下载R的源代码：
建议使用的参数：
--enable-R-shlib最好开启，否则libR.so将不会生成，而很多程序依赖本这个库。
tcktk问题：
sudo apt-get install tcl-dev，sudo apt-get install tk-dev
yum install tcl tcl-devel tk,tk-devel
为了解决后面使用Rstudio X11无法画图问题，建议yum install cairo-devel来安装cairo的库。后续通过Rstudio的global options里面的页面，设置用cairo来显示图形。
R编译和安装命令：
sudo ./configure --enable-R-shlib --with-x --with-tcltk CFLAGS="-fPIC" CXXFLAGS="-fPIC"
或者./configure --enable-R-shlib --with-x --with-tcltk
./configure --enable-R-shlib --with-x --with-tcltk --with-libtiff --with-libpng --with-jpeglib --with-x --with-cairo --with-pcre1 --with-tiff --with-jpeg
./configure --enable-R-shlib --with-x --with-tcltk --with-libtiff --with-libpng --with-jpeglib --with-cairo --with-pcre1 --with-tiff --with-jpeg --with-blas --with-lapack --with-readline
make
make install
安装完后的总结：
R is now configured for x86_64-pc-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -g -O2
Fortran fixed-form compiler: gfortran -g -O2
Default C++ compiler: g++ -std=gnu++17 -g -O2
C++11 compiler: g++ -std=gnu++11 -g -O2
C++14 compiler: g++ -std=gnu++14 -g -O2
C++17 compiler: g++ -std=gnu++17 -g -O2
C++20 compiler:
C++23 compiler:
Fortran free-form compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries: pcre2, readline, curl
Additional capabilities: PNG, NLS
Options enabled: shared R library, shared BLAS, R profiling
Capabilities skipped: JPEG, TIFF, cairo, ICU
Options not enabled: memory profiling
Recommended packages: yes
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
X11图形显示的问题：
这个比较容易有问题。暂时未找到好的解决方法
其他由于缺少依赖的而需要安装的：
No Fortran compiler found：
yum install gcc-gfortran
error: --with-readline=yes (default) and headers/libs are not available：
yum install readline-devel
error: --with-x=yes (default) and X11 headers/libs are not available：
yum install libXt-devel
configure: error: libcurl >= 7.28.0 library and headers are required with support for https：yum install libcurl-devel(注意看版本)
#include <jni.h>
编译中断。
make[2]: *** [/home/dongxj/R-4.3.2/etc/Makeconf:191：conftest.o] 错误 1
make[2]: 离开目录“/tmp/Rjavareconf.fSHbh4”
Unable to compile a JNI program：
yum -y install java-1.8.0-openjdk java-1.8.0-openjdk-devel
checking for BZ2_bzlibVersion in -lbz2... no
checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required：
yum install bzip2-devel
其他推荐的系统基础库安装：(centos stream)
yum install libxml2-devel
yum install harfbuzz-devel
yum install fribidi-devel
yum install freetype-devel libpng-devel libtiff-devel libjpeg-devel
单细胞分析常用R包安装：
harmony：
install.packages("harmony")
infercnv：
先安装lapack和blas：
https://www.netlib.org/lapack/#_lapack_version_3_10_0
http://www.netlib.org/blas/
安装的时候，遇到问题：
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/8/../../../liblapack.a(dlarf.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: //usr/local/lib/libblas.a(dgemv.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
可能是R安装时，配置时没有加--with-blas和--with-lapack的参数？gcc版本太低？
于是yum install lapack，后重新编译了R。也不行。
使用新的gcc，版本
https://blog.csdn.net/qq_37329349/article/details/82385012
https://www.jianshu.com/p/d5a03fca267e
https://www.cnblogs.com/snake553/p/7151787.html
安装JAGS遇到的问题：(centos8,gcc8.5.0)
checking for Fortran 77 libraries of gfortran... (cached) -L/usr/lib/gcc/x86_64-redhat-linux/8 -L/usr/lib/gcc/x86_64-redhat-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/8/../../.. -lgfortran -lm -lquadmath
checking for sgemm_ in /usr/lib64... no
checking if sgemm_ is being linked in already... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lmkl... no
checking for sgemm_ in -framework vecLib... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
configure: error: "You need to install the LAPACK library"
可是明明已经yum install lapack。他搜索KAPACK库的地址应该是在gcc里的。
GSVA:
BiocManager::install("GSVA")
GSEABase:
BiocManager::install("GSEABase")
msigdbr:
BiocManager::install("msigdbr")
COSG：
remotes::install_github(repo = 'genecell/COSGR')
https://cloud.tencent.com/developer/article/2320105
dittoSeq:
BiocManager::install("dittoSeq")
VISION:
yum install libsodium-devel
BiocManager::install("VISION")
harmony：
library("devtools")
install_github("immunogenomics/harmony")
SCENIC：
需要安装GENIE3’, ‘RcisTarget’, ‘AUCell
BiocManager::install("AUCell")
BiocManager::install("GENIE3")
devtools::install_github("aertslab/RcisTarget")
devtools::install_github("aertslab/SCENIC")
Cellchat：
要安装ComplexHeatmap’, ‘BiocNeighbors
BiocManager::install("ComplexHeatmap")
BiocManager::install("BiocNeighbors")
devtools::install_github("sqjin/CellChat")
scMetabolism：
wget https://cloud.r-project.org/src/contrib/magick_2.8.3.tar.gz
devtools::install_github("wu-yc/scMetabolism")
scRNAtoolVis:
yum install ImageMagick-c++-devel
wget https://cloud.r-project.org/src/contrib/magick_2.8.3.tar.gz（注意下载地址可能会变动，到时到https://cloud.r-project.org/src/contrib搜索magick的最新地址）
R CMD INSTALL magick_2.8.3.tar.gz
devtools::install_github('junjunlab/scRNAtoolVis')
monocle2：
BiocManager::install(c("leidenbase","viridis","biocViews","RANN"))
BiocManager::install("monocle")
参考：https://zhuanlan.zhihu.com/p/669186759，https://www.jianshu.com/p/e7c02697e015
monocle3：
yum install udunits2-devel
参考：https://www.jianshu.com/p/78eeae93c5a0
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