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Package 224/419HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.6.9
Gordon Smyth
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/limma
Last Changed Rev: 51155 / Revision: 54281
Last Changed Date: 2010-11-30 19:05:51 -0800 (Tue, 30 Nov 2010)
lamb2 Linux (openSUSE 11.2) / 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: 3.6.9
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.6.9.tar.gz
StartedAt: 2011-03-31 06:52:51 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:54:24 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 93.7 seconds
RetCode: 0
Status:  OK 
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/limma.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘3.6.9’
* 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 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 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 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 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’ ...920,921c920,921
< 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 package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

limma.Rcheck/00install.out:

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:153: warning: floating constant exceeds range of ‘double’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o limma.so normexp.o -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/limma.Rcheck/limma/libs
** 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
PrintLayout0.0000.0000.001
TestResults000
alias2Symbol2.6480.0442.741
arrayWeights0.0040.0000.004
arrayWeightsQuick000
asMatrixWeights0.0000.0000.001
auROC000
avearrays0.0040.0000.001
avereps0.0000.0000.001
backgroundcorrect0.0120.0000.010
blockDiag0.0000.0000.001
cbind0.0080.0000.007
channel2M0.0000.0000.002
classifytests0.0000.0000.003
contrasts.fit0.0240.0040.036
controlStatus0.0040.0040.008
convest2.6360.0082.649
dim0.0040.0000.002
dupcor0.0000.0000.001
ebayes0.0120.0000.010
genas0.0840.0040.087
geneSetTest0.0040.0000.006
getSpacing000
getlayout000
heatdiagram0.0040.0000.003
helpMethods000
imageplot0.0280.0040.033
intraspotCorrelation000
isfullrank000
isnumeric0.0000.0000.001
kooperberg000
limmaUsersGuide0.0000.0000.002
lm.series000
lmFit1.5440.0241.570
lmscFit0.0040.0000.005
loessfit0.5520.0120.577
ma3x30.0000.0000.001
makeContrasts0.0000.0000.001
makeunique0.0000.0000.001
merge0.0080.0000.008
mergeScansRG0.0000.0000.001
modelMatrix0.0040.0000.002
modifyWeights000
nec000
neqc000
normalizeMedianAbsValues000
normalizeRobustSpline0.0040.0000.003
normalizeVSN0.4400.0120.451
normalizeWithinArrays000
normalizebetweenarrays0.0040.0000.003
normalizeprintorder0.0040.0000.003
normexpfit0.0040.0000.001
normexpfitcontrol000
normexpsignal000
plotDensities0.0080.0000.006
plotMDS0.0080.0040.015
plotRLDF0.7120.0080.722
plotma0.0160.0000.013
poolvar0.0000.0000.001
printorder0.0160.0040.017
printtipWeights0.0040.0000.005
propexpr0.0000.0040.000
protectMetachar000
qqt0.0000.0000.002
qualwt000
read.ilmn000
read.maimages000
readImaGeneHeader000
readgal0.0000.0000.001
removeext0.0040.0000.001
roast0.0840.0000.084
romer0.4520.0000.451
selectmodel0.0240.0000.024
squeezeVar0.0000.0000.001
strsplit20.0040.0000.001
subsetting0.0040.0000.005
targetsA2C0.0080.0000.006
topRomer000
toptable0.0000.0000.001
trigammainverse0.0000.0000.001
trimWhiteSpace0.0000.0040.001
uniquegenelist0.0000.0000.001
unwrapdups0.0000.0000.001
venn0.0440.0080.051
volcanoplot000
weightedmedian0.0000.0000.001
zscore000