R包安装方法整理

我们布置了单细胞数据分析环境，提供公共的Rstudio server分析平台，欢迎有需要的老师联系使用。在安装R包的过程中我们遇到各种问题，也尝试了很多种方法，在这里对R包的安装方法做个总结，供大家参考！
R语言安装包主要来自CRAN网站、Bioconductor、GitHub及一些个人开发的R语言功能模块。
一、CRAN来源
1、常规安装
CRAN来源的R包一般可以用如下安装方法如下。该方法可以自动安装相关的依赖包。

> install.packages('ggplot2')

2、下载源文件本地安装

如不能顺利安装，可以下载R包源码本地安装，下载方法就是找到包的官方网站下载源文件。


image.png

源文件下载到本地之后，用如下方法安装：

> install.packages('ggplot2_3.5.1.tar.gz',type = 'source',repo=NULL)

3、在linux系统中也可以用命令行的方式安装：

$ R CMD INSTALL ggplot2_3.5.1.tar.gz

本地安装可能无法自动处理R包依赖问题，需要在安装过程中自行安装目的包依赖的其它R包。
二、Bioconductor来源的R包一般可以直接用如下方法安装。

> if (!require("BiocManager", quietly = TRUE))

如果不能顺利安装的话，参考进行前边介绍的本地安装方法。

三、在linux服务器中，CRAN和Bioconductor来源的R包可以通过conda安装，该方法也可以自动处理R包的相互依赖问题。方法如下：

$ conda search ggplot2

# Name                       Version           Build  Channel             
r-stringi                      0.4_1        r3.1.3_0  anaconda/pkgs/r     
r-stringi                      0.4_1        r3.1.3_0  pkgs/r              
r-stringi                      0.4_1       r3.1.3_0a  anaconda/pkgs/r     
r-stringi                      0.4_1       r3.1.3_0a  pkgs/r              
r-stringi                      0.5_5        r3.2.0_0  anaconda/pkgs/r     
r-stringi                      0.5_5        r3.2.0_0  pkgs/r              
r-stringi                      0.5_5       r3.2.0_0a  anaconda/pkgs/r     
r-stringi                      0.5_5       r3.2.0_0a  pkgs/r              
r-stringi                      0.5_5        r3.2.1_0  anaconda/pkgs/r     
r-stringi                      0.5_5        r3.2.1_0  pkgs/r              
r-stringi                      0.5_5       r3.2.1_0a  anaconda/pkgs/r     
r-stringi                      0.5_5       r3.2.1_0a  pkgs/r              
r-stringi                      0.5_5        r3.2.2_0  anaconda/pkgs/r     
r-stringi                      0.5_5        r3.2.2_0  pkgs/r              
r-stringi                      0.5_5       r3.2.2_0a  anaconda/pkgs/r     
r-stringi                      0.5_5       r3.2.2_0a  pkgs/r              
r-stringi                      1.0_1        r3.2.2_0  anaconda/pkgs/r     
r-stringi                      1.0_1        r3.2.2_0  pkgs/r              
r-stringi                      1.0_1       r3.2.2_0a  anaconda/pkgs/r     
r-stringi                      1.0_1       r3.2.2_0a  pkgs/r              
r-stringi                      1.1.1        r3.3.1_0  anaconda/pkgs/r     
r-stringi                      1.1.1        r3.3.1_0  pkgs/r              
r-stringi                      1.1.2        r3.3.1_0  anaconda/pkgs/r     
r-stringi                      1.1.2        r3.3.1_0  pkgs/r              
r-stringi                      1.1.2        r3.3.2_0  anaconda/pkgs/r     
r-stringi                      1.1.2        r3.3.2_0  anaconda/cloud/conda-forge
r-stringi                      1.1.2        r3.3.2_0  pkgs/r              
r-stringi                      1.1.2        r3.4.1_0  anaconda/cloud/conda-forge
r-stringi                      1.1.5        r3.4.1_0  anaconda/pkgs/r     
r-stringi                      1.1.5        r3.4.1_0  pkgs/r              
r-stringi                      1.1.5  r342h15434fd_0  anaconda/pkgs/r     
r-stringi                      1.1.5  r342h15434fd_0  pkgs/r              
r-stringi                      1.1.6 mro343h599a50d_0  anaconda/pkgs/r     
r-stringi                      1.1.6 mro343h599a50d_0  pkgs/r              
r-stringi                      1.1.6        r3.3.2_0  anaconda/cloud/conda-forge
r-stringi                      1.1.6        r3.4.1_0  anaconda/cloud/conda-forge
r-stringi                      1.1.6  r342hf484d3e_0  anaconda/pkgs/r     
r-stringi                      1.1.6  r342hf484d3e_0  pkgs/r              
r-stringi                      1.1.6  r343h599a50d_0  anaconda/pkgs/r     
r-stringi                      1.1.6  r343h599a50d_0  pkgs/r              
r-stringi                      1.1.7 mro350hc05d2f9_0  anaconda/pkgs/r     
r-stringi                      1.1.7 mro350hc05d2f9_0  pkgs/r              
r-stringi                      1.1.7        r3.3.2_0  anaconda/cloud/conda-forge
r-stringi                      1.1.7        r3.3.2_1  anaconda/cloud/conda-forge
r-stringi                      1.1.7        r3.4.1_0  anaconda/cloud/conda-forge
r-stringi                      1.1.7        r3.4.1_1  anaconda/cloud/conda-forge
r-stringi                      1.1.7  r350hebe7666_0  anaconda/pkgs/r     
r-stringi                      1.1.7  r350hebe7666_0  pkgs/r              
r-stringi                      1.2.3          r341_0  anaconda/cloud/conda-forge
r-stringi                      1.2.3  r341hfc679d8_1  anaconda/cloud/conda-forge
r-stringi                      1.2.4 mro351hebc1506_0  anaconda/pkgs/r     
r-stringi                      1.2.4 mro351hebc1506_0  pkgs/r              
r-stringi                      1.2.4  r341h9d2a408_0  anaconda/cloud/conda-forge
r-stringi                      1.2.4  r341h9d2a408_1  anaconda/cloud/conda-forge
r-stringi                      1.2.4  r351h29659fb_0  anaconda/pkgs/r     
r-stringi                      1.2.4  r351h29659fb_0  pkgs/r              
r-stringi                      1.2.4 r351h29659fb_1001  anaconda/cloud/conda-forge
r-stringi                      1.2.4  r351h9d2a408_0  anaconda/cloud/conda-forge
r-stringi                      1.2.4  r351h9d2a408_1  anaconda/cloud/conda-forge
r-stringi                      1.4.3  r351h0357c0b_0  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r35h0357c0b_1  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r35h0357c0b_2  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r35h0e574ca_3  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r36h0357c0b_1  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r36h0357c0b_2  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r36h0e574ca_3  anaconda/cloud/conda-forge
r-stringi                      1.4.3   r36h29659fb_0  anaconda/pkgs/r     
r-stringi                      1.4.3   r36h29659fb_0  pkgs/r              
r-stringi                      1.4.4   r35h0e574ca_0  anaconda/cloud/conda-forge
r-stringi                      1.4.4   r36h0e574ca_0  anaconda/cloud/conda-forge
r-stringi                      1.4.5   r35h0e574ca_0  anaconda/cloud/conda-forge
r-stringi                      1.4.5   r36h0e574ca_0  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r35h0e574ca_0  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r35h0e574ca_1  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r36h0e574ca_0  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r36h0e574ca_1  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r36h0e574ca_2  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r36h604b29c_3  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r40h0e574ca_2  anaconda/cloud/conda-forge
r-stringi                      1.4.6   r40h604b29c_3  anaconda/cloud/conda-forge
r-stringi                      1.5.3   r36h604b29c_0  anaconda/cloud/conda-forge
r-stringi                      1.5.3   r36hca8494e_0  anaconda/cloud/conda-forge
r-stringi                      1.5.3   r36hcabe038_1  anaconda/cloud/conda-forge
r-stringi                      1.5.3   r40h604b29c_0  anaconda/cloud/conda-forge
r-stringi                      1.5.3   r40hca8494e_0  anaconda/cloud/conda-forge
r-stringi                      1.5.3   r40hcabe038_1  anaconda/cloud/conda-forge
r-stringi                      1.6.1   r36hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.6.1   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.6.2   r36hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.6.2   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.6.2   r41hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.2   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.2   r41hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.3   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.3   r41hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.4   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.4   r41hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.5   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.5   r41hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r40h30a9eb7_2  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r40h337692f_1  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r40hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r41h30a9eb7_2  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r41h337692f_1  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r41hcabe038_0  anaconda/cloud/conda-forge
r-stringi                      1.7.6   r42h884c59f_0  anaconda/pkgs/r     
r-stringi                      1.7.6   r42h884c59f_0  pkgs/r              
r-stringi                      1.7.8   r40h30a9eb7_0  anaconda/cloud/conda-forge
r-stringi                      1.7.8   r41h30a9eb7_0  anaconda/cloud/conda-forge
r-stringi                      1.7.8   r41h30a9eb7_1  anaconda/cloud/conda-forge
r-stringi                      1.7.8   r42h30a9eb7_1  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r41h1ae9187_0  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r41hc0c3e09_1  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r42h1ae9187_0  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r42h9facbd6_3  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r42hc0c3e09_1  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r42hc0c3e09_2  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r43h884c59f_0  anaconda/pkgs/r     
r-stringi                     1.7.12   r43h884c59f_0  pkgs/r              
r-stringi                     1.7.12   r43h9facbd6_3  anaconda/cloud/conda-forge
r-stringi                     1.7.12   r43hc0c3e09_2  anaconda/cloud/conda-forge
r-stringi                      1.8.1   r42h9facbd6_0  anaconda/cloud/conda-forge
r-stringi                      1.8.1   r43h9facbd6_0  anaconda/cloud/conda-forge
r-stringi                      1.8.2   r42h9facbd6_0  anaconda/cloud/conda-forge
r-stringi                      1.8.2   r43h9facbd6_0  anaconda/cloud/conda-forge
r-stringi                      1.8.3   r42h9facbd6_0  anaconda/cloud/conda-forge
r-stringi                      1.8.3   r43h9facbd6_0  anaconda/cloud/conda-forge
r-stringi                      1.8.4   r42hbd1cc82_0  anaconda/cloud/conda-forge
r-stringi                      1.8.4   r43hbd1cc82_0  anaconda/cloud/conda-forge
ucsc-stringify                   324               0  anaconda/cloud/bioconda
ucsc-stringify                   332               0  anaconda/cloud/bioconda
ucsc-stringify                   357               0  anaconda/cloud/bioconda
ucsc-stringify                   357               1  anaconda/cloud/bioconda
ucsc-stringify                   366      h5eb252a_0  anaconda/cloud/bioconda
ucsc-stringify                   377      h0b8a92a_2  anaconda/cloud/bioconda
ucsc-stringify                   377      h199ee4e_0  anaconda/cloud/bioconda
ucsc-stringify                   377      h446ed27_1  anaconda/cloud/bioconda
ucsc-stringify                   377      ha8a8165_3  anaconda/cloud/bioconda

$ conda install r-ggplot2

$ conda install r-ggplot2 ##指定特定版本R包安装

四、GitHub来源R包
1、常规安装，如下所示：

> if (!require("remotes", quietly = TRUE))

2、下载源码安装
源文件一般在Releases中可以找到。


image.png

3、无源码文件
可以下载zip格式压缩包用如下方法尝试本地安装：


image.png
> devtools::install_local('gwasvcf-master.zip')

4、无源文件的还可以在服务器中解压zip包，本地创建源文件的方法安装


$ unzip presto-master.zip 

Archive:  presto-master.zip
7636b3d0465c468c35853f82f1717d3a64b3c8f6
   creating: presto-master/
  inflating: presto-master/.Rbuildignore  
   creating: presto-master/.github/
   creating: presto-master/.github/workflows/
  inflating: presto-master/.github/workflows/R-CMD-check.yaml  
  inflating: presto-master/.gitignore  
  inflating: presto-master/CRAN-RELEASE  
  inflating: presto-master/DESCRIPTION  
  inflating: presto-master/NAMESPACE  
 extracting: presto-master/NEWS.md   
   creating: presto-master/R/
  inflating: presto-master/R/RcppExports.R  
  inflating: presto-master/R/data.R  
  inflating: presto-master/R/presto-package.R  
  inflating: presto-master/R/pseudobulk.R  
  inflating: presto-master/R/utils.R  
  inflating: presto-master/R/wilcoxauc.R  
  inflating: presto-master/README.md  
  inflating: presto-master/cran-comments.md  
   creating: presto-master/data/
 extracting: presto-master/data/exprs.rda  
  inflating: presto-master/data/object_sce.rda  
  inflating: presto-master/data/object_seurat.rda  
 extracting: presto-master/data/y.rda  
   creating: presto-master/docs/
 extracting: presto-master/docs/.nojekyll  
  inflating: presto-master/docs/404.html  
   creating: presto-master/docs/articles/
  inflating: presto-master/docs/articles/getting-started.html  
  inflating: presto-master/docs/articles/index.html  
  inflating: presto-master/docs/authors.html  
  inflating: presto-master/docs/bootstrap-toc.css  
  inflating: presto-master/docs/bootstrap-toc.js  
  inflating: presto-master/docs/docsearch.css  
  inflating: presto-master/docs/docsearch.js  
  inflating: presto-master/docs/index.html  
  inflating: presto-master/docs/link.svg  
   creating: presto-master/docs/news/
  inflating: presto-master/docs/news/index.html  
  inflating: presto-master/docs/pkgdown.css  
  inflating: presto-master/docs/pkgdown.js  
  inflating: presto-master/docs/pkgdown.yml  
   creating: presto-master/docs/reference/
  inflating: presto-master/docs/reference/Rplot001.png  
  inflating: presto-master/docs/reference/collapse_counts.html  
  inflating: presto-master/docs/reference/compute_hash.html  
  inflating: presto-master/docs/reference/exprs.html  
  inflating: presto-master/docs/reference/index.html  
  inflating: presto-master/docs/reference/nnzeroGroups.html  
  inflating: presto-master/docs/reference/object_sce.html  
  inflating: presto-master/docs/reference/object_seurat.html  
  inflating: presto-master/docs/reference/pipe.html  
  inflating: presto-master/docs/reference/presto.html  
  inflating: presto-master/docs/reference/pseudobulk_deseq2.html  
  inflating: presto-master/docs/reference/pseudobulk_one_vs_all.html  
  inflating: presto-master/docs/reference/pseudobulk_pairwise.html  
  inflating: presto-master/docs/reference/pseudobulk_within.html  
  inflating: presto-master/docs/reference/rank_matrix.html  
  inflating: presto-master/docs/reference/sumGroups.html  
  inflating: presto-master/docs/reference/summarize_dge_pairs.html  
  inflating: presto-master/docs/reference/top_markers.html  
  inflating: presto-master/docs/reference/top_markers_dds.html  
  inflating: presto-master/docs/reference/wilcoxauc.html  
  inflating: presto-master/docs/reference/y.html  
  inflating: presto-master/docs/sitemap.xml  
   creating: presto-master/man/
  inflating: presto-master/man/collapse_counts.Rd  
  inflating: presto-master/man/compute_hash.Rd  
  inflating: presto-master/man/exprs.Rd  
  inflating: presto-master/man/nnzeroGroups.Rd  
  inflating: presto-master/man/object_sce.Rd  
  inflating: presto-master/man/object_seurat.Rd  
  inflating: presto-master/man/pipe.Rd  
  inflating: presto-master/man/presto.Rd  
  inflating: presto-master/man/pseudobulk_deseq2.Rd  
  inflating: presto-master/man/pseudobulk_one_vs_all.Rd  
  inflating: presto-master/man/pseudobulk_pairwise.Rd  
  inflating: presto-master/man/pseudobulk_within.Rd  
  inflating: presto-master/man/rank_matrix.Rd  
  inflating: presto-master/man/sumGroups.Rd  
  inflating: presto-master/man/summarize_dge_pairs.Rd  
  inflating: presto-master/man/top_markers.Rd  
  inflating: presto-master/man/top_markers_dds.Rd  
  inflating: presto-master/man/wilcoxauc.Rd  
  inflating: presto-master/man/y.Rd  
   creating: presto-master/src/
 extracting: presto-master/src/Makevars  
 extracting: presto-master/src/Makevars.win  
  inflating: presto-master/src/RcppExports.cpp  
  inflating: presto-master/src/fast_wilcox.cpp  
   creating: presto-master/tests/
  inflating: presto-master/tests/testthat.R  
   creating: presto-master/tests/testthat/
  inflating: presto-master/tests/testthat/test_correctness.R  
  inflating: presto-master/tests/testthat/test_datatypes.R  
   creating: presto-master/vignettes/
  inflating: presto-master/vignettes/getting-started.Rmd  
  inflating: presto-master/vignettes/pseudobulk.ipynb 

$ R CMD build gwasvcf-master

* checking for file ‘presto-master/DESCRIPTION’ ... OK
* preparing ‘presto’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘presto_1.0.0.tar.gz’

$ R CMD INSTALL gwasvcf-master.tar.gz

* installing to library ‘/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library’
* installing *source* package ‘presto’ ...
** using staged installation
** libs
using C++ compiler: ‘x86_64-conda-linux-gnu-c++ (conda-forge gcc 13.2.0-7) 13.2.0’
using C++11
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/include" -DNDEBUG  -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/Rcpp/include' -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/RcppArmadillo/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -I/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -Wl,-rpath-link,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib    -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1706308578445/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/include" -DNDEBUG  -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/Rcpp/include' -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/RcppArmadillo/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -I/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -Wl,-rpath-link,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib    -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1706308578445/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2=/usr/local/src/conda-prefix  -c fast_wilcox.cpp -o fast_wilcox.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -shared -L/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib -Wl,-rpath-link,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib -L/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib -o presto.so RcppExports.o fast_wilcox.o -L/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/lib -lR
installing to /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/00LOCK-presto/00new/presto/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (presto)

5、git clone到服务器安装


image.png
$ git clone https://github.com/immunogenomics/presto.git 

正克隆到 'presto'...
remote: Enumerating objects: 693, done.
remote: Counting objects: 100% (177/177), done.
remote: Compressing objects: 100% (86/86), done.
remote: Total 693 (delta 84), reused 145 (delta 79), pack-reused 516
接收对象中: 100% (693/693), 3.15 MiB | 1.10 MiB/s, done.
处理 delta 中: 100% (410/410), done.

$ R CMD build gwasvcf

* checking for file ‘presto/DESCRIPTION’ ... OK
* preparing ‘presto’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘presto_1.0.0.tar.gz’

$ R CMD INSTALL gwasvcf-master.tar.gz

* installing to library ‘/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library’
* installing *source* package ‘presto’ ...
** using staged installation
** libs
using C++ compiler: ‘x86_64-conda-linux-gnu-c++ (conda-forge gcc 13.2.0-7) 13.2.0’
using C++11
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/include" -DNDEBUG  -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/Rcpp/include' -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/RcppArmadillo/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -I/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -Wl,-rpath-link,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib    -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1706308578445/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/include" -DNDEBUG  -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/Rcpp/include' -I'/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/RcppArmadillo/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -I/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -Wl,-rpath-link,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib    -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1706308578445/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2=/usr/local/src/conda-prefix  -c fast_wilcox.cpp -o fast_wilcox.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -shared -L/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib -Wl,-rpath-link,/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib -L/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib -o presto.so RcppExports.o fast_wilcox.o -L/PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/lib -lR
installing to /PUBLIC/personal/xings/softwares/anaconda/conda/envs/r4.3.2/lib/R/library/00LOCK-presto/00new/presto/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (presto)

6、有一些R包很有特点，需要将zip文件解压，删除某些文件后才能安装，如CellChat。参考博客：

https://blog.csdn.net/siyan156/article/details/132778833

五、个人编写的R模块
自己可以把一些可复用的功能写成模块保存，重复使用的时候在R环境中加载使用。

> source('bayesreg.R')

总结：在安装R包时优先使用推荐的安装方法，自动处理依赖关系可以节省很多时间，遇到一些无法自动也装的R包也建议多试几次，这样可以自动安装一些依赖R包。实在无法安装时，可以尝试以上介绍的几种本地安装方法。

最后编辑于 ：
©著作权归作者所有,转载或内容合作请联系作者
  • 人面猴
    序言：七十年代末，一起剥皮案震惊了整个滨河市，随后出现的几起案子，更是在滨河造成了极大的恐慌，老刑警刘岩，带你破解...
    沈念sama阅读 216,544评论 6赞 501
  • 死咒
    序言：滨河连续发生了三起死亡事件，死亡现场离奇诡异，居然都是意外死亡，警方通过查阅死者的电脑和手机，发现死者居然都...
    沈念sama阅读 92,430评论 3赞 392
  • 救了他两次的神仙让他今天三更去死
    文/潘晓璐 我一进店门，熙熙楼的掌柜王于贵愁眉苦脸地迎上来，“玉大人，你说我怎么就摊上这事。” “怎么了？”我有些...
    开封第一讲书人阅读 162,764评论 0赞 353
  • 道士缉凶录：失踪的卖姜人
    文/不坏的土叔 我叫张陵，是天一观的道长。 经常有香客问我，道长，这世上最难降的妖魔是什么？ 我笑而不...
    开封第一讲书人阅读 58,193评论 1赞 292
  • 港岛之恋（遗憾婚礼）
    正文 为了忘掉前任，我火速办了婚礼，结果婚礼上，老公的妹妹穿的比我还像新娘。我一直安慰自己，他们只是感情好，可当我...
    茶点故事阅读 67,216评论 6赞 388
  • 恶毒庶女顶嫁案：这布局不是一般人想出来的
    文/花漫 我一把揭开白布。 她就那样静静地躺着，像睡着了一般。 火红的嫁衣衬着肌肤如雪。 梳的纹丝不乱的头发上，一...
    开封第一讲书人阅读 51,182评论 1赞 299
  • 城市分裂传说
    那天，我揣着相机与录音，去河边找鬼。 笑死，一个胖子当着我的面吹牛，可吹牛的内容都是我干的。 我是一名探鬼主播，决...
    沈念sama阅读 40,063评论 3赞 418
  • 双鸳鸯连环套：你想象不到人心有多黑
    文/苍兰香墨 我猛地睁开眼，长吁一口气：“原来是场噩梦啊……” “哼！你这毒妇竟也来了？” 一声冷哼从身侧响起，我...
    开封第一讲书人阅读 38,917评论 0赞 274
  • 万荣杀人案实录
    序言：老挝万荣一对情侣失踪，失踪者是张志新（化名）和其女友刘颖，没想到半个月后，有当地人在树林里发现了一具尸体，经...
    沈念sama阅读 45,329评论 1赞 310
  • 护林员之死
    正文 独居荒郊野岭守林人离奇死亡，尸身上长有42处带血的脓包…… 初始之章·张勋 以下内容为张勋视角 年9月15日...
    茶点故事阅读 37,543评论 2赞 332
  • 白月光启示录
    正文 我和宋清朗相恋三年，在试婚纱的时候发现自己被绿了。 大学时的朋友给我发了我未婚夫和他白月光在一起吃饭的照片。...
    茶点故事阅读 39,722评论 1赞 348
  • 活死人
    序言：一个原本活蹦乱跳的男人离奇死亡，死状恐怖，灵堂内的尸体忽然破棺而出，到底是诈尸还是另有隐情，我是刑警宁泽，带...
    沈念sama阅读 35,425评论 5赞 343
  • 日本核电站爆炸内幕
    正文 年R本政府宣布，位于F岛的核电站，受9级特大地震影响，放射性物质发生泄漏。R本人自食恶果不足惜，却给世界环境...
    茶点故事阅读 41,019评论 3赞 326
  • 男人毒药：我在死后第九天来索命
    文/蒙蒙 一、第九天 我趴在偏房一处隐蔽的房顶上张望。 院中可真热闹，春花似锦、人声如沸。这庄子的主人今日做“春日...
    开封第一讲书人阅读 31,671评论 0赞 22
  • 一桩弑父案，背后竟有这般阴谋
    文/苍兰香墨 我抬头看了看天上的太阳。三九已至，却和暖如春，着一层夹袄步出监牢的瞬间，已是汗流浃背。 一阵脚步声响...
    开封第一讲书人阅读 32,825评论 1赞 269
  • 情欲美人皮
    我被黑心中介骗来泰国打工， 没想到刚下飞机就差点儿被人妖公主榨干…… 1. 我叫王不留，地道东北人。 一个月前我还...
    沈念sama阅读 47,729评论 2赞 368
  • 代替公主和亲
    正文 我出身青楼，却偏偏与公主长得像，于是被迫代替她去往敌国和亲。 传闻我的和亲对象是个残疾皇子，可洞房花烛夜当晚...
    茶点故事阅读 44,614评论 2赞 353

推荐阅读更多精彩内容