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Package 278/516HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.10.0
Gordon Smyth
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/limma
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: limma
Version: 3.10.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch limma_3.10.0.tar.gz
StartedAt: 2012-01-09 03:57:20 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 03:58:51 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 91.1 seconds
RetCode: 0
Status:  OK  
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '3.10.0'
* 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 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 ... NOTE
'library' or 'require' call not declared from: 'sma'
* 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'marray'
* checking tests ...
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ... OK
 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  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -shared -s -static-libgcc -o limma.dll tmp.def normexp.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/limma.Rcheck/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'limma.Rnw' 
** testing if installed package can be loaded

* DONE (limma)

limma.Rcheck/limma-Ex.timings:

nameusersystemelapsed
LargeDataObject000
PrintLayout000
TestResults000
alias2Symbol4.270.034.64
arrayWeights000
arrayWeightsQuick000
asMatrixWeights000
auROC000
avearrays000
avereps000
backgroundcorrect0.020.000.02
blockDiag000
cbind000
channel2M000
classifytests000
contrasts.fit0.030.000.03
controlStatus0.010.000.01
convest2.530.002.54
dim000
dupcor000
ebayes000
genas0.060.000.06
geneSetTest000
getSpacing000
getlayout000
heatdiagram0.020.000.02
helpMethods000
imageplot0.090.000.09
intraspotCorrelation000
isfullrank000
isnumeric000
kooperberg000
limmaUsersGuide000
lm.series000
lmFit0.670.000.67
lmscFit0.000.020.02
loessfit0.640.000.64
ma3x3000
makeContrasts000
makeunique000
merge000
mergeScansRG000
modelMatrix000
modifyWeights000
nec000
normalizeMedianAbsValues000
normalizeRobustSpline0.020.000.01
normalizeVSN0.360.030.39
normalizebetweenarrays000
normalizeprintorder000
normexpfit000
normexpfitcontrol000
normexpfitdetectionp000
normexpsignal000
plotDensities000
plotMDS0.030.000.22
plotRLDF0.440.000.43
plotma0.010.000.27
poolvar000
printorder0.020.000.01
printtipWeights0.010.000.01
propexpr000
protectMetachar000
qqt000
qualwt000
read.ilmn000
read.maimages000
readImaGeneHeader000
readgal000
removeext000
roast0.050.020.07
romer0.560.000.56
selectmodel0.020.000.01
squeezeVar000
strsplit2000
subsetting0.010.000.02
targetsA2C000
topRomer000
toptable000
trigammainverse000
trimWhiteSpace000
uniquegenelist000
unwrapdups000
venn0.030.000.03
volcanoplot000
weightedmedian000
zscore000