R devtools安裝yyplot(解決了mac安裝錯(cuò)誤問題)

R version 3.6.0
重點(diǎn)在4.yyplot安裝

1.設(shè)置默認(rèn)的國(guó)內(nèi)鏡像地址

從https://mirrors.tuna.tsinghua.edu.cn/CRAN/中添加
原則就是越近越好

image.png

2.安裝devtools(支持從github上下載開源的包)

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

結(jié)果報(bào)錯(cuò)，顯示

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

仔細(xì)看錯(cuò)誤提示：dependency ‘ggtree’ is not available for package ‘gglayer’

于是直接到github上搜Y叔（yuguangchang）的ggtree，因?yàn)橄认螺dggtree才能下gglayer

結(jié)果沒搜到Y(jié)叔的ggtree，只搜到gglayer
https://github.com/GuangchuangYu/gglayer

直接把gglayer改成ggtree，成功跳轉(zhuǎn)到Y(jié)叔的ggtree
https://github.com/YuLab-SMU/ggtree

image.png

各種嘗試后推薦方法三，因?yàn)榉椒ㄒ欢碚摽尚?，但是?shí)際操作過程中外網(wǎng)速度太慢容易導(dǎo)致下載失敗

方法一：

命令：

devtools::install_git("url")

直接克隆github ggtree的地址，下載ggtree


image.png

在Rstudio中輸入命令devtools::install_git("url"),一定記得url上有“ ”，不然會(huì)提示

devtools::install_git(https://github.com/YuLab-SMU/ggtree.git)
錯(cuò)誤: 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上直接復(fù)制即可
or：

library(devtools)
install_github("GuangchuangYu/yyplot")
image.png

方法三-biomanager安裝ggtree(R>=3.5)-推薦

biomanager的安裝見下方3.

去官網(wǎng)找安裝代碼
http://bioconductor.org/packages/release/bioc/html/ggtree.html

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

BiocManager::install("ggtree")
image.png

wow！安裝成功！并提示是否更新相關(guān)的包

image.png

3.安裝biomanager (好處是每半年會(huì)對(duì)R包upgrade&debug)

Bioconductor在R3.5版本以后，終于放棄了source() 這種危險(xiǎn)的鏈接方式，改為用新的安裝方式BiocManager進(jìn)行安裝：

對(duì)于R 3.5 以下的版本，依舊需要使用BiocLite：

代碼已經(jīng)給好，不再需要source()：

去官網(wǎng)https://bioconductor.org/install/上查R對(duì)應(yīng)的安裝命令，例如我的是R 3.6，對(duì)應(yīng)bioconductor 3.10

image.png
>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'
試開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 bytes


The downloaded binary packages are in
    /var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/downloaded_packages

Bioconductor的 bioc-devel 每六個(gè)月（其實(shí)是每年四月和十月）會(huì)對(duì)旗下的生物相關(guān)的R包進(jìn)行更新和debug，install.packages在很多時(shí)候檢測(cè)不到這些更新，導(dǎo)致使用者總是安裝過時(shí)的版本

4.安裝yyplot-重點(diǎn) 

> 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
錯(cuò)誤: Failed to install 'unknown package' from GitHub:
  Failed to install 'gglayer' from GitHub:
  Failed to connect to api.github.com port 443: Connection refused

報(bào)錯(cuò)：
錯(cuò)誤: Failed to install 'unknown package' from GitHub: Failed to install 'gglayer' from GitHub: Failed to connect to api.github.com port 443: Connection refused

于是單獨(dú)安裝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)

結(jié)果顯示package ‘gglayer’ is not available (for R version 3.6.2)

R3.6不能安裝gglayer？于是跑到Y(jié)叔的github上看支持的R版本，明明支持R>=3.5呀?。?/p>

image.png

于是重新用devtools安裝

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

網(wǎng)絡(luò)問題？于是設(shè)置了代理

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

再次用devtools安裝...

> 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

按照提示來

> 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':
  method     from
  root.phylo ape 
** testing if installed package keeps a record of temporary installation path
* DONE (gglayer)

wow！gglayer終于安裝成功?。?/p>

于是動(dòng)手再重新安裝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: 無法載入共享目標(biāo)對(duì)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
錯(cuò)誤: unable to load R code in package ‘yyplot’
停止執(zhí)行
ERROR: lazy loading failed for package ‘yyplot’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/yyplot’
錯(cuò)誤: Failed to install 'yyplot' from GitHub:
  (由警告轉(zhuǎn)換成)installation of package ‘/var/folders/rr/3hs35sxn0lsfwvx91_w0vfhr0000gn/T//RtmpH6X08I/file173772d895fef/yyplot_0.0.8.tar.gz’ had non-zero exit status

仔細(xì)看報(bào)錯(cuò)的信息：

Error : .onLoad failed in loadNamespace() for 'sysfonts', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: 無法載入共享目標(biāo)對(duì)

錯(cuò)誤: unable to load R code in package ‘yyplot’
停止執(zhí)行
ERROR: lazy loading failed for package ‘yyplot’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/yyplot’
錯(cuò)誤: Failed to install 'yyplot' from GitHub:

google了Y叔的github yyplot的issue，看有沒有人遇到類似的問題，結(jié)果，確實(shí)mac上有安裝錯(cuò)誤的issue
發(fā)現(xiàn)了類似的問題

image.png

有人提出解決方法，下載XQuartz，地址https://www.xquartz.org/
image.png

出現(xiàn)的問題叫：
sysfonts not loading/Image not found
解答參考https://github.com/yixuan/showtext/issues/13

并重新配置了經(jīng)測(cè)試能登github的proxy
git config --global http.proxy http://10X.1X6.1X5.1X9:443

再次重新安裝yyplot，終于安裝成功！！

> 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.直接下載packages.tar.gz安裝

install.packages("/Users/quyue/Desktop/adipocyteData/Course/ifnb.SeuratData_3.0.0.tar.gz", repos = NULL, type = "source")
library(ifnb.SeuratData)

說明：原創(chuàng)聲明，部分觀點(diǎn)參考https://zhuanlan.zhihu.com/p/50345757

最后編輯于 ：
?著作權(quán)歸作者所有,轉(zhuǎn)載或內(nèi)容合作請(qǐng)聯(lián)系作者
【社區(qū)內(nèi)容提示】社區(qū)部分內(nèi)容疑似由AI輔助生成，瀏覽時(shí)請(qǐng)結(jié)合常識(shí)與多方信息審慎甄別。
平臺(tái)聲明：文章內(nèi)容（如有圖片或視頻亦包括在內(nèi)）由作者上傳并發(fā)布，文章內(nèi)容僅代表作者本人觀點(diǎn)，簡(jiǎn)書系信息發(fā)布平臺(tái)，僅提供信息存儲(chǔ)服務(wù)。

相關(guān)閱讀更多精彩內(nèi)容

友情鏈接更多精彩內(nèi)容