Package: AnnotationFuncs

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AnnotationFuncs_1.1.2.tar.gz

StartedAt: 2011-05-09 13:04:35 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:05:20 -0700 (Mon, 09 May 2011)

EllapsedTime: 45.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: AnnotationFuncs.Rcheck

Warnings: NA

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/AnnotationFuncs.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationFuncs/DESCRIPTION’ ... OK
* this is package ‘AnnotationFuncs’ version ‘1.1.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘AnnotationFuncs’ can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object ‘/Users/biocbuild/bbs-2.9-bioc/meat/AnnotationFuncs.Rcheck/00_pkg_src/AnnotationFuncs/man/getOrthologs.Rd’:
  ‘‘getTableName’’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getOrthologs’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'getHomolog' but not in code:
  getHomolog

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'getHomolog'
  ‘threshold’ ‘from’ ‘to’
Documented arguments not in \usage in documentation object 'getHomolog':
  ‘thershold’ ‘pre.from’ ‘pre.to’ ‘post.from’ ‘post.to’

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 the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ call not declared from: ‘org.Hs.eg.db’
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘AnnotationFuncs-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getHomolog
> ### Title: Performs quicker lookup in homologe data packages...
> ### Aliases: getHomolog
> 
> ### ** Examples
> library(hom.Hs.inp.db)
Loading required package: DBI

> library(org.Hs.eg.db)

> library(org.Bt.eg.db)
> getHomolog("ENSBTAP00000024572", revmap(hom.Hs.inpBOSTA), 'BOSTA') 
Error: could not find function "getHomolog"
Execution halted

* installing *source* package ‘AnnotationFuncs’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘AnnotationFuncsUserguide.Rnw’ 
** testing if installed package can be loaded

* DONE (AnnotationFuncs)

name	user	system	elapsed
AnnotationFuncs-package	0.745	0.070	0.948
getEvidenceCodes	0.002	0.001	0.001