安装R bioconductor基因组包

时间:2016-09-23 15:35:33

标签: r bioinformatics bioconductor

我一直在尝试使用名为seqplots的工具来分析一些测序数据。该工具通过bioconductor运行,需要安装基因组包。 bioconductor网站提供以下安装说明:

  

要安装此软件包,请启动R并输入:

source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Dmelanogaster.UCSC.dm6")`

如果我在R终端输入此内容,我会得到以下内容:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.4 Revised (2016-03-16
r70336).
Installing package(s) ‘BSgenome.Dmelanogaster.UCSC.dm6’
installing the source package ‘BSgenome.Dmelanogaster.UCSC.dm6’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34147677 bytes (32.6 MB)
downloaded 32.6 MB

'\\icnas4.cc.ic.ac.uk\gaughey'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'BSgenome.Dmelanogaster.UCSC.dm6' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'BSgenome.Dmelanogaster.UCSC.dm6'
Error: loading failed
Execution halted
*** arch - x64
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'BSgenome.Dmelanogaster.UCSC.dm6'
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\icnas4.cc.ic.ac.uk/gaughey/R/win-library/3.2/BSgenome.Dmelanogaster.UCSC.dm6'

The downloaded source packages are in
    ‘C:\Users\gaughey\AppData\Local\Temp\Rtmpcdmz8E\downloaded_packages’`

我已经尝试安装其他类似结果的基因组,并且不知道如何解决这个问题。 有人能帮忙吗?很有可能我忽略了一些简单的事情 - 我是R的完全新手(或任何编程)。我非常感谢任何帮助。

谢谢, 加布里埃尔

2 个答案:

答案 0 :(得分:1)

Seens就像hereherehere所描述的问题一样。

我没有在Windows机器中使用R的经验,但希望它可以提供帮助。

答案 1 :(得分:0)

我建议您在尝试biocLite("BSgenome")之前尝试运行library(BSgenome)biocLite(pkgs = "BSgenome.Hsapiens.NCBI.GRCh38", dependencies = TRUE)(它存储给定生物体的完整基因组序列)。