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Package 303/553HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.12.3
Gordon Smyth
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/limma
Last Changed Rev: 69129 / Revision: 69725
Last Changed Date: 2012-09-05 21:09:39 -0700 (Wed, 05 Sep 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: limma
Version: 3.12.3
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.12.3.tar.gz
StartedAt: 2012-09-24 01:54:32 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:56:07 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 95.6 seconds
RetCode: 0
Status:  OK 
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/limma.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘3.12.3’
* 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 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 ... OK
* 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.   :-5.82498   Min.   :-5.69877  
>  1st Qu.:-1.19140   1st Qu.:-1.55421  
>  Median :-0.19318   Median : 0.06267  
>  Mean   : 0.08691   Mean   :-0.05369  
>  3rd Qu.: 1.48646   3rd Qu.: 1.41900  
>  Max.   : 7.16195   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,] -1.0618269  4.5343276
> [2,]  0.8507603  0.3495635
> [3,]  2.7703696  1.4459533
> [4,] -1.8511286  0.4894799
> [5,]  1.9180276 -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,] -1.0618269  4.5343276
> [2,]  0.8507603  0.3495635
> [3,]  2.7703696  1.4459533
> [4,] -1.8511286  0.4894799
> [5,]  1.9180276 -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
 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

limma.Rcheck/00install.out:

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:153:3: warning: floating constant exceeds range of ‘double’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/limma.Rcheck/limma/libs
** 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)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject000
PrintLayout0.0000.0000.001
TestResults000
alias2Symbol5.7920.1285.965
arrayWeights0.0000.0000.001
arrayWeightsQuick0.0000.0000.001
asMatrixWeights0.0040.0000.001
auROC000
avearrays0.0000.0000.001
avereps0.0000.0000.001
backgroundcorrect0.0080.0000.009
barcodeplot0.0080.0000.005
blockDiag0.0000.0000.001
camera0.0360.0040.040
cbind0.0040.0000.007
channel2M0.0000.0000.002
classifytests0.0040.0000.002
contrasts.fit0.0280.0000.028
controlStatus0.0080.0000.011
dim0.0000.0000.001
dupcor000
ebayes0.0080.0040.010
genas0.0800.0000.081
geneSetTest0.0000.0000.001
getSpacing0.0000.0000.001
getlayout000
heatdiagram000
helpMethods000
imageplot0.0560.0000.057
intraspotCorrelation000
isfullrank0.0040.0000.001
isnumeric0.0000.0000.001
kooperberg000
limmaUsersGuide0.0040.0000.003
lm.series000
lmFit1.1240.0241.154
lmscFit000
loessfit0.0360.0000.038
ma3x30.0040.0000.001
makeContrasts0.0000.0000.001
makeunique0.0000.0000.001
merge0.0040.0000.006
mergeScansRG000
modelMatrix0.0000.0000.002
modifyWeights000
nec000
normalizeMedianAbsValues0.0000.0000.001
normalizeRobustSpline000
normalizeVSN0.4640.0320.495
normalizebetweenarrays0.0040.0000.003
normalizeprintorder000
normexpfit0.0040.0000.002
normexpfitcontrol000
normexpfitdetectionp000
normexpsignal000
plotDensities0.0000.0040.001
plotMDS0.0120.0000.019
plotRLDF0.6600.0120.675
plotma0.0160.0000.018
poolvar0.0040.0000.001
printorder0.0120.0000.015
printtipWeights000
propTrueNull0.8000.0040.806
propexpr0.0000.0000.001
protectMetachar0.0000.0000.001
qqt0.0040.0000.004
qualwt0.0000.0000.001
rankSumTestwithCorrelation0.0080.0000.007
read.ilmn000
read.maimages000
readImaGeneHeader0.0040.0000.000
readgal000
removeext000
roast0.0600.0040.062
romer0.4080.0000.408
selectmodel0.0200.0000.019
squeezeVar000
strsplit2000
subsetting0.0040.0000.004
targetsA2C0.0040.0000.006
topRomer0.0000.0000.001
toptable000
trigammainverse000
trimWhiteSpace000
uniquegenelist0.0000.0000.001
unwrapdups0.0000.0000.001
venn0.0280.0000.028
volcanoplot000
weightedmedian0.0000.0000.001
zscore0.0000.0000.001