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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
35 stars 11 forks source link

Crass compilation error #96

Closed Russel88 closed 5 years ago

Russel88 commented 5 years ago

Hi

I have a problem with compilation of crass

Hope you can help me pinpointing how to solve the problem. I looked through the other compilation issues, but they didn't seem related to this.

autogen.sh runs fine configure.sh runs fine make fails

Dist: CentOS release 6.8 gcc 4.8.4 zlib 1.2.11 xerces-c 3.1.4

libcrispr compiled succesfully.

**This is the make output and error:**
make  all-recursive
make[1]: Entering directory `/home/russel/software/libcrispr'
Making all in libcrispr
make[2]: Entering directory `/home/russel/software/libcrispr/libcrispr'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/russel/software/libcrispr/libcrispr'
make[2]: Entering directory `/home/russel/software/libcrispr'
make[2]: Leaving directory `/home/russel/software/libcrispr'
make[1]: Leaving directory `/home/russel/software/libcrispr'
(crass) [russel@eofe5 libcrispr]$ cd ..
(crass) [russel@eofe5 software]$ cd crass/
(crass) [russel@eofe5 crass]$ make
make  all-recursive
make[1]: Entering directory `/home/russel/software/crass'
Making all in src
make[2]: Entering directory `/home/russel/software/crass/src'
Making all in aho-corasick
make[3]: Entering directory `/home/russel/software/crass/src/aho-corasick'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/russel/software/crass/src/aho-corasick'
Making all in crass
make[3]: Entering directory `/home/russel/software/crass/src/crass'
/bin/sh ../../libtool --tag=CXX   --mode=link g++ -I/home/russel/software/miniconda3/envs/crass//include -I/home/russel/software/miniconda3/envs/crass//include/xercesc -pedantic -Wall -g -O2 libcrass.a ../../src/aho-corasick/libacism.a -L/home/russel/software/miniconda3/envs/crass//lib  -lz -lxerces-c   -o crass crass.o
libtool: link: g++ -I/home/russel/software/miniconda3/envs/crass//include -I/home/russel/software/miniconda3/envs/crass//include/xercesc -pedantic -Wall -g -O2 -o crass crass.o  libcrass.a ../../src/aho-corasick/libacism.a -L/home/russel/software/miniconda3/envs/crass//lib -lz /home/russel/software/miniconda3/envs/crass/lib/libxerces-c.so -lpthread -Wl,-rpath -Wl,/home/russel/software/miniconda3/envs/crass/lib -Wl,-rpath -Wl,/home/russel/software/miniconda3/envs/crass/lib
/home/russel/.linuxbrew/bin/ld: libcrass.a(WorkHorse.o): in function `WorkHorse::addDataToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, int)':
/home/russel/software/crass/src/crass/WorkHorse.cpp:2076: undefined reference to `NodeManager::generateAllsourceTags(crispr::xml::writer*, std::set<int, std::less<int>, std::allocator<int> >&, xercesc_3_1::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2064: undefined reference to `NodeManager::addSpacersToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2072: undefined reference to `NodeManager::addFlankersToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(WorkHorse.o): in function `WorkHorse::outputResults(std::string)':
/home/russel/software/crass/src/crass/WorkHorse.cpp:2021: undefined reference to `NodeManager::printAssemblyToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, bool)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::appendSourcesForSpacer(xercesc_3_0::DOMElement*, std::set<int, std::less<int>, std::allocator<int> >&, crispr::xml::writer*)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1736: undefined reference to `crispr::xml::writer::addSpacerSource(std::string, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::generateAllsourceTags(crispr::xml::writer*, std::set<int, std::less<int>, std::allocator<int> >&, xercesc_3_0::DOMElement*)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1751: undefined reference to `crispr::xml::writer::addSource(std::string, std::string, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::printAssemblyToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, bool)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1567: undefined reference to `crispr::xml::writer::addContig(std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1581: undefined reference to `crispr::xml::writer::addSpacerToContig(std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1611: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1645: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1625: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1659: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1617: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1665: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1651: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1631: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::addFlankersToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1548: undefined reference to `crispr::xml::writer::addFlanker(std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::addSpacersToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1522: undefined reference to `crispr::xml::writer::addSpacer(std::string&, std::string&, xercesc_3_0::DOMElement*, std::string)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `xercesc_3_0::XMLAttDefList::~XMLAttDefList()':
/usr/include/xercesc/framework/XMLAttDefList.hpp:158: undefined reference to `xercesc_3_0::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `xercesc_3_0::DTDEntityDecl::~DTDEntityDecl()':
/usr/include/xercesc/validators/DTD/DTDEntityDecl.hpp:160: undefined reference to `xercesc_3_0::XMLEntityDecl::~XMLEntityDecl()'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `xercesc_3_0::DTDEntityDecl::~DTDEntityDecl()':
/usr/include/xercesc/validators/DTD/DTDEntityDecl.hpp:160: undefined reference to `xercesc_3_0::XMLEntityDecl::~XMLEntityDecl()'
/home/russel/.linuxbrew/bin/ld: /usr/include/xercesc/validators/DTD/DTDEntityDecl.hpp:162: undefined reference to `xercesc_3_0::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTIN11xercesc_3_013DTDEntityDeclE[_ZTIN11xercesc_3_013DTDEntityDeclE]+0x10): undefined reference to `typeinfo for xercesc_3_0::XMLEntityDecl'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTVN11xercesc_3_013XMLAttDefListE[_ZTVN11xercesc_3_013XMLAttDefListE]+0x20): undefined reference to `xercesc_3_0::XMLAttDefList::isSerializable() const'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTVN11xercesc_3_013XMLAttDefListE[_ZTVN11xercesc_3_013XMLAttDefListE]+0x28): undefined reference to `xercesc_3_0::XMLAttDefList::serialize(xercesc_3_0::XSerializeEngine&)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTVN11xercesc_3_013XMLAttDefListE[_ZTVN11xercesc_3_013XMLAttDefListE]+0x30): undefined reference to `xercesc_3_0::XMLAttDefList::getProtoType() const'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTVN11xercesc_3_013DTDEntityDeclE[_ZTVN11xercesc_3_013DTDEntityDeclE]+0x20): undefined reference to `xercesc_3_0::DTDEntityDecl::isSerializable() const'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTVN11xercesc_3_013DTDEntityDeclE[_ZTVN11xercesc_3_013DTDEntityDeclE]+0x28): undefined reference to `xercesc_3_0::DTDEntityDecl::serialize(xercesc_3_0::XSerializeEngine&)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o):(.rodata._ZTVN11xercesc_3_013DTDEntityDeclE[_ZTVN11xercesc_3_013DTDEntityDeclE]+0x30): undefined reference to `xercesc_3_0::DTDEntityDecl::getProtoType() const'
/home/russel/.linuxbrew/bin/ld: libcrass.a(libcrispr.o): in function `findSingletons(char const*, options const&, std::vector<std::string, std::allocator<std::string> >*, std::map<std::string, bool, std::less<std::string>, std::allocator<std::pair<std::string const, bool> > >&, std::map<int, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*, std::less<int>, std::allocator<std::pair<int const, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*> > >*, StringCheck*, long&)':
/home/russel/software/crass/src/crass/libcrispr.cpp:473: undefined reference to `kseq_init(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(libcrispr.o): in function `searchFile(char const*, options const&, std::map<int, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*, std::less<int>, std::allocator<std::pair<int const, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*> > >*, StringCheck*, std::map<std::string, bool, std::less<std::string>, std::allocator<std::pair<std::string const, bool> > >&, std::map<std::string, bool, std::less<std::string>, std::allocator<std::pair<std::string const, bool> > >&, long&)':
/home/russel/software/crass/src/crass/libcrispr.cpp:88: undefined reference to `kseq_init(void*)'
ctSkennerton commented 5 years ago

I think it has something to do with you installing libcrispr. Originally I had libcrispr as a separate library that needed to be installed, but somewhere along the line I changed it and just moved all of the source code under crass. I think because you installed it separately there are now two versions of that code.

Maybe if you uninstall libcrispr and then try reinstalling crass it will work.

Russel88 commented 5 years ago

I actually tried installing libcrispr because of this error, it didn't change anything

ctSkennerton commented 5 years ago

I'm not sure, but I wonder if it's because you're mixing linuxbrew with miniconda. Since the linker is installed under linuxbrew but xerces is installed under miniconda, maybe it's not able to find the library

Russel88 commented 5 years ago

I tried compiling Xerces-c 3.1.0 from source, and make'ing crass without conda activated. And with ./configure --with-xerces=/my/newly/compiled/xerces-c

Now I get another error:

make  all-recursive
make[1]: Entering directory `/home/russel/software/crass'
Making all in src
make[2]: Entering directory `/home/russel/software/crass/src'
Making all in aho-corasick
make[3]: Entering directory `/home/russel/software/crass/src/aho-corasick'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/russel/software/crass/src/aho-corasick'
Making all in crass
make[3]: Entering directory `/home/russel/software/crass/src/crass'
/bin/sh ../../libtool --tag=CXX   --mode=link g++ -I/home/russel/software/xerces-c-3.1.0/include -I/home/russel/software/xerces-c-3.1.0/include/xercesc -pedantic -Wall -g -O2 libcrass.a ../../src/aho-corasick/libacism.a -L/home/russel/software/xerces-c-3.1.0/lib  -lz -lxerces-c   -o crass crass.o
libtool: link: g++ -I/home/russel/software/xerces-c-3.1.0/include -I/home/russel/software/xerces-c-3.1.0/include/xercesc -pedantic -Wall -g -O2 -o crass crass.o  libcrass.a ../../src/aho-corasick/libacism.a -L/home/russel/software/xerces-c-3.1.0/lib -lz -lxerces-c
/home/russel/.linuxbrew/bin/ld: crass.o: in function `xercesc_3_1::XMLAttDefList::~XMLAttDefList()':
/home/russel/software/miniconda3/envs/crass/include/xercesc/framework/XMLAttDefList.hpp:158: undefined reference to `xercesc_3_1::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: crass.o: in function `xercesc_3_1::DTDEntityDecl::~DTDEntityDecl()':
/home/russel/software/miniconda3/envs/crass/include/xercesc/validators/DTD/DTDEntityDecl.hpp:160: undefined reference to `xercesc_3_1::XMLEntityDecl::~XMLEntityDecl()'
/home/russel/.linuxbrew/bin/ld: crass.o: in function `xercesc_3_1::DTDEntityDecl::~DTDEntityDecl()':
/home/russel/software/miniconda3/envs/crass/include/xercesc/validators/DTD/DTDEntityDecl.hpp:160: undefined reference to `xercesc_3_1::XMLEntityDecl::~XMLEntityDecl()'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/miniconda3/envs/crass/include/xercesc/validators/DTD/DTDEntityDecl.hpp:162: undefined reference to `xercesc_3_1::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTIN11xercesc_3_113DTDEntityDeclE[_ZTIN11xercesc_3_113DTDEntityDeclE]+0x10): undefined reference to `typeinfo for xercesc_3_1::XMLEntityDecl'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTVN11xercesc_3_113XMLAttDefListE[_ZTVN11xercesc_3_113XMLAttDefListE]+0x20): undefined reference to `xercesc_3_1::XMLAttDefList::isSerializable() const'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTVN11xercesc_3_113XMLAttDefListE[_ZTVN11xercesc_3_113XMLAttDefListE]+0x28): undefined reference to `xercesc_3_1::XMLAttDefList::serialize(xercesc_3_1::XSerializeEngine&)'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTVN11xercesc_3_113XMLAttDefListE[_ZTVN11xercesc_3_113XMLAttDefListE]+0x30): undefined reference to `xercesc_3_1::XMLAttDefList::getProtoType() const'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTVN11xercesc_3_113DTDEntityDeclE[_ZTVN11xercesc_3_113DTDEntityDeclE]+0x20): undefined reference to `xercesc_3_1::DTDEntityDecl::isSerializable() const'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTVN11xercesc_3_113DTDEntityDeclE[_ZTVN11xercesc_3_113DTDEntityDeclE]+0x28): undefined reference to `xercesc_3_1::DTDEntityDecl::serialize(xercesc_3_1::XSerializeEngine&)'
/home/russel/.linuxbrew/bin/ld: crass.o:(.rodata._ZTVN11xercesc_3_113DTDEntityDeclE[_ZTVN11xercesc_3_113DTDEntityDeclE]+0x30): undefined reference to `xercesc_3_1::DTDEntityDecl::getProtoType() const'
/home/russel/.linuxbrew/bin/ld: libcrass.a(WorkHorse.o): in function `WorkHorse::addDataToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, int)':
/home/russel/software/crass/src/crass/WorkHorse.cpp:2076: undefined reference to `NodeManager::generateAllsourceTags(crispr::xml::writer*, std::set<int, std::less<int>, std::allocator<int> >&, xercesc_3_1::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2064: undefined reference to `NodeManager::addSpacersToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2072: undefined reference to `NodeManager::addFlankersToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2081: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2081: undefined reference to `xercesc_3_1::XMLString::transcode(unsigned short const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2084: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/WorkHorse.cpp:2084: undefined reference to `xercesc_3_1::XMLString::release(char**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(WorkHorse.o): in function `WorkHorse::outputResults(std::string)':
/home/russel/software/crass/src/crass/WorkHorse.cpp:2021: undefined reference to `NodeManager::printAssemblyToDOM(crispr::xml::writer*, xercesc_3_1::DOMElement*, bool)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(WorkHorse.o):(.gcc_except_table+0x464): undefined reference to `typeinfo for xercesc_3_1::DOMException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(WorkHorse.o):(.gcc_except_table+0x760): undefined reference to `typeinfo for xercesc_3_1::XMLException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::createDOMDocument(std::string, std::string, int&)':
/home/russel/software/crass/src/crass/writer.cpp:48: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:48: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:49: undefined reference to `xercesc_3_1::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:50: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:50: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:55: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:55: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:56: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:57: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:57: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:62: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:62: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:65: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:65: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::createDOMDocument(char const*, char const*, int&)':
/home/russel/software/crass/src/crass/writer.cpp:97: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:97: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:98: undefined reference to `xercesc_3_1::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:99: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:99: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:104: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:104: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:105: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:107: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:107: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:112: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:112: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:116: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:116: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addMetaData(std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:157: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:157: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:159: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:159: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addFileToMetadata(std::string, std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:171: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:171: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:172: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:172: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:175: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:175: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:176: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:176: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addNotesToMetadata(std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:183: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:183: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:185: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:185: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addGroup(std::string&, std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:195: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:195: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:196: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:196: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:201: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:201: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:202: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:202: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addDirectRepeat(std::string&, std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:230: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:230: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:231: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:231: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:236: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:236: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:237: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:237: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addSpacer(std::string&, std::string&, xercesc_3_1::DOMElement*, std::string)':
/home/russel/software/crass/src/crass/writer.cpp:244: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:244: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:245: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:245: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:246: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:246: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:252: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:252: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:253: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:253: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:254: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:254: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addFlanker(std::string&, std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:267: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:267: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:268: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:268: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:274: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:274: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:275: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:275: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addContig(std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:284: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:284: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:286: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:286: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::createConsensus(std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:293: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:293: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:296: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:296: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addSpacerToContig(std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:304: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:304: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:306: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:306: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::createSpacers(std::string)':
/home/russel/software/crass/src/crass/writer.cpp:312: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:312: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:314: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:314: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:325: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:325: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:326: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:326: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:327: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:327: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:328: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:328: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:335: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:335: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:336: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:336: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:337: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:337: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:338: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:338: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:344: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:344: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:345: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:345: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:346: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:346: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:347: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:347: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:354: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:354: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:355: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:355: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:356: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:356: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:357: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:357: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addSource(std::string, std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:374: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:374: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:376: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:376: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:379: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:379: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:380: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:380: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addSpacerSource(std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:388: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:388: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:391: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:391: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addStartAndEndPos(std::string, std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:401: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:401: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:402: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:402: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:409: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:409: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:410: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:410: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addProgName(std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:425: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:425: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:429: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:429: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addProgVersion(std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:436: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:436: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:440: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:440: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::addProgCommand(std::string, xercesc_3_1::DOMElement*)':
/home/russel/software/crass/src/crass/writer.cpp:447: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:447: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:451: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:451: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::printDOMToFile(std::string)':
/home/russel/software/crass/src/crass/writer.cpp:466: undefined reference to `xercesc_3_1::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:467: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:468: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:471: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:471: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:473: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:473: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:478: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:479: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:481: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:482: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:484: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:485: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:487: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:488: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:498: undefined reference to `xercesc_3_1::XMemory::operator new(unsigned long)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:498: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:498: undefined reference to `xercesc_3_1::LocalFileFormatTarget::LocalFileFormatTarget(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:523: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:523: undefined reference to `xercesc_3_1::XMLString::transcode(unsigned short const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:528: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:528: undefined reference to `xercesc_3_1::XMLString::release(char**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:498: undefined reference to `xercesc_3_1::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::printDOMToScreen()':
/home/russel/software/crass/src/crass/writer.cpp:543: undefined reference to `xercesc_3_1::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:544: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:545: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:548: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:548: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:550: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:550: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:555: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:556: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:558: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:559: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:561: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:562: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:564: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:565: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:575: undefined reference to `xercesc_3_1::XMemory::operator new(unsigned long)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:575: undefined reference to `xercesc_3_1::StdOutFormatTarget::StdOutFormatTarget()'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:599: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:599: undefined reference to `xercesc_3_1::XMLString::transcode(unsigned short const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:604: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:604: undefined reference to `xercesc_3_1::XMLString::release(char**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:575: undefined reference to `xercesc_3_1::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::printDOMToFile(std::string, xercesc_3_1::DOMDocument*)':
/home/russel/software/crass/src/crass/writer.cpp:619: undefined reference to `xercesc_3_1::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:620: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:621: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:624: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:624: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:626: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:626: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:632: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:633: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:635: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:636: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:638: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:639: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:641: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:642: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:652: undefined reference to `xercesc_3_1::XMemory::operator new(unsigned long)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:652: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:652: undefined reference to `xercesc_3_1::LocalFileFormatTarget::LocalFileFormatTarget(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:677: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:677: undefined reference to `xercesc_3_1::XMLString::transcode(unsigned short const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:682: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:682: undefined reference to `xercesc_3_1::XMLString::release(char**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:652: undefined reference to `xercesc_3_1::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o): in function `crispr::xml::writer::printDOMToScreen(xercesc_3_1::DOMDocument*)':
/home/russel/software/crass/src/crass/writer.cpp:697: undefined reference to `xercesc_3_1::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:698: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:699: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:702: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:702: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:705: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:705: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:711: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:712: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTSplitCdataSections'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:714: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:715: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTDiscardDefaultContent'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:717: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:718: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTFormatPrettyPrint'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:720: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:721: undefined reference to `xercesc_3_1::XMLUni::fgDOMWRTBOM'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:731: undefined reference to `xercesc_3_1::XMemory::operator new(unsigned long)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:731: undefined reference to `xercesc_3_1::StdOutFormatTarget::StdOutFormatTarget()'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:755: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:755: undefined reference to `xercesc_3_1::XMLString::transcode(unsigned short const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:760: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:760: undefined reference to `xercesc_3_1::XMLString::release(char**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/writer.cpp:731: undefined reference to `xercesc_3_1::XMemory::operator delete(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o):(.gcc_except_table+0x50): undefined reference to `typeinfo for xercesc_3_1::DOMException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o):(.gcc_except_table+0x98): undefined reference to `typeinfo for xercesc_3_1::DOMException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o):(.gcc_except_table+0xe8): undefined reference to `typeinfo for xercesc_3_1::XMLException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o):(.gcc_except_table+0x128): undefined reference to `typeinfo for xercesc_3_1::XMLException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o):(.gcc_except_table+0x168): undefined reference to `typeinfo for xercesc_3_1::XMLException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(writer.o):(.gcc_except_table+0x1a8): undefined reference to `typeinfo for xercesc_3_1::XMLException'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::appendSourcesForSpacer(xercesc_3_0::DOMElement*, std::set<int, std::less<int>, std::allocator<int> >&, crispr::xml::writer*)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1736: undefined reference to `crispr::xml::writer::addSpacerSource(std::string, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::generateAllsourceTags(crispr::xml::writer*, std::set<int, std::less<int>, std::allocator<int> >&, xercesc_3_0::DOMElement*)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1751: undefined reference to `crispr::xml::writer::addSource(std::string, std::string, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::printAssemblyToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, bool)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1567: undefined reference to `crispr::xml::writer::addContig(std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1581: undefined reference to `crispr::xml::writer::addSpacerToContig(std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1611: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1645: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1625: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1659: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1617: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1665: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1651: undefined reference to `crispr::xml::writer::addFlanker(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/NodeManager.cpp:1631: undefined reference to `crispr::xml::writer::addSpacer(std::string, std::string&, std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::addFlankersToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1548: undefined reference to `crispr::xml::writer::addFlanker(std::string&, std::string&, xercesc_3_0::DOMElement*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(NodeManager.o): in function `NodeManager::addSpacersToDOM(crispr::xml::writer*, xercesc_3_0::DOMElement*, bool, std::set<int, std::less<int>, std::allocator<int> >&)':
/home/russel/software/crass/src/crass/NodeManager.cpp:1522: undefined reference to `crispr::xml::writer::addSpacer(std::string&, std::string&, xercesc_3_0::DOMElement*, std::string)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(libcrispr.o): in function `findSingletons(char const*, options const&, std::vector<std::string, std::allocator<std::string> >*, std::map<std::string, bool, std::less<std::string>, std::allocator<std::pair<std::string const, bool> > >&, std::map<int, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*, std::less<int>, std::allocator<std::pair<int const, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*> > >*, StringCheck*, long&)':
/home/russel/software/crass/src/crass/libcrispr.cpp:473: undefined reference to `kseq_init(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(libcrispr.o): in function `searchFile(char const*, options const&, std::map<int, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*, std::less<int>, std::allocator<std::pair<int const, std::vector<ReadHolder*, std::allocator<ReadHolder*> >*> > >*, StringCheck*, std::map<std::string, bool, std::less<std::string>, std::allocator<std::pair<std::string const, bool> > >&, std::map<std::string, bool, std::less<std::string>, std::allocator<std::pair<std::string const, bool> > >&, long&)':
/home/russel/software/crass/src/crass/libcrispr.cpp:88: undefined reference to `kseq_init(void*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::init()':
/home/russel/software/crass/src/crass/base.cpp:66: undefined reference to `xercesc_3_1::XMLUni::fgXercescDefaultLocale'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::alloc()':
/home/russel/software/crass/src/crass/base.cpp:72: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:72: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:73: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:73: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:74: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:74: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:75: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:75: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:76: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:76: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:77: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:77: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:78: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:78: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:79: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:79: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:80: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:80: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:81: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:81: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:82: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:82: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:83: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:83: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:84: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:84: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:85: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:85: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:86: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:86: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:87: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:87: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:88: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:88: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:89: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:89: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:90: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:90: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:91: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:91: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:92: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:92: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:93: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:93: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:94: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:94: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:95: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:95: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:96: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:96: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:97: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:97: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:98: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:98: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:99: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:99: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:100: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:100: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:101: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:101: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:102: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:102: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:103: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:103: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:105: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:105: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:106: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:106: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:107: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:107: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:108: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:108: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:109: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:109: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:110: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:110: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:111: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:111: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:112: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:112: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:113: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:113: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:114: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:114: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:115: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:115: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:116: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:116: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:117: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:117: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:118: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:118: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:119: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:119: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:120: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:120: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:121: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:121: undefined reference to `xercesc_3_1::XMLString::transcode(char const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::base()':
/home/russel/software/crass/src/crass/base.cpp:66: undefined reference to `xercesc_3_1::XMLUni::fgXercescDefaultLocale'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:66: undefined reference to `xercesc_3_1::XMLPlatformUtils::Initialize(char const*, char const*, xercesc_3_1::PanicHandler*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:50: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:50: undefined reference to `xercesc_3_1::XMLString::transcode(unsigned short const*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:52: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:52: undefined reference to `xercesc_3_1::XMLString::release(char**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::dealloc()':
/home/russel/software/crass/src/crass/base.cpp:128: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:128: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:129: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:129: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:130: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:130: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:131: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:131: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:132: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:132: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:133: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:133: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:134: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:134: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:135: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:135: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:136: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:136: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:137: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:137: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:138: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:138: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:139: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:139: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:140: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:140: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:141: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:141: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:142: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:142: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:143: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:143: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:144: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:144: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:145: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:145: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:146: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:146: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:147: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:147: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:148: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:148: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:149: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:149: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:150: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:150: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:151: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:151: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:152: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:152: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:153: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:153: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:154: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:154: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:155: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:155: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:156: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:156: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:157: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:157: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:158: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:158: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:159: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:159: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:161: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:161: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:162: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:162: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:163: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:163: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:164: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:164: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:165: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:165: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:166: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:166: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:167: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:167: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:168: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:168: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:169: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:169: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:170: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:170: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:171: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:171: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:172: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:172: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:173: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:173: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:174: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:174: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:175: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:175: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:176: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:176: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:177: undefined reference to `xercesc_3_1::XMLPlatformUtils::fgMemoryManager'
/home/russel/.linuxbrew/bin/ld: /home/russel/software/crass/src/crass/base.cpp:177: undefined reference to `xercesc_3_1::XMLString::release(unsigned short**, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::init()':
/home/russel/software/crass/src/crass/base.cpp:66: undefined reference to `xercesc_3_1::XMLPlatformUtils::Initialize(char const*, char const*, xercesc_3_1::PanicHandler*, xercesc_3_1::MemoryManager*)'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::release()':
/home/russel/software/crass/src/crass/base.cpp:188: undefined reference to `xercesc_3_1::XMLPlatformUtils::Terminate()'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o): in function `crispr::xml::base::~base()':
/home/russel/software/crass/src/crass/base.cpp:188: undefined reference to `xercesc_3_1::XMLPlatformUtils::Terminate()'
/home/russel/.linuxbrew/bin/ld: libcrass.a(base.o):(.gcc_except_table+0x20): undefined reference to `typeinfo for xercesc_3_1::XMLException'
collect2: error: ld returned 1 exit status
make[3]: *** [crass] Error 1
make[3]: Leaving directory `/home/russel/software/crass/src/crass'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/russel/software/crass/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/russel/software/crass'
make: *** [all] Error 2
ctSkennerton commented 5 years ago

It's mostly the same thing, the linker still can't find the right objects. It looks like though it's not compiling anything and going straight to linking so maybe you could try make clean && make all

Russel88 commented 5 years ago

It works now!

Thank you for taking your time to solve this!

I got the following warning, but I assume it's not fatal: g++ -DHAVE_CONFIG_H -I. -I../.. -I/home/russel/software/xerces-c-3.1.0/include -I/home/russel/software/xerces-c-3.1.0/include/xercesc -pedantic -Wall -g -O2 -MT libcrispr.o -MD -MP -MF .deps/libcrispr.Tpo -c -o libcrispr.o libcrispr.cpp libcrispr.cpp: In function ‘unsigned int extendPreRepeat(ReadHolder&, int, int)’: libcrispr.cpp:614:129: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if((last_repeat_start_index + searchWindowLength + right_extension_length) >= static_cast(tmp_holder.getSeqLength())) { ^ libcrispr.cpp:756:81: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(*(repeat_iter+1) + right_extension_length >= tmp_holder.getSeqLength()) ^

ctSkennerton commented 5 years ago

you can normally ignore warnings.