satoken / dafs Goto Github PK

(...)
[ 65%] Building CXX object src/CMakeFiles/dafs.dir/dafs.cpp.o
/workspaces/src/dafs.cpp:59:10: fatal error: cxxopts.hpp: No such file or directory
   59 | #include "cxxopts.hpp"
      |          ^~~~~~~~~~~~~
compilation terminated.
make[2]: *** [src/CMakeFiles/dafs.dir/build.make:121: src/CMakeFiles/dafs.dir/dafs.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:177: src/CMakeFiles/dafs.dir/all] Error 2
make: *** [Makefile:149: all] Error 2

./configure --prefix=/usr --with-vienna-rna=/usr/include/ViennaRNA --with-glpk

# https://github.com/SIPp/sipp/issues/61
touch configure.ac aclocal.m4 configure Makefile.am Makefile.in

make CXXFLAGS="-Wall -O2 -fpermissive" CFLAGS="$CFLAGS -I/usr/include/ViennaRNA" PREFIX=/usr

...
alifold.cpp: In member function ‘float Alifold::energy_of_struct(const ALN&, const std::vector<Fasta>&, const string&, float&) const’:
alifold.cpp:140:79: warning: invalid conversion from ‘char**’ to ‘const char**’ [-fpermissive]
   float min_en = Vienna::energy_of_alistruct(seqs, str.c_str(), N, &cv_temp[0]);
                                                                               ^
In file included from alifold.cpp:30:0:
/usr/include/ViennaRNA/alifold.h:148:9: note:   initializing argument 1 of ‘float Vienna::energy_of_alistruct(const char**, const char*, int, float*)’
 float   energy_of_alistruct(const char **sequences,
         ^
mv -f .deps/alifold.Tpo .deps/alifold.Po
gcc -DHAVE_CONFIG_H -I. -I..   -I/usr/include/ViennaRNA/include -DWITH_GLPK -D_FORTIFY_SOURCE=2 -I/usr/include  -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -I/usr/include/ViennaRNA -MT boltzmann_param.o -MD -MP -MF .deps/boltzmann_param.Tpo -c -o boltzmann_param.o boltzmann_param.c
boltzmann_param.c: In function ‘copy_MLparams’:
boltzmann_param.c:5981:3: error: ‘TerminalAU’ undeclared (first use in this function)
   TerminalAU = values[3];
   ^
boltzmann_param.c:5981:3: note: each undeclared identifier is reported only once for each function it appears in
boltzmann_param.c: In function ‘copy_ninio’:
boltzmann_param.c:5990:3: error: ‘F_ninio37’ undeclared (first use in this function)
   F_ninio37[2] = values[0];
   ^
boltzmann_param.c: In function ‘copy_Tetra_loop’:
boltzmann_param.c:6004:5: error: ‘TETRA_ENERGY37’ undeclared (first use in this function)
     TETRA_ENERGY37[i] = tl[i].e;
     ^
Makefile:419: recipe for target 'boltzmann_param.o' failed
make[3]: *** [boltzmann_param.o] Error 1
make[3]: Leaving directory '/home/keith/Dropbox/linux/AUR/dafs-git/src/dafs/src'
Makefile:453: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/keith/Dropbox/linux/AUR/dafs-git/src/dafs/src'
Makefile:355: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/keith/Dropbox/linux/AUR/dafs-git/src/dafs'
Makefile:295: recipe for target 'all' failed
make: *** [all] Error 2