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Package 113/233HostnameOS / ArchBUILDCHECKBUILD BIN
limma 2.12.0
Gordon Smyth
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/limma
Last Changed Rev: 30676 / Revision: 30966
Last Changed Date: 2008-03-25 17:47:32 -0700 (Tue, 25 Mar 2008)
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 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: limma
Version: 2.12.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check limma_2.12.0.tar.gz
StartedAt: 2008-04-09 19:59:30 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 20:06:03 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 392.4 seconds
RetCode: 0
Status: OK
CheckDir: limma.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/limma.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '2.12.0'
* 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 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 limma-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/limma.Rcheck/tests'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...OK
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/limma.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating limma-manual.tex ... OK
* checking limma-manual.tex ... OK

limma.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/limma.Rcheck


---------- Making package limma ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  preparing package limma for lazy loading
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'limma'
     Formats: text html latex example chm 
  01Introduction                    text    html    latex           chm
  02classes                         text    html    latex           chm
  03reading                         text    html    latex           chm
  04Background                      text    html    latex           chm
  05Normalization                   text    html    latex           chm
  06linearmodels                    text    html    latex           chm
  07SingleChannel                   text    html    latex           chm
  08Tests                           text    html    latex           chm
  09Diagnostics                     text    html    latex           chm
  10Other                           text    html    latex           chm
  LargeDataObject                   text    html    latex   example chm
  PrintLayout                       text    html    latex   example chm
  TestResults                       text    html    latex   example chm
  anova-method                      text    html    latex           chm
  arrayWeights                      text    html    latex   example chm
  arrayWeightsQuick                 text    html    latex   example chm
  asMatrixWeights                   text    html    latex   example chm
  asdataframe                       text    html    latex           chm
  asmalist                          text    html    latex           chm
  asmatrix                          text    html    latex           chm
  auROC                             text    html    latex   example chm
  avedups                           text    html    latex           chm
  backgroundcorrect                 text    html    latex   example chm
  blockDiag                         text    html    latex   example chm
  bwss                              text    html    latex           chm
  bwss.matrix                       text    html    latex           chm
  cbind                             text    html    latex   example chm
  changelog                         text    html    latex           chm
  channel2M                         text    html    latex   example chm
  classifytests                     text    html    latex   example chm
  contrasts.fit                     text    html    latex   example chm
  controlStatus                     text    html    latex   example chm
  convest                           text    html    latex   example chm
  decideTests                       text    html    latex           chm
  dim                               text    html    latex   example chm
  dimnames                          text    html    latex           chm
  dnormexp                          text    html    latex           chm
  dupcor                            text    html    latex   example chm
  ebayes                            text    html    latex   example chm
  exprsMA                           text    html    latex           chm
  exprset2                          text    html    latex           chm
  fitfdist                          text    html    latex           chm
  fitted.MArrayLM                   text    html    latex           chm
  geneSetTest                       text    html    latex   example chm
  getSpacing                        text    html    latex   example chm
  getlayout                         text    html    latex   example chm
  gls.series                        text    html    latex           chm
  gridspotrc                        text    html    latex           chm
  heatdiagram                       text    html    latex   example chm
  helpMethods                       text    html    latex   example chm
  imageplot                         text    html    latex   example chm
  imageplot3by2                     text    html    latex           chm
  intraspotCorrelation              text    html    latex   example chm
  isfullrank                        text    html    latex   example chm
  isnumeric                         text    html    latex   example chm
  kooperberg                        text    html    latex   example chm
  limmaUsersGuide                   text    html    latex   example chm
  lm.series                         text    html    latex           chm
  lmFit                             text    html    latex   example chm
  lmscFit                           text    html    latex   example chm
  loessfit                          text    html    latex   example chm
  m.spot                            text    html    latex           chm
  ma3x3                             text    html    latex   example chm
  makeContrasts                     text    html    latex   example chm
  makeunique                        text    html    latex   example chm
  malist                            text    html    latex           chm
  marraylm                          text    html    latex           chm
  mdplot                            text    html    latex           chm
  merge                             text    html    latex   example chm
  mergeScansRG                      text    html    latex   example chm
  modelMatrix                       text    html    latex   example chm
  modifyWeights                     text    html    latex   example chm
  mrlm                              text    html    latex           chm
  normalizeMedianAbsValues          text    html    latex   example chm
  normalizeRobustSpline             text    html    latex   example chm
  normalizeWithinArrays             text    html    latex   example chm
  normalizebetweenarrays            text    html    latex   example chm
  normalizeprintorder               text    html    latex   example chm
  normalizequantiles                text    html    latex           chm
  normexp                           text    html    latex           chm
  normexpfit                        text    html    latex   example chm
  normexpsignal                     text    html    latex   example chm
  plotDensities                     text    html    latex   example chm
  plotFB                            text    html    latex           chm
  plotlines                         text    html    latex           chm
  plotma                            text    html    latex   example chm
  plotma3by2                        text    html    latex           chm
  plotprinttiploess                 text    html    latex           chm
  poolvar                           text    html    latex   example chm
  printHead                         text    html    latex           chm
  printorder                        text    html    latex   example chm
  printtipWeights                   text    html    latex   example chm
  protectMetachar                   text    html    latex   example chm
  qqt                               text    html    latex   example chm
  qualwt                            text    html    latex   example chm
  read.columns                      text    html    latex           chm
  read.maimages                     text    html    latex   example chm
  read.matrix                       text    html    latex           chm
  read.series                       text    html    latex           chm
  readGPRHeader                     text    html    latex           chm
  readImaGeneHeader                 text    html    latex   example chm
  readSpotTypes                     text    html    latex           chm
  readTargets                       text    html    latex           chm
  readgal                           text    html    latex   example chm
  removeext                         text    html    latex   example chm
  residuals.MArrayLM                text    html    latex           chm
  rg.genepix                        text    html    latex           chm
  rg.quantarray                     text    html    latex           chm
  rg.series.spot                    text    html    latex           chm
  rg.spot                           text    html    latex           chm
  rglist                            text    html    latex           chm
  splitName                         text    html    latex           chm
  squeezeVar                        text    html    latex   example chm
  strsplit2                         text    html    latex   example chm
  subsetting                        text    html    latex   example chm
  summary                           text    html    latex           chm
  targetsA2C                        text    html    latex   example chm
  tmixture                          text    html    latex           chm
  toptable                          text    html    latex   example chm
  trigammainverse                   text    html    latex   example chm
  trimWhiteSpace                    text    html    latex   example chm
  uniquegenelist                    text    html    latex   example chm
  unwrapdups                        text    html    latex   example chm
  venn                              text    html    latex   example chm
  volcanoplot                       text    html    latex   example chm
  weightedmedian                    text    html    latex   example chm
  writefit                          text    html    latex           chm
  zscore                            text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\limma.Rcheck\00_pkg_src\limma\chm\limma.chm

HHC4016: Warning: Cannot open "GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".


The following files were not compiled:
  adding MD5 sums

* DONE (limma)