R|R devtools安装yyplot(解决了mac安装错误问题) Rdevtools安装yyplot(解决了mac安装

R version 3.6.0
重点在4.yyplot安装
1.设置默认的国内镜像地址
从https://mirrors.tuna.tsinghua.edu.cn/CRAN/中添加
原则就是越近越好

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2.安装devtools(支持从github上下载开源的包)

install.packages("devtools") library(devtools) #先library以后才能用devtools！！ install_github("GuangchuangYu/yyplot")

结果报错，显示

ERROR: dependency ‘ggtree’ is not available for package ‘gglayer’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gglayer’ 错误: Failed to install 'yyplot' from GitHub: Failed to install 'gglayer' from GitHub: (由警告转换成)installation of package ‘/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmptB3H8r/file170cd22121a08/gglayer_0.0.1.tar.gz’ had non-zero exit status

仔细看错误提示：dependency ‘ggtree’ is not available for package ‘gglayer’
于是直接到github上搜Y叔（yuguangchang）的ggtree，因为先下载ggtree才能下gglayer
结果没搜到Y叔的ggtree，只搜到gglayer
https://github.com/GuangchuangYu/gglayer

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直接把gglayer改成ggtree，成功跳转到Y叔的ggtree
https://github.com/YuLab-SMU/ggtree

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image.png 各种尝试后推荐方法三，因为方法一二理论可行，但是实际操作过程中外网速度太慢容易导致下载失败
方法一：命令：

devtools::install_git("url")

直接克隆github ggtree的地址，下载ggtree

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image.png 在Rstudio中输入命令devtools::install_git("url"),一定记得url上有“ ”，不然会提示

devtools::install_git(https://github.com/YuLab-SMU/ggtree.git) 错误: 意外的'/' in "devtools::install_git(https:/"

devtools::install_git("https://github.com/YuLab-SMU/ggtree.git")
方法二：命令：

devtools::install_github("author/packagesname")

"author/packagesname"在url上直接复制即可
or：

library(devtools) install_github("GuangchuangYu/yyplot")

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image.png 方法三-biomanager安装ggtree(R>=3.5)-推荐

biomanager的安装见下方3.

去官网找安装代码
http://bioconductor.org/packages/release/bioc/html/ggtree.html

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("ggtree")

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wow！安装成功！并提示是否更新相关的包

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image.png 3.安装biomanager (好处是每半年会对R包upgrade&debug)
Bioconductor在R3.5版本以后，终于放弃了source() 这种危险的链接方式，改为用新的安装方式BiocManager进行安装：
对于R 3.5 以下的版本，依旧需要使用BiocLite：
代码已经给好，不再需要source()：
去官网https://bioconductor.org/install/上查R对应的安装命令，例如我的是R 3.6，对应bioconductor 3.10

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>if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.10")Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12) Installing package(s) 'BiocVersion' 试开URL’https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/BiocVersion_3.10.1.tgz' Content type 'application/x-gzip' length 5574 bytes ================================================== downloaded 5574 bytesThe downloaded binary packages are in /var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/downloaded_packages

Bioconductor的 bioc-devel 每六个月（其实是每年四月和十月）会对旗下的生物相关的R包进行更新和debug，install.packages在很多时候检测不到这些更新，导致使用者总是安装过时的版本
4.安装yyplot-重点

> install_github("GuangchuangYu/yyplot")

>install_github("GuangchuangYu/yyplot") Downloading GitHub repo GuangchuangYu/yyplot@master Downloading GitHub repo GuangchuangYu/gglayer@master Skipping 1 packages not available: ggtree The downloaded binary packages are in /var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/downloaded_packages 错误: Failed to install 'unknown package' from GitHub: Failed to install 'gglayer' from GitHub: Failed to connect to api.github.com port 443: Connection refused

报错：

错误: Failed to install 'unknown package' from GitHub: Failed to install 'gglayer' from GitHub: Failed to connect to api.github.com port 443: Connection refused

于是单独安装gglayer，先用的biomanager

> BiocManager::install("gglayer") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12) Installing package(s) 'gglayer' Warning message: package ‘gglayer’ is not available (for R version 3.6.2)

结果显示package ‘gglayer’ is not available (for R version 3.6.2)
R3.6不能安装gglayer？于是跑到Y叔的github上看支持的R版本，明明支持R>=3.5呀！！

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image.png 于是重新用devtools安装

> devtools::install_github("GuangchuangYu/gglayer") 错误: Failed to install 'gglayer' from GitHub: Failed to connect to api.github.com port 443: Connection refused

网络问题？于是设置了代理

git config --global http.proxy http://144.4X.1X.1X:443

再次用devtools安装...

> devtools::install_github("GuangchuangYu/gglayer") Skipping install of 'gglayer' from a github remote, the SHA1 (aa7dab85) has not changed since last install. Use `force = TRUE` to force installation

按照提示来

> devtools::install_github("GuangchuangYu/gglayer",force = TRUE)

> devtools::install_github("GuangchuangYu/gglayer",force = TRUE) Downloading GitHub repo GuangchuangYu/gglayer@master Skipping 1 packages not available: ggtree ?checking for file ‘/private/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T/RtmpH6X08I/remotes1737714e28d74/GuangchuangYu-gglayer-aa7dab8/DESCRIPTION’ ... ─preparing ‘gglayer’: ?checking DESCRIPTION meta-information ... ─checking for LF line-endings in source and make files and shell scripts ─checking for empty or unneeded directories ─building ‘gglayer_0.0.1.tar.gz’* installing *source* package ‘gglayer’ ... ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location Registered S3 method overwritten by 'treeio': methodfrom root.phylo ape ** testing if installed package keeps a record of temporary installation path * DONE (gglayer)

wow！gglayer终于安装成功！！
于是动手再重新安装yyplot

> devtools::install_github("GuangchuangYu/yyplot") Downloading GitHub repo GuangchuangYu/yyplot@master ?checking for file ‘/private/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T/RtmpH6X08I/remotes1737726ddd400/GuangchuangYu-yyplot-91d2d33/DESCRIPTION’ ... ─preparing ‘yyplot’: ?checking DESCRIPTION meta-information ... ─checking for LF line-endings in source and make files and shell scripts ─checking for empty or unneeded directories ─building ‘yyplot_0.0.8.tar.gz’* installing *source* package ‘yyplot’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading Error : .onLoad failed in loadNamespace() for 'sysfonts', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: 无法载入共享目标对象‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so’：: dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so, 6): Library not loaded: /opt/X11/lib/libfreetype.6.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/sysfonts/libs/sysfonts.so Reason: image not found 错误: unable to load R code in package ‘yyplot’ 停止执行 ERROR: lazy loading failed for package ‘yyplot’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/yyplot’ 错误: Failed to install 'yyplot' from GitHub: (由警告转换成)installation of package ‘/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/file173772d895fef/yyplot_0.0.8.tar.gz’ had non-zero exit status

仔细看报错的信息：

Error : .onLoad failed in loadNamespace() for 'sysfonts', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: 无法载入共享目标对错误: unable to load R code in package ‘yyplot’ 停止执行 ERROR: lazy loading failed for package ‘yyplot’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/yyplot’ 错误: Failed to install 'yyplot' from GitHub:

google了Y叔的github yyplot的issue，看有没有人遇到类似的问题，结果，确实mac上有安装错误的issue
发现了类似的问题

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有人提出解决方法，下载XQuartz，地址 https://www.xquartz.org/

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出现的问题叫：
sysfonts not loading/Image not found
解答参考 https://github.com/yixuan/showtext/issues/13
并重新配置了经测试能登github的proxy
git config --global http.proxy http://10X.1X6.1X5.1X9:443
再次重新安装yyplot，终于安装成功！！

> devtools::install_github("GuangchuangYu/yyplot") Downloading GitHub repo GuangchuangYu/yyplot@master ?checking for file ‘/private/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T/RtmpH6X08I/remotes173776ebf2b1f/GuangchuangYu-yyplot-91d2d33/DESCRIPTION’ ... ─preparing ‘yyplot’: ?checking DESCRIPTION meta-information ... ─checking for LF line-endings in source and make files and shell scripts ─checking for empty or unneeded directories ─building ‘yyplot_0.0.8.tar.gz’* installing *source* package ‘yyplot’ ... ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (yyplot)

6.直接下载packages.tar.gz安装