BioC 2.13: CHECK report for limma on zin1

Package: limma

Version: 3.18.13

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.18.13.tar.gz

StartedAt: 2014-04-05 02:08:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:09:34 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 75.9 seconds

RetCode: 0

Status: OK

CheckDir: limma.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/limma.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.18.13’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘limma-Tests.R’ [1s/1s]
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...631,636c631,636
<  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  
647,651c647,651
< [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
662,666c662,666
< [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
994,995c994,995
< 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
 [2s/2s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c normexp.c -o normexp.o
gcc -std=gnu99 -shared -L/usr/local/lib -o limma.so normexp.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.000	0.000	0.001
PrintLayout	0.004	0.000	0.004
TestResults	0.004	0.000	0.002
alias2Symbol	3.712	0.060	3.803
arrayWeights	0.024	0.000	0.021
arrayWeightsQuick	0.012	0.000	0.015
asMatrixWeights	0.112	0.000	0.111
auROC	0.008	0.000	0.011
avearrays	0.012	0.000	0.011
avereps	0.012	0.000	0.012
backgroundcorrect	0.016	0.000	0.018
barcodeplot	0.016	0.000	0.015
beadCountWeights	0.008	0.000	0.010
blockDiag	0.012	0.000	0.011
camera	0.040	0.004	0.042
cbind	0.028	0.000	0.026
channel2M	0.012	0.000	0.012
classifytests	0.012	0.004	0.013
contrastAsCoef	0.024	0.000	0.024
contrasts.fit	0.036	0.000	0.039
controlStatus	0.024	0.000	0.022
dim	0.020	0.000	0.021
dupcor	0.008	0.000	0.010
ebayes	0.048	0.000	0.049
fitGammaIntercept	0.008	0.000	0.011
fitfdist	0.012	0.000	0.012
genas	0.152	0.004	0.158
geneSetTest	0.016	0.004	0.018
getSpacing	0.016	0.000	0.013
getlayout	0.008	0.004	0.012
heatdiagram	0.020	0.000	0.019
helpMethods	0.008	0.000	0.007
imageplot	0.036	0.000	0.039
intraspotCorrelation	0.012	0.000	0.011
isfullrank	0.020	0.000	0.021
isnumeric	0.016	0.000	0.017
kooperberg	0.008	0.004	0.012
limmaUsersGuide	0.016	0.000	0.015
lm.series	0.012	0.000	0.011
lmFit	0.568	0.008	0.577
lmscFit	0.016	0.000	0.016
loessfit	0.108	0.000	0.108
ma3x3	0.012	0.000	0.013
makeContrasts	0.020	0.000	0.021
makeunique	0.012	0.000	0.012
merge	0.020	0.000	0.023
mergeScansRG	0.012	0.000	0.011
modelMatrix	0.020	0.000	0.018
modifyWeights	0.008	0.000	0.010
nec	0.008	0.000	0.011
normalizeMedianAbsValues	0.008	0.000	0.008
normalizeRobustSpline	0.060	0.004	0.063
normalizeVSN	0.288	0.024	0.315
normalizebetweenarrays	0.012	0.004	0.014
normalizeprintorder	0.012	0.000	0.011
normexpfit	0.028	0.000	0.027
normexpfitcontrol	0.012	0.000	0.011
normexpfitdetectionp	0.012	0.000	0.011
normexpsignal	0.012	0.000	0.011
plotDensities	0.012	0.000	0.011
plotMDS	0.032	0.000	0.029
plotRLDF	0.208	0.000	0.211
plotma	0.032	0.000	0.032
poolvar	0.008	0.000	0.007
predFCm	0.044	0.000	0.043
printorder	0.008	0.004	0.014
printtipWeights	0.012	0.000	0.012
propTrueNull	0.016	0.000	0.015
propexpr	0.004	0.000	0.005
protectMetachar	0.004	0.000	0.007
qqt	0.016	0.000	0.014
qualwt	0.012	0.000	0.011
rankSumTestwithCorrelation	0.024	0.000	0.025
read.ilmn	0.012	0.000	0.012
read.maimages	0.136	0.000	0.137
readImaGeneHeader	0.004	0.000	0.006
readgal	0.004	0.000	0.006
removeext	0.008	0.000	0.006
roast	0.068	0.000	0.065
romer	0.248	0.000	0.244
selectmodel	0.028	0.000	0.027
squeezeVar	0.004	0.000	0.006
strsplit2	0.008	0.000	0.007
subsetting	0.012	0.004	0.016
targetsA2C	0.012	0.000	0.011
topRomer	0.004	0.000	0.005
toptable	0.004	0.000	0.006
trigammainverse	0.004	0.000	0.005
trimWhiteSpace	0.004	0.000	0.006
uniquegenelist	0.008	0.000	0.006
unwrapdups	0.008	0.000	0.007
venn	0.040	0.000	0.042
volcanoplot	0.004	0.000	0.005
weightedmedian	0.008	0.000	0.007
zscore	0.016	0.000	0.012

BioC 2.13: CHECK report for limma on zin1

Summary

Command output