【软件安装】treepl的安装
我这里用的是brew安装的(为什么没用另一种办法,因为没走通)。
首先,下载原始文件,https://github.com/Homebrew/brew.git
由于网络问题,我下载的是zip文件,下载后解压。
unzip brew-master.zip
解压完成后,配置环境(注意:brew要求使用用户账号装软件)。
配置环境:
export LINUXBREWHOME=/abyss/git/treePL/Dependencies/brew-master
export PATH=$LINUXBREWHOME/bin:$PATH
export MANPATH=$LINUXBREWHOME/man:$MANPATH
export PKG_CONFIG_PATH=$LINUXBREWHOME/lib64/pkgconfig:$LINUXBREWHOME/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=$LINUXBREWHOME/lib64:$LINUXBREWHOME/lib:$LD_LIBRARY_PATH
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/local/lib64/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib64/pkgconfig:/usr/share/pkgconfig:$PKG_CONFIG_PATH
上述环境参考了前人的blog。
然后安装:
brew install brewsci/bio/treepl
brew/bin/brew update
Error: Please update your system curl.
Minimum required version: 7.41.0
Your curl version: 7.29.0
Your curl executable: /usr/bin/curl
Error: Please update your system Git.
Minimum required version: 2.7.0
Your Git version: 1.8.3.1
Your Git executable: /usr/bin/git
Error: 'curl' must be installed and in your PATH!
当然不会顺利:
切换为root账户。
更新curl:
curl http://curl.haxx.se/ca/cacert.pem -o /etc/pki/tls/certs/ca-bundle.crt
yum update curl --enablerepo=CityFanforCurl -y
vi /etc/yum.repos.d/city-fan-for-curl.repo #并写入下列内容
[CityFanforCurl]
name=City Fan Repo
baseurl=http://www.city-fan.org/ftp/contrib/yum-repo/rhel7/x86_64/
enabled=0
gpgcheck=0
yum update curl --enablerepo=CityFanforCurl -y
更新git:git clone https://github.com/git/git.git
还是用的下载的zip文件:
unzip git-master.zip
cd git-master
make prefix=/usr/local/git all
rpm -e --nodeps git
make prefix=/usr/local/git install
ln -s /usr/local/git/bin/git /usr/bin/git
好了,切换为普通用户:
brew install brewsci/bio/treepl
出现了新的报错:
ld: cannot find crti.o: No such file or directory
collect2: error: ld returned 1 exit status
make[3]: *** [libgcc_s.so] Error 1
make[3]: Leaving directory `/tmp/gccA5-20210913-48366-1fzd36k/gcc-5.5.0/build/x86_64-unknown-linux-gnu/libgcc'
make[2]: *** [all-stage1-target-libgcc] Error 2
make[2]: Leaving directory `/tmp/gccA5-20210913-48366-1fzd36k/gcc-5.5.0/build'
make[1]: *** [stage1-bubble] Error 2
make[1]: Leaving directory `/tmp/gccA5-20210913-48366-1fzd36k/gcc-5.5.0/build'
make: *** [bootstrap] Error 2
READ THIS: https://docs.brew.sh/Troubleshooting
报错找不到这个文件,找一下,重新加入静态库。
find /usr/ -name crti*
/usr/lib64/crti.o
export LIBRARY_PATH=/usr/lib64:$LIBRARY_PATH
brew install brewsci/bio/treepl
当然还是不行的,报错和上面的一样。
https://github.com/Homebrew/linuxbrew-core/issues/23460
说实话,没看懂这个帖子,反正就是gcc的安装有问题。
brew install gcc # 没啥用
sudo apt-get install libc6-dev #都说用这个命令,可是我的系统是centos(yum install glibc-devel,显示已经安装过了)
chmod 755 /usr/lib64/crti.o
再来,。。。
继续在错误的边缘作死,网上说安装32位的可以解决,试试:
yum install glibc-devel.i686 libgcc.i686 libstdc++-devel.i686 ncurses-devel.i686
再来,。。。
ld: i386 architecture of input file `/lib/crti.o' is incompatible with i386:x86-64 output
ld: i386 architecture of input file `/lib/crtn.o' is incompatible with i386:x86-64 output
collect2: error: ld returned 1 exit status
make[3]: *** [libgcc_s.so] Error 1
make[3]: Leaving directory `/tmp/gccA5-20210913-174084-1ta7b9t/gcc-5.5.0/build/x86_64-unknown-linux-gnu/libgcc'
make[2]: *** [all-stage1-target-libgcc] Error 2
make[2]: Leaving directory `/tmp/gccA5-20210913-174084-1ta7b9t/gcc-5.5.0/build'
make[1]: *** [stage1-bubble] Error 2
make[1]: Leaving directory `/tmp/gccA5-20210913-174084-1ta7b9t/gcc-5.5.0/build'
make: *** [bootstrap] Error 2
READ THIS: https://docs.brew.sh/Troubleshooting
删掉重来,。。。
ln -s /usr/lib64/crti.o /usr/lib/crti.o
ln -s /usr/lib64/crtn.o /usr/lib/crtn.o
checking for C compiler default output file name...
configure: error: in `/tmp/gccA5-20210913-40796-eiywp6/gcc-5.5.0/build/x86_64-unknown-linux-gnu/libgomp':
configure: error: C compiler cannot create executables
See `config.log' for more details.
make[2]: *** [configure-stage1-target-libgomp] Error 77
make[2]: Leaving directory `/tmp/gccA5-20210913-40796-eiywp6/gcc-5.5.0/build'
make[1]: *** [stage1-bubble] Error 2
make[1]: Leaving directory `/tmp/gccA5-20210913-40796-eiywp6/gcc-5.5.0/build'
make: *** [bootstrap] Error 2
READ THIS: https://docs.brew.sh/Troubleshooting
再重来
export LIBS=
export CFLAGS=
不行的。。
理论上就是用yum install glibc-devel安装相应库,然而我的提示之前就安装过了,所以并不知道什么情况,我还是重装一次吧。
最后还是放弃了,后来师兄师姐安装上了。
如下图:https://anaconda.org/genomedk/treepl
除了一句万物皆可conda,只能对自己的智商感到捉急了。
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最近公众号没有更新,等有文章了的吧,不过广告还是要打一下:
网站服务器没有续费,等攒一点素材了再去续吧。
以上,
abysw
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posted on 2021-09-13 17:03 Yuan-SW-F(abysw) 阅读(980) 评论(0) 编辑 收藏 举报