R source file로 설치 in linux

👉 R version 4 homepage

TL;DR

wget https://cran.r-project.org/src/base/R-4/R-4.3.1.tar.gz

tar -xvzf R-4.3.1.tar.gz 
cd R-4.3.1

mkdir /source/R-4.3.1
./configure --prefix=/source/R-4.3.1 
make -j 10 & make install

# bashrc에 path설정 추가
echo -e "PATH=/source/R-4.3.1/bin:$PATH" >> ~/.bash_profile

같이 설치하면 좋은..

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.17")

Error 모음집

PCRE2

🚨 configure: error: PCRE2 library and headers are required, or use --with-pcre1 and PCRE >= 8.32 with UTF-8 support

💡 PCRE2 설치해준다

PCRE2 homepage

https://www.linuxfromscratch.org/blfs/view/svn/general/pcre2.html

wget https://github.com/PCRE2Project/pcre2/releases/download/pcre2-10.42/pcre2-10.42.tar.bz2
tar -xvf pcre2-10.42.tar.bz2
cd pcre2-10.42

mkdir /source/pcre2
./configure --prefix=/source/pcre2
make & make install

# bash_profile이나 bashrc에 path 잡아주자 OR R ./configure할때 --with-pcre2='/source/pcre2' 옵션주기
# CFLAGS, LDFLAGS가 중요한듯
export LD_LIBRARY_PATH=/source/pcre2/lib:$LD_LIBRARY_PATH
export CFLAGS="-I/source/pcre2/include"
export LDFLAGS="-L//source/pcre2/lib" 

이후 실패한 부분으로 돌아가서 다시시도, R 압축풀었던 폴더 지우고 처음부터 다시 돌리는 것도 추천

Fortran

🚨 configure: error: Maybe check LDFLAGS for paths to Fortran libraries?

💡 gfortran 위치 잡아주자

# gfortran 위치 확인
which gfortran

> /hpc/packages/minerva-centos7/gcc/11.2.0/bin/gfortran # 난 이런식으로 나옴

# LDFLAGS 에 위치 설정 추가 (잘보고 본인환경에 맞게 수정해서 넣기!)
export LDFLAGS="-L/hpc/packages/minerva-centos7/gcc/11.2.0/lib64 -L/hpc/packages/minerva-centos7/gcc/11.2.0/lib  -lgfortran"

이후 실패한 부분으로 돌아가서 다시시도, R 압축풀었던 폴더 지우고 처음부터 다시 돌리는 것도 추천

C compiler

이건 .configure 이후, make 시도하면서 생긴 에러

configure: error: cannot run C compiled programs.

gcc 분명 잘 설치 돼있는데 왜 이런 에러가 생기는지 이해할 수 없구요. gcc 경로 확인하고 bash_profile에 넣어준다.

export PATH=/hpc/packages/minerva-centos7/gcc/11.2.0/bin:$PATH
export LD_LIBRARY_PATH=/hpc/packages/minerva-centos7/gcc/11.2.0/lib64/:$LD_LIBRARY_PATH

R 다시 설치하는데 그래도 안되면.. --host=arm 옵션을 넣어보자.

readline & GLIBC

🚨 /usr/lib64/libc.so.6: version GLIBC_2.33’ not found `

wget https://ftp.gnu.org/gnu/make/make-4.4.tar.gz tar -xvzf make-4.4.tar.gz cd make-4.4 ./configure –prefix=/sc/arion/projects/scMultiscale/chos14/source/make-4.4 make -j10 make install PATH=/source/make-4.4/bin:$PATH

wget https://github.com/westes/flex/releases/download/v2.6.4/flex-2.6.4.tar.gz tar -xvzf flex-2.6.4.tar.gz cd flex-2.6.4 ./configure –prefix=/sc/arion/projects/scMultiscale/chos14/source/flex-2.6.4 make -j 10 & make install

wget https://ftp.gnu.org/gnu/bison/bison-3.8.2.tar.gz tar -xvzf bison-3.8.2.tar.gz cd bison-3.8.2 ./configure –prefix=/sc/arion/projects/scMultiscale/chos14/source/bison-3.8.2 make -j10 make install

wget https://ftp.gnu.org/gnu/glibc/glibc-2.40.tar.gz tar -xvzf glibc-2.40.tar.gz cd glibc-2.40 mkdir build cd build ../configure –prefix=/source/glibc-2.40

Reference

• Fortran error 해결방법