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Package 123/251HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: lumi
Version: 1.5.10
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check lumi_1.5.10.tar.gz
StartedAt: 2007-12-11 03:58:24 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 04:01:43 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 198.4 seconds
RetCode: 0
Status: WARNINGS
CheckDir: lumi.Rcheck
Warnings: 1

Command output

* 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

lumi.Rcheck/00install.out:

/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
Note: removing empty section \references
Note: removing empty section \references
Note: removing empty section \examples
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Note: removing empty section \details
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Note: removing empty section \references
Note: removing empty section \seealso
Note: removing empty section \examples
Note: removing empty section \note
Note: removing empty section \references
Note: removing empty section \references
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \references
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Note: removing empty section \references
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Note: removing empty section \references
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \note
Note: removing empty section \references
Note: removing empty section \examples
Note: removing empty section \references
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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)