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This article introduces the relevant knowledge of "how to install pennCNV software in linux system". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

PennCNV is mainly used for chip data analysis CNV software.

PennCNV installation

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

But will report an error:

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

Solution:

Sed-I-e'/ # undef bool/d' khmm_wrap.c

Then:

Make cleanmake

Or report an error:

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

I Google and find the documentation, saying that the GCC must be version 4, and the perl version must be less than 5.14.2 perl, so install the lower version of 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

Then add this version of perl to the beginning of PATH, and the make installation is successful.

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