Centos7_miniconda_devtools安装_R语言入门之R包的安装_in install.packages("devtools") : 安装程序包‘systemfont

因为有同事反馈安装R包很慢或卡住，提供了一个安装R包的命令给我测试，在安装过程中复现报错信息，把下载慢或卡顿的链接中的域名在防火墙中调整出口。

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

下载安装miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh #给下载下来的安装文件添加执行权限
sudo bash Miniconda3-latest-Linux-x86_64.sh

一路Enter----yes—yes直到安装完成
进入conda环境

source ~/.bashrc
conda

国内换源

#全部清华园，备用
 
 
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/MindSpore
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/Paddle
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/auto
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biobakery
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/c4aarch64
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/caffe2
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/deepmodeling
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/dglteam
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/fastai
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/fermi
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/idaholab
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/intel
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/matsci
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/mordred-descriptor
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/numba
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/ohmeta
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/omnia
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/peterjc123
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/plotly
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/psi4
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch-lts
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch-test
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch3d
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pyviz
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/qiime2
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/rapidsai
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/rdkit
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/simpleitk
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/stackless
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/ursky

 安装下R语言运行环境，安装R4.0.0(开始时安装R4.3.1提示不支持某个插件，具体不记得了)

conda search R

 创建R4.0环境

conda create -n r4.0

进入R4.0环境 

conda activate r4.0

安装R4.0

conda install R=4.0 -y

 

进入R程序 

 

安装devtools

install.packages("devtools")

 安装R包报错：

1) grab failed: window not viewable.

Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
[tcl] grab failed: window not viewable.

一般发生在远程linux系统中安装R包，是因为R调用窗口失败，解决方法是

chooseCRANmirror(graphics=FALSE)

输入16回车，再运行一次安装命令。

install.packages("devtools")

 可能还会有下面出错信息

1: In install.packages("devtools", dependencies = TRUE) :
  安装程序包‘systemfonts’时退出狀態的值不是0
2: In install.packages("devtools", dependencies = TRUE) :
  安装程序包‘textshaping’时退出狀態的值不是0
3: In install.packages("devtools", dependencies = TRUE) :
  安装程序包‘ragg’时退出狀態的值不是0
4: In install.packages("devtools", dependencies = TRUE) :
  安装程序包‘pkgdown’时退出狀態的值不是0
5: In install.packages("devtools", dependencies = TRUE) :
  安装程序包‘devtools’时退出狀態的值不是0

解决办法： 

 1.install.packages('fontconfig')根据报错提示安装

    yum install fontconfig-devel
   
 2.install.packages('textshaping')根据报错提示安装

   yum install -y  harfbuzz-devel fribidi-devel
   
 3.install.packages('ragg')根据报错提示安装

yum install -y freetype-devel libpng-devel libtiff-devel libjpeg-devel

 4.处理完1.2.3再安装下面包已经不再提示错误了。
 install.packages('pkgdown')

处理完再试试安装devtools.

在R中使用devtools安装R包

devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

 例如生信分析常用到的Bioconductor，可使用BiocManager::install()来进行安装，例如安装DESeq2包

if (!require("BiocManager", quietly = TRUE))
       install.packages("BiocManager")
   
   BiocManager::install("DESeq2")

又报出错。

ERROR: dependencies ‘SummarizedExperiment’, ‘rhdf5’, ‘motifmatchr’, ‘chromVAR’, ‘uwot’, ‘Rsamtools’, ‘Biostrings’, ‘ComplexHeatmap’, ‘GenomicRanges’ are not available for package ‘ArchR’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/ArchR’

使用pacman包来批量安装依赖包

install.packages("pacman")

使用p_install函数，并通过packages参数传入要安装的包名列表：

pacman::p_install(packages = c("SummarizedExperiment", "rhdf5", "motifmatchr", "chromVAR", "uwot", "Rsamtools", "Biostrings", "ComplexHeatmap", "GenomicRanges"))

出现ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’ 的报错。此时往往是由于默认安装的locfit版本的问题导致的，所以通过指定低一点的版本（例如1.5-9.2）即可安装。

install.packages('https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz',repos = NULL)

出错揭示：

checking for gcc... no
checking for cc... no
checking for cl.exe... no
checking for clang... no
configure: error: in `/tmp/RtmpuOjLUv/R.INSTALLe06dd4f1f4256/XML':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details
ERROR: configuration failed for package ‘XML’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/XML’
* installing *source* package ‘BiocParallel’ ...
** using staged installation
checking for gcc... no
checking for cc... no
checking for cl.exe... no
configure: error: in `/tmp/RtmpsFlbCG/R.INSTALLe075b1e0ffb7b/BiocParallel':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details

由于本机缺少gcc编译环境，通过yum安装gcc编译环境：

yum install -y gcc

再次运行安装，提示出错信息如下

* DONE (BiocParallel)
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/DESeq2’

 安装xml

install.packages('XML')

提示出错：

You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories.
ERROR: configuration failed for package ‘XML’
* removing ‘/root/miniconda3/envs/r4.0/lib/R/library/XML’
 
下载的程序包在
        ‘/tmp/Rtmp6sGhlh/downloaded_packages’里
更新'.Library'里的HTML程序包列表
Making 'packages.html' ... 做完了。
Warning message:
In install.packages("XML") : 安装程序包‘XML’时退出狀態的值不是0

进入R，

>Sys.setenv(XML_CONFIG="/usr/bin/xml2-config") #指定安装时libxml2的目录

>install.packages("XML")

xml安装完成。

再运行一次

if (!require("BiocManager", quietly = TRUE))
       install.packages("BiocManager")
   
   BiocManager::install("DESeq2")

全部安装成功。

参考文章：Miniconda3环境配置，换国内源_miniconda换源-CSDN博客

参考文章：没有人比我更懂R包安装 - 知乎 

参考文章：DEseq2和edgeR的安装问题记录_deseq2安装报错-CSDN博客

参考文章：https://www.cnblogs.com/shuaihe/p/11379361.html