Back to the "Multiple platform build/check report"

NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
Package 17/238HostnameOSArchBUILDCHECKBUILD BIN

annotate

1.15.2

Biocore Team
Last Changed Date: 2007-06-09 10:46:20 -0700
Last Changed Rev: 25295
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
churchill Solaris 2.9 sparc  ERROR skipped
lemming Windows Server 2003 (32-bit) x64  OK [ OK ]skipped
Package: annotate
Version: 1.15.2
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check annotate_1.15.2.tar.gz
RetCode: 0
Time: 461.0 seconds
Status: OK
CheckDir: annotate.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/annotate.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.15.2'
* 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 ... NOTE
.handleXML: no visible global function definition for 'xmlTreeParse'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
buildPubMedAbst: no visible global function definition for
  'xmlChildren'
getGOChildren: no visible binding for global variable 'GOMFCHILDREN'
getGOChildren: no visible binding for global variable 'GOBPCHILDREN'
getGOChildren: no visible binding for global variable 'GOCCCHILDREN'
getGOOntology: no visible binding for global variable 'GOTERM'
getGOParents: no visible binding for global variable 'GOMFPARENTS'
getGOParents: no visible binding for global variable 'GOBPPARENTS'
getGOParents: no visible binding for global variable 'GOCCPARENTS'
getGOTerm: no visible binding for global variable 'GOTERM'
getPMInfo : tagVals : tagNames : add: no visible global function
  definition for 'xmlName'
getPMInfo : tagVals : tagNames : add: no visible global function
  definition for 'xmlValue'
getPMInfo : tagVals: no visible global function definition for
  'xmlDOMApply'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlChildren'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlName'
getPMInfo : arts : add: no visible global function definition for
  'xmlValue'
getPMInfo: no visible global function definition for 'xmlDOMApply'
getPMInfo: no visible global function definition for 'xmlRoot'
homoData: no visible global function definition for 'mapOrgs'
neighborGeneFinder : elementSelected: no visible global function
  definition for 'tkselection.clear'
neighborGeneFinder : elementSelected: no visible global function
  definition for 'tksize'
neighborGeneFinder : elementSelected: no visible global function
  definition for 'tkselection.set'
neighborGeneFinder : elementSelected: no visible global function
  definition for 'tkcurselection'
neighborGeneFinder : bindLists: no visible global function definition
  for 'tkbind'
neighborGeneFinder : upDateNames: no visible global function definition
  for 'writeList'
neighborGeneFinder : end: no visible global function definition for
  'tkdestroy'
neighborGeneFinder : collect: no visible global function definition for
  'tclvalue'
neighborGeneFinder : collect: no visible global function definition for
  'tkget'
neighborGeneFinder : collect: no visible global function definition for
  'tkcurselection'
neighborGeneFinder : collect: no visible global function definition for
  'tkconfigure'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkdelete'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkdelete'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tclvalue'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkget'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkcurselection'
neighborGeneFinder : findUDGenes: no visible binding for global
  variable 'humanLLMappingsUG2LL'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkmessageBox'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tclvalue'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tclvalue'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'writeList'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'writeList'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkconfigure'
neighborGeneFinder : findUDGenes: no visible global function definition
  for 'tkconfigure'
neighborGeneFinder: no visible global function definition for
  'tktoplevel'
neighborGeneFinder: no visible global function definition for
  'tkdestroy'
neighborGeneFinder: no visible global function definition for
  'tktitle<-'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tklabel'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for
  'oneVScrList'
neighborGeneFinder: no visible global function definition for
  'tkconfigure'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tklabel'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tclVar'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkentry'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tklabel'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for
  'makeViewer'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for 'tclVar'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkentry'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tklabel'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for
  'makeViewer'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkframe'
neighborGeneFinder: no visible global function definition for
  'tkbutton'
neighborGeneFinder: no visible global function definition for
  'tkbutton'
neighborGeneFinder: no visible global function definition for 'tkgrid'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for
  'tkbutton'
neighborGeneFinder: no visible global function definition for 'tkpack'
neighborGeneFinder: no visible global function definition for
  'tkwait.window'
pm.getabst: no visible global function definition for 'xmlRoot'
pm.getabst: no visible global function definition for 'xmlChildren'
pmid2MIAME: no visible global function definition for 'xmlRoot'
pmid2MIAME: no visible global function definition for 'xmlChildren'
pmid2MIAME: no visible global function definition for 'xmlChildren'
pmid2MIAME: no visible global function definition for 'xmlChildren'
pmid2MIAME: no visible global function definition for 'xmlValue'
pmid2MIAME: no visible global function definition for 'xmlValue'
pmid2MIAME: no visible global function definition for 'xmlChildren'
pmid2MIAME: no visible global function definition for 'xmlValue'
pmid2MIAME: no visible global function definition for 'xmlValue'
pmid2MIAME: no visible global function definition for 'xmlValue'
pmid2MIAME: no visible global function definition for 'xmlChildren'
pmid2MIAME: no visible global function definition for 'xmlValue'
pmid2MIAME: no visible global function definition for 'xmlChildren'
* 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 ... OK

annotate.Rcheck/00install.out:

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


---------- Making package annotate ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R 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: DBI
Loading required package: RSQLite
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
Note: unmatched right brace in 'dropECode' on or after line 44
Note: unmatched right brace in 'dropECode.Rd' on or after line 44
Note: unmatched right brace in 'getEvidence' on or after line 32
Note: unmatched right brace in 'getEvidence.Rd' on or after line 32
Note: unmatched right brace in 'getOntology' on or after line 38
Note: unmatched right brace in 'getOntology.Rd' on or after line 38
 >>> Building/Updating help pages for package 'annotate'
     Formats: text html latex example chm 
  ACCNUMStats                       text    html    latex   example chm
  GO2heatmap                        text    html    latex   example chm
  GOTerms-class                     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
  PWAmat                            text    html    latex   example chm
  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
  filterGOByOntology                text    html    latex   example chm
  findNeighbors                     text    html    latex   example chm
  genbank                           text    html    latex   example chm
  genelocator                       text    html    latex   example chm
  getAnnMap                         text    html    latex   example chm
  getEvidence                       text    html    latex   example chm
  getGOTerm                         text    html    latex   example chm
  getOntology                       text    html    latex   example chm
  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
  installDataPackage                text    html    latex   example chm
  locuslinkById                     text    html    latex   example chm
  locuslinkQuery                    text    html    latex   example chm
  makeAnchor                        text    html    latex   example 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
  usedChromGenes                    text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

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


Compile time: 0 minutes, 0 seconds
59	Topics
304	Local links
7	Internet links
1	Graphic


Created d:\biocbld\bbs-2.1-bioc\meat\annotate.Rcheck\00_pkg_src\annotate\chm\annotate.chm, 93,043 bytes
Compression decreased file by 138,640 bytes.
  adding MD5 sums

* DONE (annotate)