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Package 22/294HostnameOS / ArchBUILDCHECKBUILD BIN
annotate 1.20.1
Biocore Team c/o BioC user list
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/annotate
Last Changed Rev: 35158 / Revision: 38965
Last Changed Date: 2008-11-07 18:27:36 -0800 (Fri, 07 Nov 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: annotate
Version: 1.20.1
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes annotate_1.20.1.tar.gz
StartedAt: 2009-04-18 18:02:58 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:05:00 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 122.0 seconds
RetCode: 0
Status: OK
CheckDir: annotate.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/annotate.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.20.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'annotate' 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
* checking data for non-ASCII characters ... OK
* creating annotate-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating annotate-manual.tex ... OK
* checking annotate-manual.tex using pdflatex ... OK

annotate.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/annotate.Rcheck


---------- Making package annotate ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing data files
  preparing package annotate 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: AnnotationDbi
Loading required package: xtable
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'annotate'
     Formats: text html latex example chm 
Note: removing empty section \value in file 'ACCNUMStats.Rd'
Note: removing empty section \value in file 'ACCNUMStats.Rd'
  ACCNUMStats                       text    html    latex   example chm
  GO2heatmap                        text    html    latex   example chm
  GOmnplot                          text    html    latex   example chm
  HTMLPage-class                    text    html    latex   example chm
  LL2homology                       text    html    latex   example chm
  PMIDAmat                          text    html    latex   example chm
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Note: removing empty section \seealso in file 'UniGeneQuery.Rd'
Note: removing empty section \seealso in file 'UniGeneQuery.Rd'
  UniGeneQuery                      text    html    latex   example chm
  accessionToUID                    text    html    latex   example chm
  annPkgName                        text    html    latex   example chm
  aqListGOIDs                       text    html    latex   example chm
  buildChromLocation                text    html    latex   example chm
  buildPubMedAbst                   text    html    latex   example chm
  chrCats                           text    html    latex   example chm
  chromLocation-class               text    html    latex   example chm
  compatibleVersions                text    html    latex   example chm
  dropECode                         text    html    latex   example chm
Note: removing empty section \seealso in file 'entrezGeneByID.Rd'
Note: removing empty section \seealso in file 'entrezGeneByID.Rd'
  entrezGeneByID                    text    html    latex   example chm
Note: removing empty section \seealso in file 'entrezGeneQuery.Rd'
Note: removing empty section \seealso in file 'entrezGeneQuery.Rd'
  entrezGeneQuery                   text    html    latex   example chm
  filterGOByOntology                text    html    latex   example chm
  findNeighbors                     text    html    latex   example chm
  genbank                           text    html    latex   example chm
Note: removing empty section \details in file 'genelocator.Rd'
Note: removing empty section \note in file 'genelocator.Rd'
Note: removing empty section \details in file 'genelocator.Rd'
Note: removing empty section \note in file 'genelocator.Rd'
  genelocator                       text    html    latex   example chm
  getAnnMap                         text    html    latex   example chm
Note: removing empty section \details in file 'getEvidence.Rd'
Note: removing empty section \details in file 'getEvidence.Rd'
  getEvidence                       text    html    latex   example chm
  getGOTerm                         text    html    latex   example chm
  getOntology                       text    html    latex   example chm
Note: removing empty section \references in file 'getPMInfo.Rd'
Note: removing empty section \seealso in file 'getPMInfo.Rd'
Note: removing empty section \references in file 'getPMInfo.Rd'
Note: removing empty section \seealso in file 'getPMInfo.Rd'
  getPMInfo                         text    html    latex   example chm
  getSYMBOL                         text    html    latex   example chm
  getSeq4Acc                        text    html    latex   example chm
  getTDRows                         text    html    latex           chm
  hasGOannote                       text    html    latex   example chm
  hgByChroms                        text    html    latex   example chm
  hgCLengths                        text    html    latex   example chm
  hgu95AProbLocs                    text    html    latex           chm
  hgu95Achroloc                     text    html    latex   example chm
  hgu95Achrom                       text    html    latex   example chm
  hgu95All                          text    html    latex   example chm
  hgu95Asym                         text    html    latex   example chm
  homoData-class                    text    html    latex   example chm
  htmlpage                          text    html    latex   example chm
  isValidkey                        text    html    latex   example chm
  makeAnchor                        text    html    latex   example chm
  mapOrgs                           text    html    latex           chm
  neighborGeneFinder                text    html    latex   example chm
  p2LL                              text    html    latex   example chm
  pm.abstGrep                       text    html    latex   example chm
  pm.getabst                        text    html    latex   example chm
  pm.titles                         text    html    latex   example chm
  pmAbst2HTML                       text    html    latex   example chm
  pmid2MIAME                        text    html    latex   example chm
  pmidQuery                         text    html    latex   example chm
  probesByLL                        text    html    latex   example chm
  pubMedAbst-class                  text    html    latex   example chm
  pubmed                            text    html    latex   example chm
  readGEOAnn                        text    html    latex   example chm
  serializeEnv                      text    html    latex   example chm
  updateSymbolsToValidKeys          text    html    latex   example chm
  usedChromGenes                    text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\annotate.Rcheck\00_pkg_src\annotate\chm\annotate.chm


Compile time: 0 minutes, 1 second
60	Topics
290	Local links
7	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-bioc\meat\annotate.Rcheck\00_pkg_src\annotate\chm\annotate.chm, 93,949 bytes
Compression decreased file by 136,759 bytes.
  adding MD5 sums

* DONE (annotate)