affycoretools 1.11.2
James W. MacDonald
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affycoretools | | Last Changed Rev: 28320 / Revision: 29143 | | Last Changed Date: 2007-10-30 14:03:22 -0700 (Tue, 30 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | [ OK ] | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/affycoretools.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.11.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affycoretools' 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
* creating affycoretools-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affycoretools_biomaRt.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affycoretools_biomaRt.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affycoretools.tex' ...
Package natbib Warning: Citation `dsc:Rossini:2001' on page 1 undefined on inpu
Package natbib Warning: Citation `ESS' on page 1 undefined on input line 55.
Package natbib Warning: Citation `Leisch:2002' on page 1 undefined on input lin
Package natbib Warning: Citation `Benjamini:1995' on page 12 undefined on input
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affycoretools.tex' ...
Package natbib Warning: Citation `dsc:Rossini:2001' on page 1 undefined on inpu
Package natbib Warning: Citation `ESS' on page 1 undefined on input line 55.
Package natbib Warning: Citation `Leisch:2002' on page 1 undefined on input lin
Package natbib Warning: Citation `Benjamini:1995' on page 12 undefined on input
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './affycoretools.tex' ...
* creating affycoretools-manual.tex ... OK
* checking affycoretools-manual.tex ... OK
/loc/home/biocbuild/bbs-2.2-bioc/meat/affycoretools.Rcheck
* Installing *source* package 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: GOstats
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: xtable
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: biomaRt
Loading required package: RCurl
Attaching package: 'biomaRt'
The following object(s) are masked from package:annotate :
getGO
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: annaffy
Loading required package: KEGG
** help
>>> Building/Updating help pages for package 'affycoretools'
Formats: text html latex example
affystart text html latex
annBM text html latex example
convert.back text html latex
extractStats text html latex
foldFilt text html latex
foldFiltBM text html latex
getCols text html latex
getIndex text html latex
getOrder text html latex
getUniqueLL text html latex
getans text html latex
houtSig text html latex
hyperG2annaffy text html latex
hyperGoutput text html latex
intNames text html latex
limma2annaffy text html latex
limma2biomaRt text html latex
make.cl text html latex
makeFCList text html latex
makeIndices text html latex
pca.legend text html latex
plotDeg text html latex example
plotMA text html latex
plotPCA text html latex
probes2table text html latex
probes2tableBM text html latex
tableFilt text html latex
vennCounts2 text html latex example
vennSelect text html latex
vennSelectBM text html latex
vennSelectFC text html latex
** building package indices ...
* DONE (affycoretools)