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[other] 安装DESeq2包求助

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发表于 2017-9-7 11:26:21 | 显示全部楼层 |阅读模式
本帖最后由 蚊子 于 2017-9-7 11:28 编辑

在做转录组7-差异表达分析的时候,在Ubuntu系统上安装了最新的RStudio,R是用$ sudo apt-get install r-base安装的,版本是3.4.1。
接着使用一下命令安装DESeq2:
source("http://bioconductor.org/biocLite.R")
biocLite('DESeq2', dependencies=T)
报错如下:
[AppleScript] 纯文本查看 复制代码
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/XML’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/GenomeInfoDb’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/hjd/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’

The downloaded source packages are in
	‘/tmp/RtmpYkflva/downloaded_packages’
installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, Matrix, mgcv, rpart, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

搜索报错原因,有人提到R版本不对,然后尝试了3.3.2等其他版本,结果还是报错啊。
不知有没有人遇到类似的问题呢?
求帮助



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发表于 2017-9-7 12:25:20 | 显示全部楼层
ERROR: configuration failed for package ‘XML’ 这句话论坛有人说过ubuntu等linux系统安装xml和RCurl包缺少关键文件
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 楼主| 发表于 2017-9-7 17:28:33 | 显示全部楼层
bioinfotrainee 发表于 2017-9-7 12:25
ERROR: configuration failed for package ‘XML’ 这句话论坛有人说过ubuntu等linux系统安装xml和RCurl包 ...

按照文中方法,居然可以了,谢谢
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发表于 2017-9-7 23:36:39 | 显示全部楼层
蚊子 发表于 2017-9-7 17:28
按照文中方法,居然可以了,谢谢

不客气,我是技能树的创始人,就是为了帮助你们的
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发表于 2017-9-9 14:25:01 | 显示全部楼层
你通过apt get 安装的r不是最新版本  好像是3.2版本  最新版本需要自己去编译 自己编译的后就会提示缺少很多关键的依赖包 pcre bzip2 xml rcurl等
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