Back to the "Multiple platform build/check report"
| Package 17/205 | OS | Arch | BUILD | CHECK | BUILD BIN |
annotate1.11.5Biocore Team | Linux (SUSE 9.2) | x86_64 | OK | [ ERROR ] | |
| Linux (SUSE 9.2) | i686 | OK | ERROR | ||
| Solaris 2.9 | sparc | OK | ERROR | ||
| Linux (SUSE 10.0) | x86_64 | OK | ERROR | ||
| Windows Server 2003 | x86_64 | OK | ERROR | OK | |
| Windows XP | i686 | OK | ERROR | OK | |
| Mac OS X (10.4.6) | i686 | OK | ERROR |
| Package: annotate |
| Version: 1.11.5 |
| Command: /loc/biocbuild/1.9d/R/bin/R CMD check annotate_1.11.5.tar.gz |
| RetCode: 1 |
| Time: 115.2 seconds |
| Status: ERROR |
| CheckDir: annotate.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/annotate.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.11.5'
* 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 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 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 ... WARNING
Undocumented S4 methods:
generic 'KEGG2heatmap' and siglist 'character,eSet,character'
generic 'KEGG2heatmap' and siglist 'character,matrix,character'
generic 'KEGGmnplot' and siglist 'character,eSet,character'
generic 'KEGGmnplot' and siglist 'character,matrix,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating annotate-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'annotate-Ex.R' failed.
The error most likely occurred in:
> ### * getSYMBOL
>
> flush(stderr()); flush(stdout())
>
> ### Name: getSYMBOL
> ### Title: Functions to deal with Data Packages
> ### Aliases: getSYMBOL getGO getGOdesc getPMID getLL lookUp getUniqAnnItem
> ### Keywords: manip
>
> ### ** Examples
>
> data(sample.exprSet.1)
> gN <- geneNames(sample.exprSet.1)[100:105]
> ## A bit of a hack to not have a package dependency on hgu95av2
> ## but need to fiddle w/ the warn level to not fail the example anyways.
> curWarn <- getOption("warn")
> options(warn=0)
> on.exit(options(warn=curWarn), add=TRUE)
NULL
> if( require("hgu95av2", character.only=TRUE)
+ && require("GO", character.only=TRUE) ) {
+ lookUp(gN, "hgu95av2", "SYMBOL")
+ # Same as lookUp for SYMBOL except the return is a vector
+ getSYMBOL(gN,"hgu95av2" )
+ gg<- getGO(gN, "hgu95av2")
+ lookUp(gg[[2]][[1]][["GOID"]], "GO", "TERM")
+ # Same as lookUp for TERM
+ getGOdesc(gg[[2]][[1]][["GOID"]], "ANY")
+ # For BP only
+ getGOdesc(gg[[2]][[1]][["GOID"]], "BP")
+ getLL(gN, "hgu95av2")
+ getPMID(gN, "hgu95av2")
+ } else
+ cat("could not run all examples\n")
Loading required package: hgu95av2
Loading required package: GO
Error in ans[names(ans) == which] : object is not subsettable
Execution halted
annotate.Rcheck/00install.out:
* Installing *source* package 'annotate' ...
** R
** data
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
** help
>>> Building/Updating help pages for package 'annotate'
Formats: text html latex example
ACCNUMStats text html latex example
GO2heatmap text html latex example
GOTerms-class text html latex example
GOmnplot text html latex example
HTMLPage-class text html latex example
LL2homology text html latex example
PMIDAmat text html latex example
PWAmat text html latex example
UniGeneQuery text html latex example
accessionToUID text html latex example
buildChromLocation text html latex example
buildPubMedAbst text html latex example
chromLocation-class text html latex example
compatibleVersions text html latex example
findNeighbors text html latex example
genbank text html latex example
genelocator text html latex example
getPMInfo text html latex example
getSYMBOL text html latex example
getSeq4Acc text html latex example
getTDRows text html latex
hgByChroms text html latex example
hgCLengths text html latex example
hgu95AProbLocs text html latex
hgu95Achroloc text html latex example
hgu95Achrom text html latex example
hgu95All text html latex example
hgu95Asym text html latex example
homoData-class text html latex example
htmlpage text html latex example
installDataPackage text html latex example
locuslinkById text html latex example
locuslinkQuery text html latex example
makeAnchor text html latex example
neighborGeneFinder text html latex example
p2LL text html latex example
pm.abstGrep text html latex example
pm.getabst text html latex example
pm.titles text html latex example
pmAbst2HTML text html latex example
pmid2MIAME text html latex example
pmidQuery text html latex example
probesByLL text html latex example
pubMedAbst-class text html latex example
pubmed text html latex example
readGEOAnn text html latex example
serializeEnv text html latex example
usedChromGenes text html latex example
** building package indices ...
* DONE (annotate)