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Package 230/436HostnameOS / ArchBUILDCHECKBUILD BIN
limma 3.7.24
Gordon Smyth
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma
Last Changed Rev: 53239 / Revision: 53255
Last Changed Date: 2011-02-23 16:23:06 -0800 (Wed, 23 Feb 2011)
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 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: limma
Version: 3.7.24
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings limma_3.7.24.tar.gz
StartedAt: 2011-02-24 20:33:26 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 20:34:49 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 83.6 seconds
RetCode: 0
Status:  OK 
CheckDir: limma.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/limma.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘3.7.24’
* 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 ... 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-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-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
LargeDataObject0.0000.0000.001
PrintLayout000
TestResults0.0000.0000.001
alias2Symbol2.3440.0522.446
arrayWeights0.0040.0000.004
arrayWeightsQuick000
asMatrixWeights000
auROC0.0000.0000.001
avearrays0.0040.0000.002
avereps0.0000.0000.001
backgroundcorrect0.0080.0000.008
blockDiag0.0000.0000.001
cbind0.0080.0000.007
channel2M0.0000.0000.002
classifytests0.0040.0000.003
contrasts.fit0.0320.0080.039
controlStatus0.0080.0000.008
convest2.3760.0082.383
dim0.0040.0000.002
dupcor0.0000.0000.001
ebayes0.0080.0040.010
genas0.0840.0000.083
geneSetTest0.0040.0000.005
getSpacing000
getlayout0.0040.0000.000
heatdiagram0.0000.0040.003
helpMethods000
imageplot0.0320.0000.032
intraspotCorrelation0.0000.0000.001
isfullrank0.0000.0000.001
isnumeric0.0000.0000.001
kooperberg0.0000.0000.001
limmaUsersGuide0.0040.0000.003
lm.series000
lmFit1.4600.0121.473
lmscFit0.0040.0000.005
loessfit0.5240.0000.524
ma3x30.0000.0000.001
makeContrasts0.0000.0000.001
makeunique0.0000.0000.001
merge0.0080.0000.007
mergeScansRG000
modelMatrix0.0000.0040.002
modifyWeights000
nec000
neqc000
normalizeMedianAbsValues0.0000.0000.001
normalizeRobustSpline0.0040.0000.002
normalizeVSN0.4160.0200.437
normalizebetweenarrays0.0000.0000.003
normalizeprintorder000
normexpfit0.0000.0000.002
normexpfitcontrol000
normexpfitdetectionp000
normexpsignal000
plotDensities000
plotMDS0.0280.0000.026
plotRLDF0.6440.0080.657
plotma0.0120.0000.013
poolvar0.0000.0000.001
printorder0.0120.0040.017
printtipWeights000
propexpr000
protectMetachar0.0000.0000.001
qqt0.0000.0000.002
qualwt000
read.ilmn0.0000.0000.001
read.maimages000
readImaGeneHeader000
readgal000
removeext0.0000.0000.001
roast0.0520.0000.052
romer0.4240.0000.425
selectmodel0.0240.0000.024
squeezeVar0.0000.0000.001
strsplit20.0000.0000.001
subsetting0.0040.0000.004
targetsA2C0.0040.0000.006
topRomer000
toptable000
trigammainverse000
trimWhiteSpace000
uniquegenelist000
unwrapdups0.0040.0000.000
venn0.0280.0000.029
volcanoplot0.0000.0000.001
weightedmedian0.0000.0000.001
zscore0.0000.0000.001