lumi 1.5.10
Pan Du
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi | | Last Changed Rev: 29097 / Revision: 29143 | | Last Changed Date: 2007-12-07 10:16:44 -0800 (Fri, 07 Dec 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | [ WARNINGS ] | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | WARNINGS | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/lumi.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '1.5.10'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'lumi' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... WARNING
Found the following file(s) with non-portable file names:
inst/doc/Control Probe Profile.txt
These are not fully portable file names
See section 'Package structure' in manual 'Writing R Extensions'.
* 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 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 data for non-ASCII characters ... OK
* creating lumi-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' './lumi.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './lumi.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './lumi.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './lumi_VST_evaluation.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './lumi_VST_evaluation.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './lumi_VST_evaluation.tex' ...
* creating lumi-manual.tex ... OK
* checking lumi-manual.tex ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/lumi.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/lumi.Rcheck
* Installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
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: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: mgcv
This is mgcv 1.3-29
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Creating a new generic function for "pairs" in "lumi"
Creating a new generic function for "plot" in "lumi"
** help
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>>> Building/Updating help pages for package 'lumi'
Formats: text html latex example
LumiBatch-class text html latex example
MAplot-methods text html latex example
addControlData2lumi text html latex example
addNuId2lumi text html latex example
affyExpresso text html latex
affyVstRma text html latex
bgAdjust text html latex example
boxplot-methods text html latex example
density-methods text html latex example
detectOutlier text html latex example
detectionCall text html latex example
estimateLumiCV text html latex example
example.lumi text html latex example
getControlData text html latex example
getControlProbe text html latex example
getControlType text html latex example
hist-methods text html latex example
id2seq text html latex example
inverseVST text html latex example
is.nuID text html latex example
lumi.package text html latex
lumiB text html latex example
lumiExpresso text html latex example
lumiN text html latex example
lumiQ text html latex example
lumiR text html latex example
lumiR.batch text html latex example
lumiT text html latex example
monoSmu text html latex example
monoSpline text html latex example
nuID2probeID text html latex example
nuID2targetID text html latex example
pairs-methods text html latex example
plot-methods text html latex example
plotControlData text html latex example
plotHousekeepingGene text html latex example
plotSampleRelation text html latex example
plotStringencyGene text html latex example
plotVST text html latex example
probeID2nuID text html latex example
rsn text html latex
seq2id text html latex example
ssn text html latex
targetID2nuID text html latex example
vst text html latex example
** building package indices ...
* DONE (lumi)