Mamba安装和常用命令

Mamba安装和常用命令

官网：https://mamba.readthedocs.io/en/latest/index.html

安装

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh

bash Miniforge3-Linux-x86_64.sh

#将安装目录下的bin路径添加到PATH环境变量中
mamba --version
mamba 1.5.5
conda 23.11.0		# 除了安装好mamba和conda，默认配置了conda的源（安装路径下.condarc 文件，后需换/添加源，可以直接修改此文件）

更换源

vim .condarc		# 添加
# 清华源
channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
ssl_verify: true
# 中科大源
channels:
  - https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
  - https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
  - https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
ssl_verify: true
# 上海交大源
channels:
  - https://mirrors.sjtug.sjtu.edu.cn/anaconda/pkgs/main/
  - https://mirrors.sjtug.sjtu.edu.cn/anaconda/pkgs/free/
  - https://mirrors.sjtug.sjtu.edu.cn/anaconda/cloud/conda-forge/
ssl_verify: true

# 此处同类型的源只需添加一个即可，如果配置多个，会在多个源里进行搜索，一个是结果会重复，第二是命令运行时间长，如果在某个源里没有需要的软件，可以通过“-c”参数，临时指定使用另外一个源。
# 源文件配置方法：https://conda.io/projects/conda/en/latest/userguide/configuration/mirroring.html

常用命令

# 初始化
mamba init		# 必须要运行一次，然后重开一个终端，才能 mamba activate/deactivate
# 环境创建
mamba create ( -n name_of_myenv | -p path_of_myenv) -c CHANNEL <list of packages>		# -n 或 -p 参数2选1
# 列出所有环境
mamba env list
# 移除环境
mamba env remove -n name_of_myenv
# 搜索软件
mamba search packages_name -c CHANNEL
mamba repoquery search packages_name
# 激活/进入环境
mamba activate name_of_myenv
# 退出环境
mamba deactivate
# 列出当前环境已安装的软件
mamba list
# 安装软件
mamba install packages_name
# 卸载软件
conda remove -n name_of_myenv packages_name

测试

mamba create -p /Software/R/R.4.2.0 r-base=4.2.0 gcc=11.1.0 gfortran=11.1.0 libgcc-ng=13.1.0
WARNING: A directory already exists at the target location '/Software/R/R.4.2.0'
but it is not a conda environment.
Continue creating environment (y/[n])? y


Looking for: ['r-base=4.2.0', 'gcc=11.1.0', 'gfortran=11.1.0', 'libgcc-ng=13.1.0']

https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pk..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..            No change
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cl..            No change
Could not solve for environment specs
The following packages are incompatible
├─ gfortran 11.1.0**  is installable and it requires
│  └─ gfortran_linux-64 11.1.0.* , which can be installed;
└─ r-base 4.2.0**  is not installable because it requires
   └─ gfortran_linux-64 10.* , which conflicts with any installable versions previously reported.
# 看来不同软件对依赖软件的版本有要求，不能无脑装

# 最后的环境创建命令
mamba create -p /Software/R/R.4.2.0 r-base=4.2.0 gcc=10.4.0 gfortran=10.4.0 libgcc-ng=13.1.0
# 测试R并安装包
mamba activate /Software/R/R.4.2.0
R
install.packages('tidyverse', repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
# 第一次偷懒，直接使用路径/Software/R/R.4.2.0/bin/R 启动R 并安装包，会报错：
/bin/sh: x86_64-conda-linux-gnu-c++: command not found
# 等包安装好了以后可以直接这样启动R
# ERROR: dependency ‘ragg’ is not available for package ‘tidyverse’
install.packages("ragg", repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
# ft_cache.h:9:10: fatal error: ft2build.h: No such file or directory
#    9 | #include <ft2build.h>
#      |          ^~~~~~~~~~~~
yum install fontconfig-devel.x86_64
# 安装ragg 再次报错
# ERROR: dependency ‘textshaping’ is not available for package ‘ragg’
mamba install r-textshaping
#mamba install freetype-devel libpng-devel libtiff-devel libjpeg-devel
yum install -y freetype-devel libpng-devel libtiff-devel

# 安装libjpeg-devel
yum install libjpeg-turbo-devel
# 继续报错
/Software/R/R.4.2.0/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lpng15: No such file or directory		# 需要安装libpng15-devel
# 下载 https://jaist.dl.sourceforge.net/project/libpng/libpng15/1.5.30/libpng-1.5.30.tar.gz
tar -xzvf libpng-1.5.30.tar.gz 
cd libpng-1.5.30
make && make install		# 安装完之后软链进环境里的lib文件夹里，或者直接安装在当前环境的lib文件夹里（/Software/R/R.4.2.0/lib）
# 再次安装ragg包，安装成功
# 再次安装tidyverse包，安装成功，真是费劲

其他

• 默认关闭bsea环境：conda config --set auto_activate_base false