bedtools软件安装报错:gzopen函数未定义(undefined reference to `gzopen64')
2017-02-22 14:07
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在如下网站下载最新版软件:https://github.com/arq5x/bedtools2/releases/tag/v2.26.0
https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
wget https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz tar xzf bedtools-2.26.0.tar.gz
cd bedtools2
vim Makefile,将第28行修改为:prefix = /ifs4/BC_COM_P5/F15FTSECKF0984/PEOahnD/PEOahnD/hlb/bin/bedtools-2.26/
make
报错:
- Building main bedtools binary.
obj/gzstream.o: In function `gzstreambuf::open(char const*, int)':
gzstream.C:(.text+0x2a2): undefined reference to `gzopen64'
collect2: ld 返回 1
make: *** [all] 错误 1
搜索系统中库文件:
locate libz.so | less
输出如下:
/lib64/libz.so.1
/lib64/libz.so.1.2.3
/root/zlib-1.2.8/libz.so
/root/zlib-1.2.8/libz.so.1
/root/zlib-1.2.8/libz.so.1.2.8
/usr/lib64/libz.so
/usr/local/lib/libz.so
/usr/local/lib/libz.so.1
/usr/local/lib/libz.so.1.2.8
分别查询上述.so文件中的函数地址,如果都找不到,则需安装最新版本的libz
objdump -T /lib64/libz.so.1 | grep gzopen64
objdump -T /lib64/libz.so.1.2.3 | grep gzopen64
objdump -T /root/zlib-1.2.8/libz.so | grep gzopen64
objdump -T /root/zlib-1.2.8/libz.so.1 | grep gzopen64
objdump -T /root/zlib-1.2.8/libz.so.1.2.8 | grep gzopen64
objdump -T /usr/lib64/libz.so | grep gzopen64
objdump -T /usr/local/lib/libz.so | grep gzopen64
objdump -T /usr/local/lib/libz.so.1.2.8 | grep gzopen64
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export LDFLAGS="-L/usr/local/lib"
make
安装成功
https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
wget https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz tar xzf bedtools-2.26.0.tar.gz
cd bedtools2
vim Makefile,将第28行修改为:prefix = /ifs4/BC_COM_P5/F15FTSECKF0984/PEOahnD/PEOahnD/hlb/bin/bedtools-2.26/
make
报错:
- Building main bedtools binary.
obj/gzstream.o: In function `gzstreambuf::open(char const*, int)':
gzstream.C:(.text+0x2a2): undefined reference to `gzopen64'
collect2: ld 返回 1
make: *** [all] 错误 1
搜索系统中库文件:
locate libz.so | less
输出如下:
/lib64/libz.so.1
/lib64/libz.so.1.2.3
/root/zlib-1.2.8/libz.so
/root/zlib-1.2.8/libz.so.1
/root/zlib-1.2.8/libz.so.1.2.8
/usr/lib64/libz.so
/usr/local/lib/libz.so
/usr/local/lib/libz.so.1
/usr/local/lib/libz.so.1.2.8
分别查询上述.so文件中的函数地址,如果都找不到,则需安装最新版本的libz
objdump -T /lib64/libz.so.1 | grep gzopen64
objdump -T /lib64/libz.so.1.2.3 | grep gzopen64
objdump -T /root/zlib-1.2.8/libz.so | grep gzopen64
objdump -T /root/zlib-1.2.8/libz.so.1 | grep gzopen64
objdump -T /root/zlib-1.2.8/libz.so.1.2.8 | grep gzopen64
objdump -T /usr/lib64/libz.so | grep gzopen64
objdump -T /usr/local/lib/libz.so | grep gzopen64
objdump -T /usr/local/lib/libz.so.1.2.8 | grep gzopen64
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export LDFLAGS="-L/usr/local/lib"
make
安装成功
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