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linux系统怎么安装pennCNV软件

发表于:2022-12-07 作者:安全数据网编辑
编辑最后更新 2022年12月07日,本篇内容介绍了"linux系统怎么安装pennCNV软件"的有关知识,在实际案例的操作过程中,不少人都会遇到这样的困境,接下来就让小编带领大家学习一下如何处理这些情况吧!希望大家仔细阅读,能够学有所成

本篇内容介绍了"linux系统怎么安装pennCNV软件"的有关知识,在实际案例的操作过程中,不少人都会遇到这样的困境,接下来就让小编带领大家学习一下如何处理这些情况吧!希望大家仔细阅读,能够学有所成!

pennCNV主要用于芯片数据分析CNV软件

PennCNV安装

wget https://github.com/WGLab/PennCNV/archive/v1.0.4.tar.gztar xvfz v1.0.4.tar.gzcd kext/make

但是会报错:

gcc `perl -MExtUtils::Embed -e ccopts` -fPIC   -c -o khmm_wrap.o khmm_wrap.ckhmm_wrap.c: In function 'SWIG_AsCharPtrAndSize':khmm_wrap.c:1576: error: 'bool' undeclared (first use in this function)khmm_wrap.c:1576: error: (Each undeclared identifier is reported only oncekhmm_wrap.c:1576: error: for each function it appears in.)khmm_wrap.c:1576: error: expected ':' before numeric constantkhmm_wrap.c: In function '_wrap_estHMMFromFile_CHMM':khmm_wrap.c:1875: error: 'bool' undeclared (first use in this function)khmm_wrap.c:1875: error: expected ':' before numeric constantkhmm_wrap.c:1875: error: expected ':' before numeric constantkhmm_wrap.c:1890: error: expected ':' before numeric constantkhmm_wrap.c:1890: error: expected ':' before numeric constantkhmm_wrap.c:1905: error: expected ':' before numeric constantkhmm_wrap.c:1905: error: expected ':' before numeric constantkhmm_wrap.c: In function '_wrap_testVit_CHMM':khmm_wrap.c:2005: error: 'bool' undeclared (first use in this function)khmm_wrap.c:2005: error: expected ':' before numeric constantkhmm_wrap.c:2005: error: expected ':' before numeric constantkhmm_wrap.c: In function '_wrap_GetStateProb_CHMM':khmm_wrap.c:2137: error: 'bool' undeclared (first use in this function)khmm_wrap.c:2137: error: expected ':' before numeric constantkhmm_wrap.c:2137: error: expected ':' before numeric constantkhmm_wrap.c: In function '_wrap_testVitTrio_CHMM':khmm_wrap.c:2325: error: 'bool' undeclared (first use in this function)khmm_wrap.c:2325: error: expected ':' before numeric constantkhmm_wrap.c:2325: error: expected ':' before numeric constantkhmm_wrap.c: In function '_wrap_reg_linear':khmm_wrap.c:2443: error: 'bool' undeclared (first use in this function)khmm_wrap.c:2443: error: expected ':' before numeric constantkhmm_wrap.c:2443: error: expected ':' before numeric constantkhmm_wrap.c:2458: error: expected ':' before numeric constantkhmm_wrap.c:2458: error: expected ':' before numeric constantkhmm_wrap.c:2473: error: expected ':' before numeric constantkhmm_wrap.c:2473: error: expected ':' before numeric constantkhmm_wrap.c:2488: error: expected ':' before numeric constantkhmm_wrap.c:2488: error: expected ':' before numeric constantmake: *** [khmm_wrap.o] Error 1

解决办法:

sed -i -e '/#undef bool/d' khmm_wrap.c

然后:

make cleanmake

还是报错:

gcc `perl -MExtUtils::Embed -e ccopts` -fPIC   -c -o khmm_wrap.o khmm_wrap.cgcc `perl -MExtUtils::Embed -e ccopts` -fPIC   -c -o khmm.o khmm.cgcc `perl -MExtUtils::Embed -e ccopts` -fPIC   -c -o kc.o kc.cgcc `perl -MExtUtils::Embed -e ccopts` -fPIC   -c -o khmmDev.o khmmDev.cgcc -shared -o khmm.so khmm_wrap.o khmm.o kc.o khmmDev.o `perl -MExtUtils::Embed -e ldopts`/usr/bin/ld: /share/work/biosoft/perl/perl-5.22.1/lib/5.22.1/x86_64-linux-thread-multi/CORE/libperl.a(op.o): relocation R_X86_64_32 against `PL_op_mutex' can not be used when making a shared object; recompile with -fPIC/share/work/biosoft/perl/perl-5.22.1/lib/5.22.1/x86_64-linux-thread-multi/CORE/libperl.a: could not read symbols: Bad valuecollect2: ld returned 1 exit statusmake: *** [khmm.so] Error 1

本人谷歌和查找说明文档,说GCC必须是4版本,而且perl版本要低于5.14.2:,于是安装低版本perl:

wget https://www.cpan.org/src/5.0/perl-5.14.2.tar.gztar xvfz perl-5.14.2.tar.gzcd perl-5.14.2./Configure -des -Dprefix=/share/work/perl/perl-v5.14.2 -Accflags='-fPIC'makemake install

然后再把这个版本的perl添加到PATH的开头就可以,顺利make 安装成功了。

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