Hi Leopold,
On Wed, Jul 08, 2015 at 10:38:57AM +0200, Leopold Palomo-Avellaneda wrote:
> El Dimecres, 8 de juliol de 2015, a les 09:41:45, Andreas Tille va escriure:
> > Hi,
> >
> > I'm working on the Debian Med target hyphy that is using cmake and I
> > tried to link against Debian packaged sqlite. I found some promising
> > code to steal from and created a patch but somehow the -lsqlite3 option
> > is missing from the linker call. I guess its a simple flaw in my patch
> > and perhaps somebody could help me fixing this. The packaging is at
> >
> > svn://anonscm.debian.org/debian-med/trunk/packages/hyphy/trunk/
> >
> > Thanks for any help
> >
> > Andreas (who wishes to find the time to dive a bit more into cmake)
>
> It worked ... at least what i have seen. The package fails for another things.
When I build with pdebuild I get
...
Linking CXX executable HYPHYMPI
/usr/bin/cmake -E cmake_link_script CMakeFiles/HYPHYMPI.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -g -fsigned-char -O3 -march=corei7-avx
-mtune=corei7-avx CMakeFiles/ HYPHYMPI.dir/src/core/list.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/
HYPHYMPI.dir/src/core/batchlan.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/ variable.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/HYPHYMPI.dir/
src/core/stack.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/regex.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o CMakeFiles/HYPHYMPI.dir/
src/core/site.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/calcnode2.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/sequence.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o CMakeFiles/HYPHYMPI.dir/
src/core/avllistxl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/ error.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/ likefuncocl.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/
new/bgm.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o
CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o
CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/Net.
cpp./usr/bin/c++ -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -g -fsigned-char
-O3 -march=corei7-avx -mtune=corei7-avx
CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o
CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/
HYPHYMCMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o: In function
`_ElementaryCommand::ExecuteCase53(_ExecutionList&)':
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:901: undefined reference to
`sqlite3_open'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:907: undefined reference to
`sqlite3_errmsg'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:908: undefined reference to
`sqlite3_close'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:904: undefined reference to
`sqlite3_exec'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:919: undefined reference to
`sqlite3_busy_timeout'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:933: undefined reference to
`sqlite3_close'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:942: undefined reference to
`sqlite3_exec'
/tmp/buildd/hyphy-2.2.4/src/core/batchlan2.cpp:943: undefined reference to
`sqlite3_errmsg'
...
What else do you get?
Kind regards
Andreas.
--
http://fam-tille.de
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