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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 122/247HostnameOSArchBUILDCHECKBUILD BIN

limma

2.11.10

Gordon Smyth
Last Changed Date: 2007-08-17 01:48:31 -0700
Last Changed Rev: 26473
lamb1 Linux (SUSE 10.1) x86_64  OK [ WARNINGS ]
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) x64  OK  WARNINGS  OK 
pitt Mac OS X (10.4.10) i386  OK  WARNINGS  OK 
Package: limma
Version: 2.11.10
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check limma_2.11.10.tar.gz
RetCode: 0
Time: 133.9 seconds
Status: WARNINGS
CheckDir: limma.Rcheck
Warnings: 3

Command output

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/limma.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '2.11.10'
* 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 ... WARNING
Rd files with unknown encoding:
  ebayes.Rd

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'subsetting' but not in code:
  [

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'subsetting':
  [

Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* creating limma-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/home/biocbuild/bbs-2.1-bioc/meat/limma.Rcheck/tests'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...908,909c908,909
< 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
make[1]: Leaving directory `/home/biocbuild/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

WARNING: There were 3 warnings, see
  /home/biocbuild/bbs-2.1-bioc/meat/limma.Rcheck/00check.log
for details

limma.Rcheck/00install.out:

* Installing *source* package 'limma' ...
** R
** inst
** preparing package for lazy loading
** help
 >>> 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
  LargeDataObject                   text    html    latex   example
  PrintLayout                       text    html    latex   example
  TestResults                       text    html    latex   example
  anova-method                      text    html    latex
  arrayWeights                      text    html    latex   example
  arrayWeightsQuick                 text    html    latex   example
  asMatrixWeights                   text    html    latex   example
  asdataframe                       text    html    latex
  asmalist                          text    html    latex
  asmatrix                          text    html    latex
  auROC                             text    html    latex   example
  avedups                           text    html    latex
  backgroundcorrect                 text    html    latex   example
  blockDiag                         text    html    latex   example
  bwss                              text    html    latex
  bwss.matrix                       text    html    latex
  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
  dnormexp                          text    html    latex
  dupcor                            text    html    latex   example
  ebayes                            text    html    latex   example
  exprsMA                           text    html    latex
  exprset2                          text    html    latex
  fitfdist                          text    html    latex
  fitted.MArrayLM                   text    html    latex
  geneSetTest                       text    html    latex   example
  getSpacing                        text    html    latex   example
  getlayout                         text    html    latex   example
  gls.series                        text    html    latex
  gridspotrc                        text    html    latex
  heatdiagram                       text    html    latex   example
  helpMethods                       text    html    latex   example
  imageplot                         text    html    latex   example
  imageplot3by2                     text    html    latex
  intraspotCorrelation              text    html    latex   example
  isfullrank                        text    html    latex   example
  isnumeric                         text    html    latex   example
  kooperberg                        text    html    latex   example
  limmaUsersGuide                   text    html    latex   example
  lm.series                         text    html    latex
  lmFit                             text    html    latex   example
  lmscFit                           text    html    latex   example
  loessfit                          text    html    latex   example
  m.spot                            text    html    latex
  ma3x3                             text    html    latex   example
  makeContrasts                     text    html    latex   example
  makeunique                        text    html    latex   example
  malist                            text    html    latex
  marraylm                          text    html    latex
  mdplot                            text    html    latex
  merge                             text    html    latex   example
  mergeScansRG                      text    html    latex   example
  modelMatrix                       text    html    latex   example
  modifyWeights                     text    html    latex   example
  mrlm                              text    html    latex
  normalizeMedianAbsValues          text    html    latex   example
  normalizeRobustSpline             text    html    latex   example
  normalizeWithinArrays             text    html    latex   example
  normalizebetweenarrays            text    html    latex   example
  normalizeprintorder               text    html    latex   example
  normalizequantiles                text    html    latex
  normexp                           text    html    latex
  normexpfit                        text    html    latex   example
  normexpsignal                     text    html    latex   example
  plotDensities                     text    html    latex   example
  plotFB                            text    html    latex
  plotlines                         text    html    latex
  plotma                            text    html    latex   example
  plotma3by2                        text    html    latex
  plotprinttiploess                 text    html    latex
  poolvar                           text    html    latex   example
  printHead                         text    html    latex
  printorder                        text    html    latex   example
  printtipWeights                   text    html    latex   example
  protectMetachar                   text    html    latex   example
  qqt                               text    html    latex   example
  qualwt                            text    html    latex   example
  read.columns                      text    html    latex
  read.maimages                     text    html    latex   example
  read.matrix                       text    html    latex
  read.series                       text    html    latex
  readGPRHeader                     text    html    latex
  readImaGeneHeader                 text    html    latex   example
  readSpotTypes                     text    html    latex
  readTargets                       text    html    latex
  readgal                           text    html    latex   example
  removeext                         text    html    latex   example
  residuals.MArrayLM                text    html    latex
  rg.genepix                        text    html    latex
  rg.quantarray                     text    html    latex
  rg.series.spot                    text    html    latex
  rg.spot                           text    html    latex
  rglist                            text    html    latex
  splitName                         text    html    latex
  squeezeVar                        text    html    latex   example
  strsplit2                         text    html    latex   example
  subsetting                        text    html    latex   example
  summary                           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)