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Package 344/631HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.15.11
Gordon Smyth
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma
Last Changed Rev: 72573 / Revision: 72575
Last Changed Date: 2013-01-15 16:52:56 -0800 (Tue, 15 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: limma
Version: 3.15.11
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.15.11.tar.gz
StartedAt: 2013-01-16 03:54:25 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 03:56:22 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 116.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: limma.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘3.15.11’
* 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 ... 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 ... WARNING
Undocumented code objects:
  ‘fitGammaIntercept’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
              user system elapsed
alias2Symbol 5.848  0.052   5.949
* 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
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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/limma.Rcheck/00check.log’
for details.

limma.Rcheck/00install.out:

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -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-2.12-bioc/R/lib -lR
installing to /loc/home/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
   ‘limma.Rnw’ 
** testing if installed package can be loaded

* DONE (limma)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject0.0040.0000.007
PrintLayout0.0600.0000.061
TestResults0.0040.0080.009
alias2Symbol5.8480.0525.949
arrayWeights0.0760.0000.077
arrayWeightsQuick0.0400.0000.038
asMatrixWeights0.0360.0000.037
auROC0.0520.0000.055
avearrays0.0560.0000.060
avereps0.0600.0000.057
backgroundcorrect0.0640.0000.063
barcodeplot0.2840.0080.293
blockDiag0.0400.0000.039
camera0.1080.0000.109
cbind0.0800.0000.081
channel2M0.0360.0040.039
classifytests0.0600.0000.059
contrasts.fit0.0920.0120.125
controlStatus0.0480.0000.047
dim0.0920.0000.092
dupcor0.0520.0000.055
ebayes0.1360.0040.140
fitfdist0.0480.0000.046
genas0.5120.0040.511
geneSetTest0.0440.0000.045
getSpacing0.0480.0040.049
getlayout0.0200.0000.021
heatdiagram0.0320.0080.040
helpMethods0.0160.0040.021
imageplot0.0520.0120.066
intraspotCorrelation0.040.000.04
isfullrank0.0360.0040.041
isnumeric0.0400.0040.040
kooperberg0.0360.0000.039
limmaUsersGuide0.0400.0000.043
lm.series0.020.000.02
lmFit0.8760.0280.903
lmscFit0.0400.0000.041
loessfit0.0920.0000.094
ma3x30.0360.0000.039
makeContrasts0.0400.0000.041
makeunique0.0440.0000.041
merge0.0640.0000.065
mergeScansRG0.0560.0000.054
modelMatrix0.0560.0000.058
modifyWeights0.0400.0000.041
nec0.040.000.04
normalizeMedianAbsValues0.0360.0000.038
normalizeRobustSpline0.1160.0080.128
normalizeVSN0.5280.0280.562
normalizebetweenarrays0.0640.0000.063
normalizeprintorder0.0120.0080.019
normexpfit0.0240.0000.023
normexpfitcontrol0.0360.0000.039
normexpfitdetectionp0.040.000.04
normexpsignal0.0200.0000.021
plotDensities0.0800.0040.086
plotMDS0.0520.0040.058
plotRLDF0.4360.0160.451
plotma0.3800.0080.386
poolvar0.040.000.04
predFCm0.1240.0080.130
printorder0.0480.0000.048
printtipWeights0.0640.0000.063
propTrueNull0.0440.0000.044
propexpr0.0200.0000.021
protectMetachar0.0200.0000.021
qqt0.0400.0000.041
qualwt0.0200.0000.023
rankSumTestwithCorrelation0.0640.0040.069
read.ilmn0.0360.0000.038
read.maimages0.040.000.04
readImaGeneHeader0.020.000.02
readgal0.0240.0000.021
removeext0.0240.0000.023
roast0.1480.0000.146
romer0.4730.0000.475
selectmodel0.080.000.08
squeezeVar0.0200.0000.021
strsplit20.040.000.04
subsetting0.0440.0000.045
targetsA2C0.0240.0000.027
topRomer0.0200.0000.021
toptable0.0200.0000.019
trigammainverse0.0240.0000.023
trimWhiteSpace0.0280.0000.028
uniquegenelist0.0400.0000.039
unwrapdups0.0240.0000.023
venn0.0880.0040.091
volcanoplot0.020.000.02
weightedmedian0.0200.0000.021
zscore0.040.000.04