, void *ex,
                                                         ^
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.12-bioc/meat/limma.Rcheck/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)

name	user	system	elapsed
LargeDataObject	0.008	0.001	0.009
PrintLayout	0.010	0.002	0.013
TestResults	0.009	0.001	0.010
alias2Symbol	8.615	0.264	9.194
arrayWeights	0.301	0.006	0.312
arrayWeightsQuick	0.038	0.005	0.044
asMatrixWeights	0.034	0.004	0.039
auROC	0.036	0.003	0.038
avearrays	0.034	0.002	0.037
avereps	0.038	0.003	0.041
backgroundcorrect	0.048	0.003	0.051
barcodeplot	0.065	0.004	0.070
blockDiag	0.034	0.002	0.036
camera	0.124	0.005	0.130
cbind	0.083	0.005	0.091
channel2M	0.051	0.001	0.053
classifytests	0.040	0.003	0.045
contrasts.fit	0.129	0.003	0.137
controlStatus	0.059	0.001	0.061
dim	0.084	0.001	0.085
dupcor	0.026	0.005	0.032
ebayes	0.088	0.010	0.099
fitGammaIntercept	0.036	0.003	0.039
fitfdist	0.035	0.002	0.037
genas	0.216	0.016	0.239
geneSetTest	0.052	0.003	0.054
getSpacing	0.034	0.001	0.037
getlayout	0.018	0.000	0.019
heatdiagram	0.055	0.002	0.058
helpMethods	0.020	0.002	0.023
imageplot	0.082	0.007	0.093
intraspotCorrelation	0.035	0.003	0.039
isfullrank	0.062	0.002	0.074
isnumeric	0.056	0.001	0.059
kooperberg	0.034	0.003	0.037
limmaUsersGuide	0.021	0.002	0.024
lm.series	0.032	0.003	0.035
lmFit	1.107	0.058	1.207
lmscFit	0.051	0.005	0.055
loessfit	0.118	0.006	0.126
ma3x3	0.040	0.004	0.046
makeContrasts	0.057	0.005	0.062
makeunique	0.020	0.003	0.025
merge	0.058	0.005	0.063
mergeScansRG	0.036	0.004	0.040
modelMatrix	0.041	0.005	0.046
modifyWeights	0.020	0.003	0.022
nec	0.037	0.004	0.041
normalizeMedianAbsValues	0.020	0.002	0.022
normalizeRobustSpline	0.149	0.011	0.164
normalizeVSN	0.668	0.062	0.753
normalizebetweenarrays	0.043	0.004	0.048
normalizeprintorder	0.046	0.002	0.050
normexpfit	0.021	0.003	0.023
normexpfitcontrol	0.035	0.002	0.038
normexpfitdetectionp	0.074	0.003	0.078
normexpsignal	0.020	0.002	0.023
plotDensities	0.091	0.007	0.099
plotMDS	0.093	0.004	0.097
plotRLDF	0.491	0.023	0.572
plotma	0.134	0.005	0.154
poolvar	0.041	0.008	0.051
predFCm	0.119	0.013	0.133
printorder	0.028	0.012	0.040
printtipWeights	0.055	0.007	0.063
propTrueNull	0.041	0.007	0.049
propexpr	0.023	0.004	0.029
protectMetachar	0.023	0.005	0.029
qqt	0.043	0.006	0.053
qualwt	0.020	0.004	0.024
rankSumTestwithCorrelation	0.047	0.008	0.057
read.ilmn	0.041	0.004	0.045
read.maimages	0.038	0.005	0.042
readImaGeneHeader	0.020	0.003	0.022
readgal	0.019	0.003	0.022
removeext	0.035	0.003	0.039
roast	0.151	0.007	0.158
romer	0.606	0.061	0.675
selectmodel	0.086	0.008	0.097
squeezeVar	0.022	0.004	0.027
strsplit2	0.041	0.005	0.047
subsetting	0.050	0.006	0.057
targetsA2C	0.050	0.004	0.074
topRomer	0.019	0.002	0.021
toptable	0.019	0.003	0.021
trigammainverse	0.038	0.004	0.051
trimWhiteSpace	0.018	0.002	0.022
uniquegenelist	0.038	0.005	0.044
unwrapdups	0.022	0.004	0.025
venn	0.090	0.007	0.098
volcanoplot	0.033	0.003	0.036
weightedmedian	0.020	0.003	0.023
zscore	0.024	0.004	0.027