安装Perl编写的RAST程序时遇符号查找错误求助

执行的安装命令 #

mkdir sas
cp ~/Downloads/sas.tgz sas
cd sas
TOP=`pwd`
tar -zxvf sas.tgz
cd modules
./BUILD_MODULES
export PERL5LIB=$PERL5LIB:$TOP/lib:$TOP/modules/lib
export PATH=$PATH:$TOP/bin

错误信息 #

perl: symbol lookup error: /usr/local/share/perl5/lib/perl5/x86_64-linux-thread-multi/auto/version/vxs/vxs.so: undefined symbol: Perl_xs_apiversion_bootcheck
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
Build URI-1.53
perl: symbol lookup error: /usr/local/share/perl5/lib/perl5/x86_64-linux-thread-multi/auto/version/vxs/vxs.so: undefined symbol: Perl_xs_apiversion_bootcheck
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
Build HTML-Tagset-3.03
perl: symbol lookup error: /usr/local/share/perl5/lib/perl5/x86_64-linux-thread-multi/auto/version/vxs/vxs.so: undefined symbol: Perl_xs_apiversion_bootcheck
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
Build HTML-Parser-3.64
perl: symbol lookup error: /usr/local/share/perl5/lib/perl5/x86_64-linux-thread-multi/auto/version/vxs/vxs.so: undefined symbol: Perl_xs_apiversion_bootcheck
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
Build libwww-perl-5.834
perl: symbol lookup error: /usr/local/share/perl5/lib/perl5/x86_64-linux-thread-multi/auto/version/vxs/vxs.so: undefined symbol: Perl_xs_apiversion_bootcheck
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.
Build Task-Weaken-1.02
perl: symbol lookup error: /usr/local/share/perl5/lib/perl5/x86_64-linux-thread-multi/auto/version/vxs/vxs.so: undefined symbol: Perl_xs_apiversion_bootcheck
make: *** No targets specified and no makefile found.  Stop.
make: *** No rule to make target `install'.  Stop.

系统环境信息 #

• 系统Perl版本：perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi
• 尝试过conda环境的perl-5.34.0，错误相同
• 非系统管理员，无法删除/usr/local下的Perl模块
• PATH变量内容：

/opt/software/miniconda3/bin
/opt/software/miniconda3/condabin
/opt/CREST
/usr/local/FastQC
/usr/local/IGV
/usr/local/IGVTools
/usr/local/MUMmer
/usr/local/TrimGalore-0.5.0
/usr/local/blast
/usr/local/bowtie2
/usr/local/circos/bin
/usr/local/fastx
/usr/local/bin/gatk
/usr/local/hisat2-2.1.0
/usr/local/mauve
/usr/local/mauve/linux-x64
/usr/local/mothur
/usr/local/mothur/blast/bin
/usr/local/ngsplot/bin
/usr/local/subread-1.6.3-Linux-x86_64/bin
/opt/jdk1.8.0_171/bin
/opt/jdk1.8.0_171/jre/bin

1. 隔离系统冲突模块，使用本地安装路径 #

错误核心是系统/usr/local下的version模块与当前Perl版本不兼容，导致符号缺失。通过修改环境变量让Perl优先使用本地模块：

在执行./BUILD_MODULES前，先运行：

# 清空原有PERL5LIB，避免加载系统冲突模块
export PERL5LIB="$TOP/lib:$TOP/modules/lib"
# 指定依赖模块安装到当前目录的local_perl文件夹
export PERL_MM_OPT="INSTALL_BASE=$TOP/local_perl"
export PERL_MB_OPT="--install_base $TOP/local_perl"
# 将本地模块路径加入优先搜索队列
export PERL5LIB="$TOP/local_perl/lib/perl5:$PERL5LIB"

再执行./BUILD_MODULES，所有依赖会安装到本地，不会调用系统中冲突的version模块。

2. 创建完全隔离的conda Perl环境 #

之前的conda环境可能继承了系统PERL5LIB，需创建纯净环境：

# 创建新conda环境，指定与系统接近的Perl版本
conda create -n rast_perl perl=5.32.1 -y
# 激活环境
conda activate rast_perl
# 重新执行安装步骤，清空PERL5LIB避免系统模块干扰
mkdir sas
cp ~/Downloads/sas.tgz sas
cd sas
TOP=`pwd`
tar -zxvf sas.tgz
cd modules
unset PERL5LIB
./BUILD_MODULES
export PERL5LIB="$TOP/lib:$TOP/modules/lib:$CONDA_PREFIX/lib/perl5/site_perl/5.32.1/x86_64-linux-thread-multi"
export PATH="$TOP/bin:$PATH"

3. 手动安装兼容的version模块 #

如果上述方法无效，手动在本地安装对应版本的version模块：

# 下载与Perl5.32兼容的version模块源码
wget https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK/version-0.9924.tar.gz
tar -zxvf version-0.9924.tar.gz
cd version-0.9924
# 安装到本地目录
perl Makefile.PL INSTALL_BASE=$TOP/local_perl
make
make install
# 加入环境变量
export PERL5LIB="$TOP/local_perl/lib/perl5:$PERL5LIB"
# 回到modules目录重新执行安装
cd ../modules
./BUILD_MODULES

内容的提问来源于stack exchange，提问作者random