[mira_talk] Compiling MIRA 3.0.3 on Mac OS X 10.6 Snow Leopard
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 16 Mar 2010 18:50:47 +0000
Hi Bastien et al,
I've recently updated my Mac to Snow Leopard, and installed Boost
1.42.0 under my home directory (most of it - there was a problem with
the python bindings), and attempted to install MIRA 3.0.3 from source
as follows:
cd mira-3.0.3
./configure --with-boost=/Users/myusername/
make
At the end of the configure step, I had:
Quote:
--------------------------------------------------------------------------------
Summary of MIRA configuration
--------------------------------------------------------------------------------
Building version .................................
3.0.3_prod_darwin10.2.0_i386_dynamic
-n Production or development version?................
production
We are building on ............................... Darwin
CPU supports 64 bit? ......... ................... yes
Compiler ......................................... gcc
-n Compiler optimisation flags used .................
-O2
Do we compile in 64 bit? ......................... yes
Building completely static? ...................... no
-n BOOST expected to compile and link?...............
yes
Can MIRA be built on this system? ................ yes (when correctly
configured)
This system has been reported as having problems.
Please help fixing if you can.
Using CFLAGS : -O2
Using CXXFLAGS : -DPUBLICQUIET -O2 -pthread -I/Users/xxx/include
Using LDFLAGS : -L/Users/xxx/lib -lboost_thread
System: Darwin xxx.local 10.2.0 Darwin Kernel Version 10.2.0: Tue Nov
3 10:37:10 PST 2009; root:xnu-1486.2.11~1/RELEASE_I386 i386
Compiler: 'gcc -v' output:
Using built-in specs.
Target: i686-apple-darwin10
Configured with: /var/tmp/gcc/gcc-5646.1~2/src/configure
--disable-checking --enable-werror --prefix=/usr --mandir=/share/man
--enable-languages=c,objc,c++,obj-c++
--program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
--with-slibdir=/usr/lib --build=i686-apple-darwin10
--with-gxx-include-dir=/include/c++/4.2.1
--program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10
--target=i686-apple-darwin10
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5646) (dot 1)
--------------------------------------------------------------------------------
end quote
I then ran make, and it started fine but ran into trouble with the XML
parsing code:
quote:
--------------------------------------------------------------------------------
Making all in examples_programming
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"3.0.3\" -DPACKAGE_STRING=\"mira\ 3.0.3\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.0.3\"
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
-DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\"
-DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1
-Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1
-DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STRFTIME=1 -DHAVE_FLOOR=1
-DHAVE_MEMSET=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_ISBLANK=1
-DHAVE_NAMESPACES= -DHAVE_STD= -DHAVE_STL= -DHAVE_BOOST=
-DHAVE_BOOST_THREAD= -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1
-DBUGTRACKFLAG=1 -DENABLE64=1 -I. -I../ -pthread -I/Users/xxx//include
-DPUBLICQUIET -O2 -pthread -I/Users/xxx//include -MT mira_101.o -MD
-MP -MF .deps/mira_101.Tpo -c -o mira_101.o mira_101.C
mv -f .deps/mira_101.Tpo .deps/mira_101.Po
/bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread
-I/Users/xxx//include -DPUBLICQUIET -O2 -pthread -I/Users/xxx//include
-L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/
-L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf -L/Users/xxx//lib
-L/Users/xxx//lib -lboost_thread -o mira_101 mira_101.o -lmira
-lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass
-lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf
-lmiraKNN_abi373 -lm -lexpat -lz -lboost_thread
libtool: link: g++ -pthread -I/Users/xxx//include -DPUBLICQUIET -O2
-pthread -I/Users/xxx//include -o mira_101 mira_101.o
-Wl,-bind_at_load -L/Users/xxx/Downloads/Software/mira-3.0.3/src/io
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/util
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/errorhandling
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/mira
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/examine
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/EdIt
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/caf
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/knn_abi373
-L/Users/xxx/Downloads/Software/mira-3.0.3/src/knn_alf
-L/Users/pjxxx//lib -lmira -lmiraEdIt -lmiraExamine -lmirasupport
-lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio
-lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz -lboost_thread -pthread
Undefined symbols:
"_eXML_Parse", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_egzopen", referenced from:
ReadPool::loadDataFromFASTQ(std::basic_string<char ,
std::char_traits<char>, std::allocator<char> > const&, unsigned char,
unsigned int&, bool, unsigned char, bool)in
libmirasupport.a(readpool.o)
ReadPool::loadDataFromFASTQ(std::basic_string<char ,
std::char_traits<char>, std::allocator<char> > const&, unsigned char,
unsigned int&, bool, unsigned char, bool)in
libmirasupport.a(readpool.o)
"_egzread", referenced from:
ks_getuntil(__kstream_t*, int, __kstring_t*, int*)in
libmirasupport.a(readpool.o)
kseq_read(kseq_t*) in libmirasupport.a(readpool.o)
kseq_read(kseq_t*) in libmirasupport.a(readpool.o)
kseq_read(kseq_t*) in libmirasupport.a(readpool.o)
kseq_read(kseq_t*) in libmirasupport.a(readpool.o)
"_egzclose", referenced from:
ReadPool::loadDataFromFASTQ(std::basic_string<char ,
std::char_traits<char>, std::allocator<char> > const&, unsigned char,
unsigned int&, bool, unsigned char, bool)in
libmirasupport.a(readpool.o)
ReadPool::loadDataFromFASTQ(std::basic_string<char ,
std::char_traits<char>, std::allocator<char> > const&, unsigned char,
unsigned int&, bool, unsigned char, bool)in
libmirasupport.a(readpool.o)
"_eXML_SetElementHandler", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_GetErrorCode", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_ParserCreate", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_SetCharacterDataHandler", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_SetUserData", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_ParserFree", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_ErrorString", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
"_eXML_GetCurrentLineNumber", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [mira_101] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
--------------------------------------------------------------------------------
end quote
Looking over the configure output it did say:
--------------------------------------------------------------------------------
checking for Expat XML Parser headers in /usr/include... found
checking for Expat XML Parser libraries... found
checking for Expat XML Parser... yes
--------------------------------------------------------------------------------
end quote
Any ideas?
I see you've been moving the documentation over to sourceforge - is
there anything specifically on installation I should be reading beyond
the INSTALL file?
Thanks,
Peter
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