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Package 209/389HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.4.5
Gordon Smyth
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/limma
Last Changed Rev: 49285 / Revision: 49923
Last Changed Date: 2010-09-07 22:57:09 -0700 (Tue, 07 Sep 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: limma
Version: 3.4.5
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings limma_3.4.5.tar.gz
StartedAt: 2010-10-04 17:26:20 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:27:49 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 88.3 seconds
RetCode: 0
Status:  OK  
CheckDir: limma.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/limma.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.4.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'limma' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...896,897c896,897
< 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 -1.821460e-17
> mu+beta    -0.3333333 -1.821460e-17  3.333333e-01
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

limma.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'limma' ...
** libs
  making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c normexp.c -o normexp.o
normexp.c: In function 'fit_saddle_nelder_mead':
normexp.c:153: warning: floating constant exceeds range of 'double'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/limma.Rcheck/limma/libs/x64
  ... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (limma)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject000
PrintLayout000
TestResults000
alias2Symbol3.310.063.96
arrayWeights0.020.000.02
arrayWeightsQuick000
asMatrixWeights000
auROC000
avereps000
backgroundcorrect0.020.000.01
blockDiag000
cbind0.010.000.02
channel2M000
classifytests000
contrasts.fit0.030.000.04
controlStatus0.010.000.01
convest2.050.002.05
dim000
dupcor000
ebayes0.010.000.02
genas0.080.020.09
geneSetTest0.010.000.01
getSpacing000
getlayout000
heatdiagram000
helpMethods000
imageplot0.060.000.07
intraspotCorrelation000
isfullrank000
isnumeric000
kooperberg000
limmaUsersGuide000
lm.series000
lmFit1.780.031.82
lmscFit000
loessfit0.480.000.48
ma3x3000
makeContrasts000
makeunique000
merge0.020.000.02
mergeScansRG000
modelMatrix000
modifyWeights000
neqc000
normalizeMedianAbsValues000
normalizeRobustSpline000
normalizeWithinArrays000
normalizebetweenarrays0.020.000.01
normalizeprintorder000
normexpfit000
normexpfitcontrol000
normexpsignal000
plotDensities0.010.000.02
plotMDS0.020.000.01
plotRLDF0.560.000.56
plotma0.020.000.02
poolvar000
printorder0.010.000.02
printtipWeights000
propexpr000
protectMetachar000
qqt000
qualwt000
read.ilmn000
read.maimages000
readImaGeneHeader000
readgal000
removeext000
roast0.100.000.09
romer0.460.000.47
selectmodel0.040.000.03
squeezeVar000
strsplit20.010.000.02
subsetting000
targetsA2C000
topRomer000
toptable000
trigammainverse000
trimWhiteSpace000
uniquegenelist000
unwrapdups000
venn0.040.000.05
volcanoplot000
weightedmedian000
zscore000