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我在安装 GenomicFeatures(R 中的一个 bioconductor 包)时遇到问题,但我尝试安装的所有其他 Bioconductor 包都可以正常工作。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’

我搜索了这个错误,发现只有两个或三个链接(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

在另一台装有 R.3.0.0 和 biocond.v 2.12 的计算机上,它安装正常。

我将不胜感激任何提示或指示下一步要尝试什么,以找出 GF 安装失败的原因。

我的环境和安装命令和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

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

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1 回答 1

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Looks like you're using the 'devel' version of Bioconductor (currently, Bioconductor version 2.13, from the output above), and you're being bitten by leading edge changes. The GenomicFeatures package has not built successfully for a couple of days, and the version available via biocLite is not working correctly with other available packages. I believe that GenomicFeatures will build successfully tonight, and that will be available after about 10am Seattle time Sunday, June 2.

The right place for this is question is the Bioconductor or Bioc-devel mailing list

于 2013-06-02T02:48:13.753 回答