annotate 1.28.1
Biocore Team c/o BioC user list
| Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/annotate | | Last Changed Rev: 53404 / Revision: 54588 | | Last Changed Date: 2011-03-03 07:28:48 -0800 (Thu, 03 Mar 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | [ ERROR ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/annotate.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.28.1’
* 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 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' calls not declared from:
GO hsahomology humanCHRLOC
* checking data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in ‘annotate-Ex.R’ failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accessionToUID
> ### Title: A function to convert accession values to NCBI UIDs.
> ### Aliases: accessionToUID
> ### Keywords: interface
>
> ### ** Examples
>
>
> ## The two returns from genbank should be the same
> xdoc <- genbank("U03397",type="accession",disp="data")
Read 410 items
Loading required package: XML
Read 645 items
> x <- accessionToUID("U03397",db="genbank")
Read 4 items
> xdoc <- genbank(x, type="uid",disp="data")
Error in genbank(x, type = "uid", disp = "data") :
No Gene ID, cannot proceed
Execution halted
* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (annotate)