limma 2.18.3
Gordon Smyth
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/limma | | Last Changed Rev: 41423 / Revision: 42512 | | Last Changed Date: 2009-08-31 01:36:40 -0700 (Mon, 31 Aug 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/limma.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '2.18.3'
* 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'removeBatchEffect':
removeBatchEffect
Code: function(x, batch, design = matrix(1, ncol(x), 1))
Docs: function(x, batch, design = NULL)
Mismatches in argument default values:
Name: 'design' Code: matrix(1, ncol(x), 1) Docs: NULL
* 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
* checking examples ... OK
* checking tests ...
Running 'limma-Tests.R'
Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...968,969c968,969
< 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
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.4-bioc/meat/limma.Rcheck/00check.log
for details
* Installing *source* package 'limma' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -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-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> 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
EList 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
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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
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helpMethods text html latex example
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kooperberg text html latex example
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lmFit text html latex example
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loessfit text html latex example
ma3x3 text html latex example
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mdplot text html latex
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normalizeWithinArrays text html latex example
normalizebetweenarrays text html latex example
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readTargets text html latex
readgal text html latex example
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removeext text html latex example
residuals.MArrayLM text html latex
rglist text html latex
roast text html latex example
romer text html latex example
selectmodel text html latex example
squeezeVar text html latex example
strsplit2 text html latex example
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summary text html latex
symbols2indices 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)