So I tried forcing p++ to the GNU version as well, instead of relying on the system version. This seemingly solved the ld issue though now I found another error:
creating build/lib.macosx-10.7-x86_64-2.7/parmed/modeller/data
copying parmed/modeller/data/standard_residues.lib -> build/lib.macosx-10.7-x86_64-2.7/parmed/modeller/data
UPDATING build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py
set build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py to '3.0.0+57.g74a84d30'
running build_ext
building 'parmed.amber._rdparm' extension
creating build/temp.macosx-10.7-x86_64-2.7
creating build/temp.macosx-10.7-x86_64-2.7/src
clang -fno-strict-aliasing -I/Users/guolaa/SOFTWARE/amber18/miniconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src -I/Users/guolaa/SOFTWARE/amber18/miniconda/include/python2.7 -c src/_rdparm.cpp -o build/temp.macosx-10.7-x86_64-2.7/src/_rdparm.o
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from src/_rdparm.cpp:17:
/Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error: 'locale' file not found
#include <locale>
^~~~~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1
make[2]: *** [parmed] Error 1
make[1]: *** [serial] Error 2
make: *** [install] Error 2
I suppose me not being a particularly skilled programmer or debugger makes this process a bit harder than it has to be and I suppose the short version here is, if your using Homebrew instead of MacPorts, do not update the OS and Xcode.
Best regards
// Gustaf
> On 8 Oct 2018, at 13:25, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> As far as I can see, I got the last couple of executions and at least one issue involving ld.
>
> gfortran -c -DBINTRAJ -DEMIL \
> \
> -O3 -mtune=native -fPIC -ffree-form -I/Users/guolaa/SOFTWARE/amber18/include -I/Users/guolaa/SOFTWARE/amber18/include \
> -o getopts_c.o getopts_c.F90
> ar rv /Users/guolaa/SOFTWARE/amber18/lib/librism.a rism1d_c.o solvmdl_c.o rism1d_potential_c.o rism1d_closure_c.o rism1d_kh_c.o rism1d_hnc_c.o rism1d_py_c.o rism1d_mv0_c.o rism1d_psen_c.o rism1d_nub_c.o rism1d_polyt_c.o rism1d_devb_c.o quaternion.o array_util.o rism_util.o rism_report_c.o rism3d_grid_c.o rism3d_closure_c.o rism3d_kh_c.o rism3d_hnc_c.o rism3d_psen_c.o rism3d_c.o rism3d_potential_c.o rism3d_restart.o rism3d_xyzv.o rism3d_opendx.o rism3d_ccp4.o rism3d_solvent_c.o rism3d_solute_c.o pubfft.o rism3d_fft.o rism_parm.o rism_io.o mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o fce_c.o erfcfun.o safemem.o blend.o rism_timer_c.o constants.o getopts_c.o bspline.o fftw3.o
> ar: creating archive /Users/guolaa/SOFTWARE/amber18/lib/librism.a
> a - rism1d_c.o
> a - solvmdl_c.o
> a - rism1d_potential_c.o
> a - rism1d_closure_c.o
> a - rism1d_kh_c.o
> a - rism1d_hnc_c.o
> a - rism1d_py_c.o
> a - rism1d_mv0_c.o
> a - rism1d_psen_c.o
> a - rism1d_nub_c.o
> a - rism1d_polyt_c.o
> a - rism1d_devb_c.o
> a - quaternion.o
> a - array_util.o
> a - rism_util.o
> a - rism_report_c.o
> a - rism3d_grid_c.o
> a - rism3d_closure_c.o
> a - rism3d_kh_c.o
> a - rism3d_hnc_c.o
> a - rism3d_psen_c.o
> a - rism3d_c.o
> a - rism3d_potential_c.o
> a - rism3d_restart.o
> a - rism3d_xyzv.o
> a - rism3d_opendx.o
> a - rism3d_ccp4.o
> a - rism3d_solvent_c.o
> a - rism3d_solute_c.o
> a - pubfft.o
> a - rism3d_fft.o
> a - rism_parm.o
> a - rism_io.o
> a - mdiis_orig_c.o
> a - mdiis_blas_c.o
> a - mdiis_blas2_c.o
> a - mdiis_c.o
> a - fce_c.o
> a - erfcfun.o
> a - safemem.o
> a - blend.o
> a - rism_timer_c.o
> a - constants.o
> a - getopts_c.o
> a - bspline.o
> a - fftw3.o
> ranlib /Users/guolaa/SOFTWARE/amber18/lib/librism.a
> gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
> -o Plumed.o Plumed.c
> gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm -I../rism -I../../../include -I/Users/guolaa/SOFTWARE/amber18/include -I/Users/guolaa/SOFTWARE/amber18/include -o /Users/guolaa/SOFTWARE/amber18/bin/sander file_io_dat.o constants.o state.o memory_module.o stack.o nose_hoover.o nose_hoover_init.o trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o remd.o findmask.o relax_mat.o nmr.o multitmd.o multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o sander_lib.o mdread.o locmem.o runmd.o relaxmd.o quench.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o shake.o rattle.o ene.o mdwrit.o minrit.o set.o dynlib.o mdfil.o nmlsrc.o ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o nonbond_list.o short_ene.o pol_gauss.o ew_recip.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o ew_bndpol.o ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.!
> o assert.o erfcfun.o sinr_t.o md_scheme.o constantph.o constante.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o emil.o mdin_emil_dat.o amoeba_valence.o amoeba_multipoles.o amoeba_recip.o amoeba_interface.o amoeba_direct.o amoeba_mdin.o amoeba_adjust.o amoeba_self.o amoeba_vdw.o amoeba_induced.o amoeba_runmd.o ../rism/amber_rism_interface.SANDER.o AmberNetcdf.o bintraj.o binrestart.o spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o charmm.o crg_reloc.o amd.o scaledMD.o barostats.o random.o les.o music_module.o abfqmmm_module.o qm_mm.o qm_ewald.o qmmm_vsolv.o qm2_extern_util_module.o qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o qm2_extern_orc_module.o qm2_extern_nw_module.o qm2_extern_qc_module.o qm2_extern_mrcc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o prn_qmmm_dipole.o sebomd_module.o sebomd_arr!
> ays.o \
> pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o lscivr_vars.o lsc_init.o lsc_xp.o force.o -L/Users/guolaa/SOFTWARE/amber18/lib -lsqm \
> nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-value.o mt19937.o xray_fftpack.o xray_FFT.o xray_fourier.o xray_globals.o xray_interface.o xray_real_space.o xray_reciprocal_space.o xray_utils.o \
> -lFpbsa ../lib/nxtsec.o /Users/guolaa/SOFTWARE/amber18/lib/libemil.a -lstdc++ \
> ../sebomd/sebomd.a \
> ../lib/sys.a /Users/guolaa/SOFTWARE/amber18/lib/libnetcdff.a /Users/guolaa/SOFTWARE/amber18/lib/libnetcdf.a \
> -lrism /Users/guolaa/SOFTWARE/amber18/lib/libfftw3.a -larpack -lxblas-amb -framework Accelerate \
> Plumed.o -ldl
> Undefined symbols for architecture x86_64:
> "std::__1::__basic_string_common<true>::__throw_length_error() const", referenced from:
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in libemil.a(inout.o)
> "std::__1::locale::has_facet(std::__1::locale::id&) const", referenced from:
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(setup.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(initialise.o)
> "std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> ...
> "std::__1::ios_base::getloc() const", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> ...
> "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::assign(char const*)", referenced from:
> stringAssignIfNonNull(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >*, char*, char const*) in libemil.a(amberInterface.o)
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> hsc::readParamFile() in libemil.a(inout.o)
> "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::resize(unsigned long, char)", referenced from:
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in libemil.a(inout.o)
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in libemil.a(setup.o)
> "std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::push_back(char)", referenced from:
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in libemil.a(inout.o)
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in libemil.a(setup.o)
> "std::__1::basic_istream<char, std::__1::char_traits<char> >::peek()", referenced from:
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::setUpFromFile() in libemil.a(setup.o)
> hsc::initWells() in libemil.a(initialise.o)
> "std::__1::basic_istream<char, std::__1::char_traits<char> >::getline(char*, long, char)", referenced from:
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::setUpFromFile() in libemil.a(setup.o)
> hsc::initWells() in libemil.a(initialise.o)
> "std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
> hsc::readParamFile() in libemil.a(inout.o)
> std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in libemil.a(inout.o)
> virtual thunk to std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in libemil.a(inout.o)
> virtual thunk to std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in libemil.a(inout.o)
> hsc::setUpNew(double*, double*, double*, double*) in libemil.a(setup.o)
> std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in libemil.a(setup.o)
> hsc::setUpFromFile() in libemil.a(setup.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::put(char)", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> hsc::writeOutBinding(char*) in libemil.a(inout.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::flush()", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> hsc::writeOutBinding(char*) in libemil.a(inout.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::sentry(std::__1::basic_ostream<char, std::__1::char_traits<char> >&)", referenced from:
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(inout.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(tools.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(reportFreeEnergy.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(setup.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(initialise.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::~sentry()", referenced from:
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(inout.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(tools.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(reportFreeEnergy.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(setup.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(initialise.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(amberInterface.o)
> virtual thunk to std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(amberInterface.o)
> virtual thunk to std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(amberInterface.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(void const*)", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> hsc::testLoop(Particle*) in libemil.a(tools.o)
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(double)", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_mcAttempt(double*, double*, double*, double*, double*, int*, double*, double*, double*) in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> hsc::writeOutBinding(char*) in libemil.a(inout.o)
> hsc::writeOutBindingToWells(char*) in libemil.a(inout.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(float)", referenced from:
> hsc::writeOutSimData(char*) in libemil.a(inout.o)
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(int)", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> hsc::writeOutBinding(char*) in libemil.a(inout.o)
> hsc::writeOutBindingToWells(char*) in libemil.a(inout.o)
> ...
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(long)", referenced from:
> hsc::setUpNew(double*, double*, double*, double*) in libemil.a(setup.o)
> hsc::setUpFromFile() in libemil.a(setup.o)
> "std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned long)", referenced from:
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> "std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> hsc::flushLog() in libemil.a(inout.o)
> std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in libemil.a(inout.o)
> hsc::setUpNew(double*, double*, double*, double*) in libemil.a(setup.o)
> std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in libemil.a(setup.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::sync()", referenced from:
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&)", referenced from:
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::uflow()", referenced from:
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::setbuf(char*, long)", referenced from:
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsgetn(char*, long)", referenced from:
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsputn(char const*, long)", referenced from:
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::showmanyc()", referenced from:
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::basic_streambuf()", referenced from:
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> hsc::flushLog() in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(inout.o)
> hsc::setUpNew(double*, double*, double*, double*) in libemil.a(setup.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(setup.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(initialise.o)
> "std::__1::basic_streambuf<char, std::__1::char_traits<char> >::~basic_streambuf()", referenced from:
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::~basic_filebuf() in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(inout.o)
> std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in libemil.a(inout.o)
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in libemil.a(inout.o)
> std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in libemil.a(inout.o)
> ...
> "std::__1::cerr", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::debugWrap(int, int) in libemil.a(tools.o)
> hsc::setupList() in libemil.a(setup.o)
> Particle::insertToCell(Cell&) in libemil.a(setup.o)
> hsc::setupListW() in libemil.a(setup.o)
> ...
> "std::__1::ctype<char>::id", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> ...
> "std::__1::locale::locale(std::__1::locale const&)", referenced from:
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(setup.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(initialise.o)
> "std::__1::locale::~locale()", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> emil_forces(double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> hsc::stepLambda(double) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> hsc::readParamFile() in libemil.a(inout.o)
> ...
> "std::__1::codecvt<char, char, __mbstate_t>::id", referenced from:
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in libemil.a(setup.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in libemil.a(setup.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in libemil.a(initialise.o)
> ...
> "std::__1::ios_base::__set_badbit_and_consider_rethrow()", referenced from:
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(inout.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(tools.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(reportFreeEnergy.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(setup.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(initialise.o)
> ...
> "std::__1::ios_base::init(void*)", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> hsc::writeOutBinding(char*) in libemil.a(inout.o)
> hsc::writeOutBindingToWells(char*) in libemil.a(inout.o)
> hsc::writeOutSimData(char*) in libemil.a(inout.o)
> ...
> "std::__1::ios_base::clear(unsigned int)", referenced from:
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(amberInterface.o)
> std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in libemil.a(stepLambda.o)
> hsc::readParamFile() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> hsc::writeOutWells() in libemil.a(inout.o)
> hsc::writeOutBinding(char*) in libemil.a(inout.o)
> hsc::writeOutBindingToWells(char*) in libemil.a(inout.o)
> ...
> "std::__1::ios_base::~ios_base()", referenced from:
> hsc::reportSystemFreeEnergy() in libemil.a(reportFreeEnergy.o)
> "std::__1::basic_ios<char, std::__1::char_traits<char> >::~basic_ios()", referenced from:
> hsc::reportSystemFreeEnergy() in libemil.a(reportFreeEnergy.o)
> "std::__1::basic_ios<char, std::__1::char_traits<char> >::~basic_ios()", referenced from:
> emil_init(int*, int*, int*, int*, int*, double*, char*, char*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, char*, char*, char*, char*, int*) in libemil.a(amberInterface.o)
> std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(amberInterface.o)
> virtual thunk to std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(amberInterface.o)
> virtual thunk to std::__1::basic_ofstream<char, std::__1::char_traits<char> >::~basic_ofstream() in libemil.a(amberInterface.o)
> hsc::readParamFile() in libemil.a(inout.o)
> std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in libemil.a(inout.o)
> hsc::writeOutConfig(char*) in libemil.a(inout.o)
> ...
> "std::bad_cast::bad_cast()", referenced from:
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::overflow(int) in libemil.a(amberInterface.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in libemil.a(inout.o)
> std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in libemil.a(inout.o)
> ...
> "typeinfo for std::__1::basic_istream<char, std::__1::char_traits<char> >", referenced from:
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> typeinfo for std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> typeinfo for std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> ...
> "typeinfo for std::__1::basic_ostream<char, std::__1::char_traits<char> >", referenced from:
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> typeinfo for std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> typeinfo for std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "typeinfo for std::__1::basic_iostream<char, std::__1::char_traits<char> >", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> typeinfo for std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> typeinfo for std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "typeinfo for std::__1::basic_streambuf<char, std::__1::char_traits<char> >", referenced from:
> typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "vtable for std::__1::basic_ios<char, std::__1::char_traits<char> >", referenced from:
> hsc::reportSystemFreeEnergy() in libemil.a(reportFreeEnergy.o)
> NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
> "non-virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "non-virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "virtual thunk to std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "virtual thunk to std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in libemil.a(initialise.o)
> "virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(amberInterface.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> "virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(inout.o)
> construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in libemil.a(setup.o)
> ld: symbol(s) not found for architecture x86_64
> collect2: error: ld returned 1 exit status
> make[2]: *** [/Users/guolaa/SOFTWARE/amber18/bin/sander] Error 1
> make[1]: *** [serial] Error 2
> make: *** [install] Error 2
>
>> On 8 Oct 2018, at 10:54, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>> Were the symbols in question mentioned in line(s) before?
>>
>> Bill
>>
>>
>> On 10/8/18 1:04 AM, Gustaf Olsson wrote:
>>> but compilation broke with error:
>>>
>>> ld: symbol(s) not found for architecture x86_64
>>> collect2: error: ld returned 1 exit status
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 08 2018 - 05:30:02 PDT
