如何在macOS Sierra上使用R studio安装biocLite和ComplexHeatmap

Question

我正在运行R studio (Anaconda) R版本3.4.1 (2017-06-30)。

尝试安装biocLite时出现以下错误：

> source("http://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) : 
  internet routines cannot be loaded
> biocLite()
Error in biocLite() : could not find function "biocLite"

尝试安装ComplexHeatmap时，出现以下错误(包括http和https)：

> source("https://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) : 
  internet routines cannot be loaded
> biocLite("ComplexHeatmap")
Error in biocLite("ComplexHeatmap") : could not find function "biocLite"

如何使用R studio或mac终端安装biocLite和ComplexHeatmaps？

谢谢

Answer 1

这篇文章在一定程度上对我有效：https://github.com/ContinuumIO/anaconda-issues/issues/4421

简要地说：

在mac终端上安装了以下三个东西：

conda install -c r r-essentials

                      (I am not sure if r-essentials was actually needed for this but it didn't harm)

conda install libssh2

 conda install krb5

(重启R studio，这对于查看变化非常重要)

要安装biocLite：

现在在R studio中运行这两个命令：

source("https://bioconductor.org/biocLite.R")
biocLite()

但是，"ComplexHeatmap“失败并给出以下警告: Code: source("https://bioconductor.org/biocLite.R") biocLite("ComplexHeatmap")

警告：

There were 11 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘mclust’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘mvtnorm’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘robustbase’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘prabclus’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘fpc’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘dendextend’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ComplexHeatmap’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘glmnet’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘openssl’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘xts’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘TTR’ had non-zero exit status