MAC安装DESeq2报错及解决方案

在R环境中安装DESeq2

1、安装DESeq2基本语法：

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source ("http://bioconductor.org/biocLite.R") # 调入安装工具Bioconductor
biocLite("DESeq2") # 安装DESeq2
library("DESeq2") # 测试是否安装成功

2、报错信息

我的系统是MacOS 10.10.5，执行安装命令后各种报错：

fatal error:
‘string.h’ file not found
include <string.h> / for memcpy, memset /
1 error generated.
make: *** [000.init.o] Error 1
ERROR: compilation failed for package ‘matrixStats’

fatal error:
‘math.h’ file not found
include_next <math.h>
1 error generated.
make: *** [DbColumn.o] Error 1
ERROR: compilation failed for package ‘RSQLite’

fatal error:
‘ctype.h’ file not found
include <ctype.h>
1 error generated.
make: *** [DocParse.o] Error 1
ERROR: compilation failed for package ‘XML’

fatal error:
‘stdlib.h’ file not found
include <stdlib.h> / Not used by R itself, but widely assumed in packages /
1 error generated.
make: *** [all_missing.o] Error 1
ERROR: compilation failed for package ‘checkmate’

fatal error:
‘string.h’ file not found
include <string.h>
/ for memcpy, memset /
1 error generated.
make: *** [AEbufs.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’

fatal error:
‘stdio.h’ file not found
include <stdio.h>
1 error generated.
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package ‘Biobase’

fatal error:
‘unistd.h’ file not found
include <unistd.h>
1 error generated.
make: *** [ipcmutex.o] Error 1
ERROR: compilation failed for package ‘BiocParallel’

fatal error:
‘stdlib.h’ file not found
include <stdlib.h>
1 error generated.
make: *** [S_enter.o] Error 1
ERROR: compilation failed for package ‘locfit’

configure: error:
cannot run C++ compiled programs.
If you meant to cross compile, use --host'. Seeconfig.log’ for more details
ERROR: configuration failed for package ‘RcppArmadillo’

There were 22 warnings (use warnings() to see them)
warnings()
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘matrixStats’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘RSQLite’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘XML’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘checkmate’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘S4Vectors’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘Biobase’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘BiocParallel’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘locfit’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘RcppArmadillo’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘htmlTable’ had non-zero exit status
11: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘IRanges’ had non-zero exit status
12: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
13: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘XVector’ had non-zero exit status
14: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘DelayedArray’ had non-zero exit status
15: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘AnnotationDbi’ had non-zero exit status
16: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘Hmisc’ had non-zero exit status
17: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘annotate’ had non-zero exit status
18: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘GenomicRanges’ had non-zero exit status
19: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
20: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘genefilter’ had non-zero exit status
21: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘geneplotter’ had non-zero exit status
22: In install.packages(pkgs = doing, lib = lib, …) :
installation of package ‘DESeq2’ had non-zero exit status

3、报错原因

根据返回的报错信息，可以知道，系统中缺乏’string.h’，’math.h’，’ctype.h’，’stdlib.h’，’stdio.h’，’unistd.h’这些文件，这些文件都是C++ library中得Header files，因此，需要安装C++，或者直接安装Xcode Command Line Tools。

安装Xcode命令行工具

Xcode Command Line Tools，包含一些命令行开发工具，例如gcc/g++编译器、make、git、nasm等，安装命令如下：

1	xcode-select --install # 安装Xcode命令行工具（Xcode Command Line Tools）

安装完成后，检查是否成功：

1	xcode-select -p # 检查是否成功安装

/Applications/Xcode.app/Contents/Developer

若看到如下信息，则表明Xcode Command Line Tools已经安装：

xcode-select: error: command line tools are already installed, use “Software Update” to install update

再次安装DESeq2

此时，就可以着手安装DESeq2软件包了，执行：

1 2	source ("http://bioconductor.org/biocLite.R") # 调入安装工具Bioconductor biocLite("DESeq2") # 安装DESeq2