limma 2.16.5
Gordon Smyth
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/limma | | Last Changed Rev: 38072 / Revision: 38965 | | Last Changed Date: 2009-03-19 16:00:17 -0700 (Thu, 19 Mar 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/limma.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '2.16.5'
* 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
* creating limma-Ex.R ... OK
* checking examples ... OK
* checking tests ...
Running 'limma-Tests.R'
Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...953,954c953,954
< 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
OK
* checking package vignettes in 'inst/doc' ... OK
* creating limma-manual.tex ... OK
* checking limma-manual.tex using pdflatex ... OK
* Installing *source* package 'limma' ...
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c normexp.c -o normexp.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c normexp.c -o normexp.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'limma'
Formats: text html latex example
01Introduction text html latex
02classes text html latex
03reading text html latex
04Background text html latex
05Normalization text html latex
06linearmodels text html latex
07SingleChannel text html latex
08Tests text html latex
09Diagnostics text html latex
10Other text html latex
LargeDataObject text html latex example
PrintLayout text html latex example
TestResults text html latex example
alias2Symbol text html latex example
anova-method text html latex
arrayWeights text html latex example
arrayWeightsQuick text html latex example
asMatrixWeights text html latex example
asdataframe text html latex
asmalist text html latex
asmatrix text html latex
auROC text html latex example
avedups text html latex
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cbind text html latex example
changelog text html latex
channel2M text html latex example
classifytests text html latex example
contrasts.fit text html latex example
controlStatus text html latex example
convest text html latex example
decideTests text html latex
dim text html latex example
dimnames text html latex
dupcor text html latex example
ebayes text html latex example
exprsMA text html latex
fitfdist text html latex
fitted.MArrayLM text html latex
geneSetTest text html latex example
getEAWP text html latex
getSpacing text html latex example
getlayout text html latex example
gls.series text html latex
gridspotrc text html latex
heatdiagram text html latex example
helpMethods text html latex example
imageplot text html latex example
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intraspotCorrelation text html latex example
isfullrank text html latex example
isnumeric text html latex example
kooperberg text html latex example
limmaUsersGuide text html latex example
lm.series text html latex
lmFit text html latex example
lmscFit text html latex example
loessfit text html latex example
ma3x3 text html latex example
makeContrasts text html latex example
makeunique text html latex example
malist text html latex
marraylm text html latex
mdplot text html latex
merge text html latex example
mergeScansRG text html latex example
modelMatrix text html latex example
modifyWeights text html latex example
mrlm text html latex
normalizeMedianAbsValues text html latex example
normalizeRobustSpline text html latex example
normalizeWithinArrays text html latex example
normalizebetweenarrays text html latex example
normalizeprintorder text html latex example
normalizequantiles text html latex
normexpfit text html latex example
normexpsignal text html latex example
plotDensities text html latex example
plotFB text html latex
plotlines text html latex
plotma text html latex example
plotma3by2 text html latex
plotprinttiploess text html latex
poolvar text html latex example
printHead text html latex
printorder text html latex example
printtipWeights text html latex example
protectMetachar text html latex example
qqt text html latex example
qualwt text html latex example
read.columns text html latex
read.maimages text html latex example
readGPRHeader text html latex
readImaGeneHeader text html latex example
readSpotTypes text html latex
readTargets text html latex
readgal text html latex example
removeBatchEffect text html latex
removeext text html latex example
residuals.MArrayLM text html latex
rglist text html latex
roast text html latex example
selectmodel text html latex example
squeezeVar text html latex example
strsplit2 text html latex example
subsetting text html latex example
summary text html latex
targetsA2C text html latex example
tmixture text html latex
toptable text html latex example
trigammainverse text html latex example
trimWhiteSpace text html latex example
uniquegenelist text html latex example
unwrapdups text html latex example
venn text html latex example
volcanoplot text html latex example
weightedmedian text html latex example
writefit text html latex
zscore text html latex example
** building package indices ...
* DONE (limma)