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Package 25/419HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: annotate
Version: 1.28.1
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.28.1.tar.gz
StartedAt: 2011-04-07 04:38:51 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 04:40:02 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 71.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: annotate.Rcheck
Warnings: NA

Command output

* 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

annotate.Rcheck/00install.out:

* 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)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.3040.0202.322
GO2heatmap0.3120.0040.315
GOmnplot0.1400.0040.146
HTMLPage-class000
LL2homology0.0040.0000.003
PMIDAmat0.2840.0040.359
PWAmat4.7680.0604.832
UniGeneQuery0.0040.0000.001