JupyterR内核在Seurat及依赖包安装时，Error: C++17 standard requested but CXX17 is not defined各种报错问题及解决方案

1 前言

这几天需要跑单细胞的数据，单位服务器只有Python的内核，搭建完R内核后开始装R包，第一个：Seurat就开始各种报错，记录大战三百回合。笔者倔起来就是肝，坚决不docker，就是要搞。报错的起因是Error: C++17 standard requested but CXX17 is not defined本篇顺带记录其他相关报错，下文一一细说，排序无先后主次之分。

2 报错类型及解决方案

2.1 “安装程序包‘RcppArmadillo’时退出狀態的值不是0”

1. 这类报错提示很泛，各种原因都有可能，最常见能解决的就是一个一个安装依赖包，将这些报错的包名称在R包官网列表里找到，安装对应的报错包的依赖包
2. 再不济，就下载对应的压缩包，选择一一本地安装，这里是在Rstudio server内进行的，

2.2 package ‘reticule’ is not available for Bioconductor version ‘3.15’

Bioconductor版本3.15，R4.2后要安装3.16，安装新版本即可

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.16")

###安装全部
Upgrade 36 packages to Bioconductor version '3.16'? [y/n]: 
y

然后就来新的包安装报错了，再继续一一安装解决，这个就是重复且机械的活。R实在太薛定谔了，除了个别明星报错，这种大类的很泛的报错，指不定现在安装不行，过两天明天安装又行了；别人的电脑可以，自己的电脑不行（多半是路径安装目录，环境配置），所以只能一个一个试，来一个解决一个，来一群解决一群

> warnings()
Warning messages:
1: In install.packages(...) :
  installation of package ‘httpuv’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘impute’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘preprocessCore’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘cluster’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘stringi’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘Matrix’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘nlme’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘RcppEigen’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘mgcv’ had non-zero exit status
10: In install.packages(...) :
  installation of package ‘Biostrings’ had non-zero exit status
11: In install.packages(...) :
  installation of package ‘interp’ had non-zero exit status

2.3 Error: C++17 standard requested but CXX17 is not defined

这个是GCC版本问题，设置一下用新版本就行了，这个在终端运行，立竿见影

module load GCC/7.2.0-2.29
然后:
mkdir -p ~/.R
  echo 'CXX17 = g++ -std=c++17 -fPIC' > ~/.R/Makevars

2.4 /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status

还是gcc的问题

# 在终端运行，把ld换成自己报错时的路径
ldconfig -p | grep ld
which ld

# 更新
sudo yum update

# 查看版本
gcc --version
gfortran --version

# 重新安装一次就行了
sudo yum install gcc-gfortran