在linux系统、conda环境下配置R软件及R包（内含fatal error: glpk.h: No such file or directory不完全解决办法:(

在第五次因为偷懒想使用本地RStudio跑scRNA-seq数据结果电脑死机蓝屏只能强制重启后——

终于开始配置linux系统服务器下的R了。

本文参考大佬教程：

https://blog.csdn.net/liangjinghui123/article/details/131494540

https://blog.csdn.net/luofunong/article/details/132870880

前情提要：服务器无sudo权限，无法修改默认目录以及各种Path

##linux配置R环境
##查看已有环境
conda info --envs
##新建conda环境
conda create -n R_temporary

中途选择默认yes

##激活环境
source activate R_temporary

##添加channels
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
conda config --set show_channel_urls yes
conda config --show
##查看R版本信息
conda search r-base
##选择合适的版本安装
conda install r-base=4.3.2

全都选择y

安装成功后（done）进入R：

##进入R
R
##退出R
#q()

 先设置镜像源：

##查看镜像
options()$repos
#    CRAN
#"@CRAN@"
##打开文件
file.edit(file.path("~",".Rprofile"))
##“a”进入编辑状态，写入代码，Esc结束编辑，“:wq”退出
#options("repos"= c(CRAN="https://mirrors.pku.edu.cn/CRAN/","http://mirrors.aliyun.com/CRAN"))
options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","https://mirrors.tuna.tsinghua.edu.cn/CRAN/","http://mirrors.aliyun.com/CRAN","https://mirrors.ustc.edu.cn/CRAN/"))
print("已设置北大阿里云镜像")
##退出再重新进入R，查看镜像是否设置好
q()
##进入R
R
##查看镜像
options()$repos
#保证镜像源设置好，装包才能顺利

然后就开始在R中安装BiocManager：

##安装BiocManager：https://www.bioconductor.org/install/
#The current release of Bioconductor is version 3.18; it works with R version 4.3.0.
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.18")

在安装BiocManager时也容易遇到千奇百怪的报错：

  URL 'https://bioconductor.org/config.yaml': status was 'Problem with the SSL CA cert (path? access rights?)'

还有：

Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
Warning messages:
1: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'Couldn't resolve host name'
2: In file(con, "r") :
  URL 'http://bioconductor.org/config.yaml': status was 'Couldn't resolve host name'
Error: Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette

一直报错，无法解决——

试试这样：https://cloud.tencent.com/developer/article/2228246

##让Bioconductor通过联网去验证版本
options(BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS=TRUE)
install.packages("BiocManager")
library(BiocManager)

（其实完全没有装好，但是我装不下去了==）

继续——

正常安装R包：

install.packages("Seurat")#没装上
#version = 5.0.1
library(Seurat)
install.packages("tidyverse")#没装上
library(tidyverse)
install.packages("patchwork")
library(patchwork)
install.packages("ggplot2")
library(ggplot2)
install.packages("clustree")#没装上
library(clustree)
install.packages("cowplot")
library(cowplot)
install.packages("dplyr")
library(dplyr)
install.packages("harmony")
library(harmony) 
BiocManager::install("monocle")#没装上
library(monocle)

可以看到，我一共想安装9个R包，最终安装成功并能顺利library调用的只有5个！！！

经过我千奇百怪的搜索和安装尝试后，报错也千奇百怪：

make: *** [/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/lib/R/etc/Makeconf:193: vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/lib/R/library/igraph’

Warning message:
In install.packages("igraph") :
  installation of package ‘igraph’ had non-zero exit status

Warning: unable to access index for repository https://mirrors.pku.edu.cn/CRAN/src/contrib:
  cannot open URL 'https://mirrors.pku.edu.cn/CRAN/src/contrib/PACKAGES'
Warning: unable to access index for repository https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib:
  cannot open URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/PACKAGES'
Warning: dependency ‘graph’ is not available

甚至还有缺少编译文件：

In file included from vendor/cigraph/src/community/optimal_modularity.c:32:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: glpk.h: No such file or directory
   39 | #include <glpk.h>
      |          ^~~~~~~~
compilation terminated.
make: *** [/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/lib/R/etc/Makeconf:193: vendor/cigraph/src/community/optimal_modularity.o] Error 1

或者又是缺少依赖库：

Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
 * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
 * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
 * csw: libharfbuzz_dev libfribidi_dev (Solaris)
 * brew: harfbuzz fribidi (OSX)
If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: hb-ft.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘textshaping’

/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lxml2: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/lib/R/share/make/shlib.mk:10: xml2.so] Error 1
ERROR: compilation failed for package ‘xml2’
* removing 

但没有sudo权限，根本无法补装依赖库……

在焦虑的驱使下，找到了这篇文章：

https://zhuanlan.zhihu.com/p/585291878

“退出R，使用conda安装”

本小白第一次知道R包还可以用conda安装……

直接开装最难搞也是最有用的Seurat包：

只需静静等待它成功：

进R试试：

注意了，Seurat包首字母可要大写啊！

好好好，又报错：

Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘htmltools’ 0.5.6.1 is already loaded, but >= 0.5.7 is required

install一下试试看呢？ 

install.packages("htmltools")

Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘htmltools’ 0.5.6.1 is already loaded, but >= 0.5.7 is required

仍然报版本错误……那把R包安装路径里的文件夹删掉再重新装呢？

#查看R包安装路径
.libPaths()
#去路径里把htmltools包文件夹删掉
#再次安装
install.packages("htmltools")

继续报错：

ERROR: failed to lock directory ‘/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/lib/R/library’ for modifying
Try removing ‘/hpc/data/home/xxx/software/miniconda3/envs/R_temporary/lib/R/library/00LOCK-htmltools’

再去路径里把00LOCK-htmltools文件夹删掉！

（如果删不掉就重新进入R再删）

删掉后再次安装：

install.packages("htmltools")

然后就很顺利地安装好啦~

再次调用Seurat：（== 你还记得安装htmltools是为了Seurat吗（（

成功~

同理，tidyverse和clustree都可以成功安装~

最后看看需要BiocManager安装的monocle：

也找到了大佬的trouble shooting：https://blog.csdn.net/wangyiqi806643897/article/details/125077367

运用一些普适性命令（别搞特殊（

在Bioconda上找到要安装的包的对应名字：

conda install -c bioconda bioconductor-monocle

好好好，又报错了：

没有sudo权限的情况下好像确实不好装包…

不装了==累了，就写到这。