GLIBC error 之小胡踩坑记

使用UCSC tool中的bedToGenePred报错glibc版本错误

在没有root权限的基础上进行一系列版本更新，耗时很长…

binutils 2.31 更新ld(后来发现没有必要…)

bison 3.1

gcc 4.9.4

gmp 6.1.2

mpfr 4.0.1

mpc 1.1.0

little trick in make binutils

1) run configure as normal

2) run 'make' it will fail in the gas directory

3) run 'mv bfd/config.h bfd/config.h.bak' this forces the compilation to select the correct config.h 

4) run 'cd gas/'

5) run 'make'

6) run 'cd ..'

7) run 'make' this will rebuild bfd, but it will skip over gas and avoid the error... however it will then descend into binutils and run into the same error...

8) run 'mv bfd/config.h bfd/config.h.bak'

9) run 'cd binutils/'

10) run 'make'

11) run 'cd ..'

12) run 'make' this will rebuild bfd, but it will skip over gas and binutils... this time everything else compiles without error

wget https://mirrors.tuna.tsinghua.edu.cn/gnu/binutils/binutils-2.31.tar.gz

tar xvzf binutils-2.31.tar.gz

cd binutils-2.31

./configure --prefix=$prefix

make

mv bfd/config.h bfd/config.h.bak

cd gas

make

cd ..

make

mv bfd/config.h bfd/config.h.bak

cd binutils

make

cd ..

make

wget ftp://ftp.gnu.org/gnu/bison/bison-3.1.tar.gz

tar xvzf bison-3.1.tar.gz

cd bison-3.1

./configure --prefix=$prefix

make

make install

gcc 依赖ftp://gcc.gnu.org/pub/gcc/infrastructure

wget https://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2

wget https://ftp.gnu.org/gnu/mpfr/mpfr-4.0.1.tar.gz

wget https://ftp.gnu.org/gnu/mpc/mpc-1.1.0.tar.gz

tar xjvf gmp-6.1.2.tar.bz2

tar xvzf mpc-1.1.0.tar.gz

tar xvzf mpfr-4.0.1.tar.gz

cd gmp-6.1.2/

./configure --prefix=$prefix

make

make install

cd mpfr-4.0.1/

./configure --prefix= --with-gmp-include=/picb/rnasys/program/include --with-gmp-lib=/picb/rnasys/program/lib

make

make install

cd mpc-1.1.0/

./configure --prefix= --with-gmp-include=/picb/rnasys/program/include --with-gmp-lib=/picb/rnasys/program/lib

make

make install

gcc编译踩坑记

未在gcc source目录外编译报错

configure: error: building out of tree but ../gcc-4.9.4 contains host-x86_64-unknown-linux-gnu.

mkdir gcc_build

cd gcc_build

../gcc-4.9.4/configure --prefix=program LDFLAGS="-L/program/lib" CPPFLAGS="-I/program/include" --disable-multilib

持久战，编译gcc需要很久

PREFIX=

export LD_LIBRARY_PATH=$PREFIX/gmp/lib:$PREFIX/mpfr/lib:$PREFIX/mpc/lib:$PREFIX/isl/lib:$PREFIX/cloog/lib

export C_INCLUDE_PATH=$PREFIX/gmp/include:$PREFIX/mpfr/include:$PREFIX/mpc/include:$PREFIX/isl/include:$PREFIX/cloog/include

export CPLUS_INCLUDE_PATH=$PREFIX/gmp/include:$PREFIX/mpfr/include:$PREFIX/mpc/include:$PREFIX/isl/include:$PREFIX/cloog/include

../configure --with-gmp=$PREFIX/gmp --with-mpfr=$PREFIX/mpfr --with-mpc=$PREFIX/mpc --with-isl=$PREFIX/isl --with-cloog=$PREFIX/cloog --enable-static --disable-multilib --prefix=/picb/rnasys/program/bin/gcc --enable-languages=c,c++,fortran

make -j $THREADS bootstrap && make install

gcc编译成功

glibc也编译成功。。

noted glibc 2.14 与高版本的gcc ld冲突。。