字体配置

字体安装

# 字体库
brew tap homebrew/cask-fonts
# 代码显示字体：用于 RStudio IDE 等代码编辑器
brew install --cask font-fira-code
# 代码排版字体：用于书籍中代码
brew install font-inconsolata
# 其它系列字体
brew install font-dejavu font-liberation
brew install font-fira-sans font-fira-mono font-fira-code 
brew install font-open-sans font-open-sans-condensed
# 中文字体
brew install --cask font-noto-sans-cjk-sc font-noto-serif-cjk-sc
brew install --cask font-alegreya-sans-sc font-alegreya-sc
# 英文字体
brew install --cask font-source-code-pro font-source-sans-pro  font-source-serif-pro
# 用于终端显示
brew install --cask font-source-code-pro-for-powerline
# 漫画字体
brew install --cask font-xkcd
# 表情字体
brew install --cask font-noto-emoji font-noto-color-emoji
# Windows 系统字体
brew install --cask font-arial font-andale-mono font-times-new-roman

编辑器

代码编辑

通用代码文本集成开发编辑环境 IDE

brew install --cask visual-studio-code atom

文本编辑

文字编辑和文档转化工具

brew install pandoc hugo
brew install --cask mark-text
brew install --cask calibre lyx

运行 LyX 内置的 knitr 模版，需要一些 LaTeX 包

tinytex::tlmgr_install(c('palatino', 'babel-english', 'mathpazo'))

R 和 R 包

R 和 RStudio 软件

brew install --cask r xquartz
brew install --cask rstudio

设置 R 软件的语言为英文¹，避免一些不必要的编码问题，中文翻译不是很好，此外，看英文最好！

defaults write org.R-project.R force.LANG en_US.UTF-8

安装一些 R 包需要的系统依赖

brew install glpk
brew install clp
brew install udunits gdal
brew install v8

安装完 apache-arrow 后，固定下来

brew install apache-arrow
brew pin apache-arrow

R 包与 X11

MacOS 从源码安装 R 软件时，配置需要指定 X11 相关库和头文件。

../source/configure --prefix=/Users/xiangyun/R-devel \
  --x-libraries=/opt/X11/lib/ --x-includes=/opt/X11/include \
  --enable-R-shlib --enable-memory-profiling

参考 SO 帖子配置 X11，先安装 XQuartz，再从源码安装 rgl 包，需要指定 X11 相关文件的路径，以便编译安装时发现。

install.packages(
  pkgs = "rgl", type = "source",
  configure.args = c(
    "--x-libraries=/opt/X11/lib/",
    "--x-includes=/opt/X11/include"
  )
)

如果不从源码编译就只能通过网页查看 3D 图形效果。rgl 包支持 WebGL 输出，特别是当环境不支持 OpenGL 的时候，比如在 Github Action 上使用 rgl 生成三维图形。

## 加载 rgl 
library(rgl)
## 准备启用 WebGL 
knitr::knit_hooks$set(webgl = rgl::hook_webgl)
## 详见帮助文档 rgl::hook_webgl
options(rgl.printRglwidget = TRUE)
options(rgl.useNULL = TRUE)

添加代码块运行控制选项 webgl=TRUE，运行示例：

example("plot3d", "rgl")

R 包与 Orca

安装 orca 将 plotly 绘制的交互式动态图形转化为静态的 SVG/PDF 格式矢量图形

brew install --cask orca

R 包与 PhantomJS

安装 phantomjs 用于 webshot 包

brew install --cask phantomjs

webshot::install_phantomjs() 将交互式图形截图放在 bookdown 书里

R 包与 OpenMP

目前，发现 R 包 data.table、RandomFields 和 RandomFieldsUtils 需启用 OpenMP 从源码编译才能获得共享内存的多线程并行计算的能力。

从源码安装 data.table

brew install pkg-config # 检查和发现 zlib
brew install libomp # OpenMP

参考 https://mac.r-project.org/openmp/ 文档，在 ~/.R/Makevars 添加两行即可。

CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp

Rmpi 包和 open-mpi

先安装外部软件依赖

brew install open-mpi

install.packages('Rmpi', type = 'source')

* installing *source* package ‘Rmpi’ ...
** package ‘Rmpi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... clang -mmacosx-version-min=11.3
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=11.3 accepts -g... yes
checking for clang -mmacosx-version-min=11.3 option to accept ISO C89... none needed
checking for pkg-config... /usr/local/bin/pkg-config
checking if pkg-config knows about OpenMPI... yes
checking for orted... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -mmacosx-version-min=11.3 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/Cellar/open-mpi/4.1.1_2/include -DMPI2 -DOPENMPI  -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rmpi.c -o Rmpi.o
clang -mmacosx-version-min=11.3 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/Cellar/open-mpi/4.1.1_2/include -DMPI2 -DOPENMPI  -I/usr/local/include   -fPIC  -Wall -g -O2  -c conversion.c -o conversion.o
clang -mmacosx-version-min=11.3 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/Cellar/open-mpi/4.1.1_2/include -DMPI2 -DOPENMPI  -I/usr/local/include   -fPIC  -Wall -g -O2  -c internal.c -o internal.o
clang -mmacosx-version-min=11.3 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rmpi.so Rmpi.o conversion.o internal.o -L/usr/local/Cellar/open-mpi/4.1.1_2/lib -L/usr/local/opt/libevent/lib -lmpi -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rmpi/00new/Rmpi/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rmpi)

stringi 包和 icu4c

安装 icu4c

brew install icu4c

配置环境变量

# brew 安装的 icu4c 优先
echo 'export PATH="/usr/local/opt/icu4c/bin:$PATH"' >> ~/.zshrc
echo 'export PATH="/usr/local/opt/icu4c/sbin:$PATH"' >> ~/.zshrc

# 用于 C++ 编译器找到 icu4c
echo 'export LDFLAGS="-L/usr/local/opt/icu4c/lib"' >> ~/.zshrc
echo 'export CPPFLAGS="-I/usr/local/opt/icu4c/include"' >> ~/.zshrc

# 用于 pkg-config 找到 icu4c 
echo 'export PKG_CONFIG_PATH="/usr/local/opt/icu4c/lib/pkgconfig"' >> ~/.zshrc

如果用 brew 安装了新版本的 gcc 编译器，在安装需要启用 gcc 编译链接的 R 包时，出现如下类似警告²：

设置 gfortran 库路径，当前安装的 gcc-11

FLIBS = -L/usr/local/Cellar/gcc/11.2.0/lib/gcc/11 -lgfortran -lquadmath -lm

openssl 包和 openssl@1.1

brew install openssl@1.1

openssl

install.packages(
  pkgs = "openssl", type = "source",
  configure.vars = c(
    "LIB_DIR=/usr/local/opt/openssl@1.1/lib",
    "INCLUDE_DIR=/usr/local/opt/openssl@1.1/include"
  )
)

常用软件

# 图像处理
brew install ghostscript imagemagick optipng graphviz
brew install --cask drawio inkscape gimp

# 视频处理
brew install ffmpeg
# GIF 制作
brew install gifski

# 视频播放
brew install --cask zy-player
brew install --cask iina

# 解压、下载软件
brew install --cask rar free-download-manager

# 数据库管理
brew install --cask dbeaver-community

# 办公软件
brew install --cask tencent-meeting zoom
brew install --cask google-chrome
brew install --cask adobe-acrobat-reader
brew install --cask microsoft-office
brew install --cask zotero

# 统计软件
brew install jags
brew install --cask qgis
brew install --cask julia
brew install --cask pycharm-ce

Internationalization of the R.app ↩︎
Mac OS X R error “ld: warning: directory not found for option”

ld: warning: directory not found for option ‘-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2’↩︎

在 MacOS 上安装数据分析软件

黄湘云