无法安装bioconductor的GenomicFeatures包："Error in setGeneric“

Question

我在安装GenomicFeatures (R中的一个bioconductor包)时遇到了问题，但我尝试安装的所有其他Bioconductor包都工作正常。GenomicFeatures的错误是：

Error in setGeneric(f, where = where) :
must supply a function skeleton for ‘cols’, explicitly or via an existing 
function Error : unable to load R code in package ‘GenomicFeatures’

我在谷歌上搜索了这个错误，发现只有两三个链接(与其他R包相关)，通常问题是由于安装了旧的R，但我有一个相当新的。

我有R 3.0.0和biocond.v 2.13

在另一台安装了R.3.0.0和biiccond.v2.12的计算机上，它安装正常。

为了找出GF安装失败的原因，我将非常感谢任何提示或指示下一步要尝试什么。

我的环境、安装命令和sessionInfo：

$ R

R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.11.1), ?biocLite for help
> biocLite("GenomicFeatures")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.11.1), R version 3.0.0.
Installing package(s) 'GenomicFeatures'
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GenomicFeatures_1.13.8.tar.gz'
Content type 'application/x-gzip' length 752535 bytes (734 Kb)
opened URL
==================================================
downloaded 734 Kb

* installing *source* package âGenomicFeaturesâ ...
** R
** inst
** preparing package for lazy loading
Error in setGeneric(f, where = where) :
  must supply a function skeleton for âcolsâ, explicitly or via an existing function
Error : unable to load R code in package âGenomicFeaturesâ
ERROR: lazy loading failed for package âGenomicFeaturesâ
* removing â/scratch_local/ugdg_software/lib/R/library/GenomicFeaturesâ
* restoring previous â/scratch_local/ugdg_software/lib/R/library/GenomicFeaturesâ


> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8   
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8  
 [7] LC_PAPER=C                 LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

正如Martin所说，今天发布的新版本(2013-06-02)修复了这个问题。

Answer 1

看起来你使用的是'devel‘版本的Bioconductor (目前，来自上面输出的Bioconductor版本2.13 )，而你正被前沿的变化所困扰。GenomicFeatures包有几天的not built successfully，可通过biocLite获得的版本不能与其他可用包一起正常工作。我相信GenomicFeatures将在今晚成功构建，这将在西雅图时间6月2日(星期日)上午10点左右提供。

这个问题的正确位置是Bioconductor或Bioc-devel mailing list