[SOLVED] No linking against a static library after an update

olenellus · 2024-05-27 14:08:57

I am quite confused. I used to link against an RNA folding library (ViennaRNA) in my programs (using Ofront+ Oberon-2 translator to C). I know almost nothing about internals guts of C/C++. The installation of ViennaRNA (from AUR or from the official distribution) provides a set of compiled programs, a static shared library libRNA.a in install-path/lib/ and a set of header files in install-path/include/ViennaRNA/ to bind to it. After one of recent updates (a month or a couple of months ago) the linking stopped working. I did not notice the error message back than. Instead I reinstalled viennarna package. It still does not work. The stand alone programs are compiled without problems and work. The inclusion of libRNA does not. Even in the examples provided with the library.

Here is an example that cannot be compiled/linked anymore

#include <stdlib.h>
#include <stdio.h>
#include <string.h>

#include <ViennaRNA/model.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/utils/basic.h>
#include <ViennaRNA/utils/strings.h>
#include <ViennaRNA/mfe.h>

int
main()
{
  /* initialize random number generator */
  vrna_init_rand();

  /* Generate a random sequence of 50 nucleotides */
  char      *seq = vrna_random_string(50, "ACGU");

  /* allocate memory for MFE structure (length + 1) */
  char      *structure = (char *)vrna_alloc(sizeof(char) * (strlen(seq) + 1));

  /* create a new model details structure to store the Model Settings */
  vrna_md_t md;

  /* ALWAYS set default model settings first! */
  vrna_md_set_default(&md);

  /* change temperature and activate G-Quadruplex prediction */
  md.temperature  = 25.0; /* 25 Deg Celcius */
  md.gquad        = 1;    /* Turn-on G-Quadruples support */

  /* create a fold compound */
  vrna_fold_compound_t  *fc = vrna_fold_compound(seq, &md, VRNA_OPTION_DEFAULT);

  /* predict Minmum Free Energy and corresponding secondary structure */
  float                 mfe = vrna_mfe(fc, structure);

  /* print sequence, structure and MFE */
  printf("%s\n%s [ %6.2f ]\n", seq, structure, mfe);

  /* cleanup memory */
  free(structure);
  vrna_fold_compound_free(fc);

  return 0;
}

An attempt to compile it with

> gcc fold_compound_md.c -lRNA -ofold_compound_md

ends up with a kiloton of error messages from /usr/bin/ld

/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:294:(.text+0x117c): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::Kernel(int, svm_node* const*, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x129b): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:284:(.text+0x12d6): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_values._omp_fn.0':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x15b2): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x15c3): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x1619): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_values._omp_fn.1':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x16ca): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x16d3): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x1709): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x1aaa): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x1ac6): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x1ae2): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:525:(.text+0x1b19): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:532:(.text+0x1b95): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:540: more undefined references to `operator new[](unsigned long)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:780:(.text+0x21f9): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:781:(.text+0x2207): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:782:(.text+0x2215): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:783:(.text+0x2223): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:784:(.text+0x2231): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:785: more undefined references to `operator delete[](void*)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:532:(.text+0x25b8): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:540:(.text+0x25ca): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:541:(.text+0x25d5): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1616:(.text+0x2c60): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svr':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1617:(.text+0x2c6b): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1618: more undefined references to `operator new[](unsigned long)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text+0x2df2): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text+0x2e00): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text+0x2e0e): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text+0x2e1c): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text+0x2e2a): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text+0x2e38): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1643: more undefined references to `operator delete[](void*)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1577:(.text+0x2ff9): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_epsilon_svr':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1578:(.text+0x3004): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1579:(.text+0x3013): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text+0x3170): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text+0x317e): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text+0x318c): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text+0x319a): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text+0x31a8): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text+0x31b6): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1455:(.text+0x3265): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_c_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1456:(.text+0x3274): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x3342): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text+0x3361): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text+0x33a1): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text+0x3476): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text+0x3497): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text+0x34a8): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_c_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1481:(.text+0x3577): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1482:(.text+0x357f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1493:(.text+0x35a2): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1516:(.text+0x3671): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x36f9): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text+0x3718): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text+0x3758): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text+0x3838): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text+0x3869): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text+0x388a): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1536:(.text+0x3965): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1537:(.text+0x3971): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1545:(.text+0x3995): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_one_class':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1546:(.text+0x39a0): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::ONE_CLASS_Q(svm_problem const&, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1329:(.text+0x3b0e): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1330:(.text+0x3b4e): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1361:(.text+0x3c26): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1362:(.text+0x3c37): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_one_class':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1568:(.text+0x3c4b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1569:(.text+0x3c53): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1516:(.text+0x3cee): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_values':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x3ec8): undefined reference to `GOMP_parallel'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x3f6a): undefined reference to `GOMP_parallel'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_probability':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1833:(.text+0x443d): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `sigmoid_predict':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1833:(.text+0x4452): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1835:(.text+0x44e2): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1738:(.text+0x6d27): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `sigmoid_train':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1747:(.text+0x6d70): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1747:(.text+0x6d7a): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1749:(.text+0x6dff): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1749:(.text+0x6e0d): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1762:(.text+0x6f18): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1762:(.text+0x6f28): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1763:(.text+0x6f48): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1767:(.text+0x7026): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1768:(.text+0x7052): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1768: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `sigmoid_train':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1802:(.text+0x73bc): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1804:(.text+0x7414): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1804:(.text+0x7427): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2084:(.text+0x7e7a): undefined reference to `sqrt'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:295:(.text+0x118b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:296:(.text+0x11b3): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::k_function(svm_node const*, svm_node const*, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:371:(.text+0x13f2): undefined reference to `tanh'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:368:(.text+0x152e): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:786:(.text+0x2276): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::~Solver()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:400:(.text._ZN6SolverD0Ev[_ZN6SolverD5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver_NU::~Solver_NU()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1013:(.text._ZN9Solver_NUD0Ev[_ZN9Solver_NUD5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::get_Q(int, int) const [clone ._omp_fn.0]':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x4d): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x56): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x8a): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::get_Q(int, int) const [clone ._omp_fn.0]':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1290:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0x50): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1293:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0xdd): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1293:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0xea): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::get_Q(int, int) const':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii[_ZNK5SVR_Q5get_QEii]+0x120): undefined reference to `GOMP_parallel'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::get_Q(int, int) const':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1290:(.text._ZNK5SVC_Q5get_QEii[_ZNK5SVC_Q5get_QEii]+0x87): undefined reference to `GOMP_parallel'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text._ZN5SVC_QD2Ev[_ZN5SVC_QD5Ev]+0x21): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text._ZN5SVC_QD2Ev[_ZN5SVC_QD5Ev]+0x3f): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text._ZN5SVC_QD2Ev[_ZN5SVC_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1361:(.text._ZN11ONE_CLASS_QD2Ev[_ZN11ONE_CLASS_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1362:(.text._ZN11ONE_CLASS_QD2Ev[_ZN11ONE_CLASS_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x5b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x69): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x77): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1361:(.text._ZN11ONE_CLASS_QD0Ev[_ZN11ONE_CLASS_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1362:(.text._ZN11ONE_CLASS_QD0Ev[_ZN11ONE_CLASS_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1363:(.text._ZN11ONE_CLASS_QD0Ev[_ZN11ONE_CLASS_QD5Ev]+0x5a): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x21): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x3f): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1316:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x68): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x5b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x69): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x77): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1436:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x92): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `clone<svm_node* const, const svm_node*>':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text.unlikely+0x1): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `clone<double const, double>':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text.unlikely+0x21): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text.unlikely+0x3a): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_c_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1455:(.text.unlikely+0x7a): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text.unlikely+0x93): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1330: more undefined references to `__cxa_throw_bad_array_new_length' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text.unlikely+0xea): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text.unlikely+0x124): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::ONE_CLASS_Q(svm_problem const&, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1329:(.text.unlikely+0x15e): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::kernel_sigmoid(int, int) const':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:249:(.text._ZNK6Kernel14kernel_sigmoidEii[_ZNK6Kernel14kernel_sigmoidEii]+0x3e): undefined reference to `tanh'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::kernel_rbf(int, int) const':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:245:(.text._ZNK6Kernel10kernel_rbfEii[_ZNK6Kernel10kernel_rbfEii]+0x60): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::SVR_Q(svm_problem const&, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1376:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x3b): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1377:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x80): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1378:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x92): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1379:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0xbb): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1389:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x169): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1390:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x18e): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1390:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1ae): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1376:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1bb): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1389:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1d0): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1379:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1d5): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1377:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1da): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI7QMatrix[_ZTI7QMatrix]+0x0): undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI6Kernel[_ZTI6Kernel]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI6Solver[_ZTI6Solver]+0x0): undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI9Solver_NU[_ZTI9Solver_NU]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI5SVC_Q[_ZTI5SVC_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI11ONE_CLASS_Q[_ZTI11ONE_CLASS_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI5SVR_Q[_ZTI5SVR_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.local.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0'
/usr/bin/ld: /usr/local/lib/libRNA.a(msa_utils.o): in function `vrna_aln_pinfo':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/msa_utils.c:145:(.text+0x8ae): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/msa_utils.c:146:(.text+0x8df): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/msa_utils.c:152:(.text+0x94b): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(msa_utils.o): in function `vrna_aln_conservation_col':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/msa_utils.c:630:(.text+0x1b6b): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_scaled_params':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:437:(.text+0x34e): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_scaled_exp_params':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:625:(.text+0x15cf): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:626:(.text+0x1625): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:627:(.text+0x167b): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:628:(.text+0x16d1): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:629:(.text+0x172c): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:637:(.text+0x17e8): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:638:(.text+0x181b): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:643:(.text+0x189e): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:646:(.text+0x191a): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:647:(.text+0x1972): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:646:(.text+0x19cc): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:625: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_scaled_exp_params':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:713:(.text+0x2844): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:712:(.text+0x2886): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:712:(.text+0x28b2): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:728:(.text+0x28e7): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:732:(.text+0x292d): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:736:(.text+0x2973): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:740:(.text+0x29bf): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:746: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_scaled_exp_params':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:746:(.text+0x2ac3): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:746:(.text+0x2aef): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:746:(.text+0x2b2b): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:750:(.text+0x2b41): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:809:(.text+0x2baa): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:817:(.text+0x2c25): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:818:(.text+0x2c59): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:819:(.text+0x2c72): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:821:(.text+0x2c9a): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:823: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_exp_params_ali':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:867:(.text+0x3082): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:868:(.text+0x30b5): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:873:(.text+0x313a): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:877:(.text+0x3181): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:877:(.text+0x3199): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:877:(.text+0x31ac): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:881: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_exp_params_ali':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:951:(.text+0x4202): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:947:(.text+0x4243): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:947:(.text+0x426f): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:973:(.text+0x42a4): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:977:(.text+0x42f0): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:981:(.text+0x4336): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:985:(.text+0x437c): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:991: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `get_exp_params_ali':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:991:(.text+0x447f): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:991:(.text+0x44ab): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:991:(.text+0x44e6): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:995:(.text+0x44fc): undefined reference to `sin'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1054:(.text+0x4564): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1063:(.text+0x45df): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1064:(.text+0x4613): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1065:(.text+0x462c): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1067:(.text+0x4654): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1069: more undefined references to `exp' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(params.o): in function `rescale_params':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/params.c:1090:(.text+0x4b55): undefined reference to `pow'
/usr/bin/ld: /usr/local/lib/libRNA.a(salt.o): in function `loop_salt_aux':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:113:(.text+0xc8): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(salt.o): in function `approx_hyper':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:99:(.text+0xe0): undefined reference to `pow'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:100:(.text+0x114): undefined reference to `pow'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:100:(.text+0x12c): undefined reference to `pow'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:101:(.text+0x144): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(salt.o): in function `loop_salt_aux':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:113:(.text+0x1fe): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(salt.o): in function `kappa':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:62:(.text+0x39f): undefined reference to `sqrt'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:62:(.text+0x3d5): undefined reference to `sqrt'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:62:(.text+0x5ae): undefined reference to `sqrt'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:62:(.text+0x5c7): undefined reference to `sqrt'
/usr/bin/ld: /usr/local/lib/libRNA.a(salt.o): in function `vrna_salt_duplex_init':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/salt.c:204:(.text+0x7a1): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `populate_sc_bp_pf':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:984:(.text+0x130): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `populate_sc_up_pf':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:821:(.text+0x5d3): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `prepare_sc_stack_pf':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:1421:(.text+0xbbd): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:1441:(.text+0xc83): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `populate_sc_up_pf':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:821:(.text+0xf5e): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `sc_reset_bp':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:1165:(.text+0x17fd): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `sc_add_bp':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:1032:(.text+0x1c33): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `sc_reset_up':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:1128:(.text+0x1fca): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `sc_add_up':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:1189:(.text+0x21a2): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o): in function `vrna_sc_set_stack':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:494:(.text+0x2319): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(soft.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/constraints/soft.c:528: more undefined references to `roundf' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(structure_utils.o): in function `vrna_dist_mountain':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/structure_utils.c:694:(.text+0x1ed6): undefined reference to `pow'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/structure_utils.c:696:(.text+0x1ef9): undefined reference to `pow'
/usr/bin/ld: /usr/local/lib/libRNA.a(unstructured_domains.o): in function `prepare_default_data':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/unstructured_domains.c:2092:(.text+0xf9a): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(unstructured_domains.o): in function `default_exp_prod_rule':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/unstructured_domains.c:2242:(.text+0x1444): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(unstructured_domains.o): in function `backtrack_MFE_matrix':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/unstructured_domains.c:1203:(.text+0x30f5): undefined reference to `roundf'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/unstructured_domains.c:1242:(.text+0x324d): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(unstructured_domains.o): in function `backtrack_MFE_matrix_exhaustive':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/unstructured_domains.c:1369:(.text+0x440b): undefined reference to `roundf'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/unstructured_domains.c:1396:(.text+0x45bb): undefined reference to `roundf'
/usr/bin/ld: /usr/local/lib/libRNA.a(expn.o): in function `expn':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/expn.c:204:(.text+0x22b): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/expn.c:100:(.text+0x24b): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/expn.c:124:(.text+0x276): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/expn.c:154:(.text+0x36d): undefined reference to `pow'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/expn.c:154:(.text+0x383): undefined reference to `tgamma'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/expn.c:113:(.text+0x447): undefined reference to `exp'
/usr/bin/ld: /usr/local/lib/libRNA.a(gquad.o): in function `exp_E_gquad_ali_penalty':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/gquad.c:1360:(.text+0x5f7): undefined reference to `pow'
/usr/bin/ld: /usr/local/lib/libRNA.a(hairpin.o): in function `E_Hairpin':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/hairpin.h:173:(.text+0xc6c): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(internal.o): in function `E_IntLoop':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/internal.h:574:(.text+0x101f): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/internal.h:523:(.text+0x111b): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/internal.h:552:(.text+0x1320): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(io.o): in function `get_array1':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/params/io.c:768:(.text+0xaf3): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(kn.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/kn.c:183: more undefined references to `log' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(kn.o): in function `kn':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/kn.c:253:(.text+0x48d): undefined reference to `exp'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/kn.c:183:(.text+0x51a): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/kn.c:183:(.text+0x5b0): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../cephes/kn.c:253:(.text+0x627): undefined reference to `sqrt'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm_utils.o): in function `sd_regression':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/utils/svm_utils.c:129:(.text+0x373): undefined reference to `sqrt'
/usr/bin/ld: /usr/local/lib/libRNA.a(eval.o): in function `E_IntLoop':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/internal.h:574:(.text+0x10f): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/internal.h:523:(.text+0x20b): undefined reference to `log'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../../src/ViennaRNA/loops/internal.h:552:(.text+0x410): undefined reference to `log'
/usr/bin/ld: /usr/local/lib/libRNA.a(eval.o): in function `energy_of_ml_pt':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/eval.c:2120:(.text+0x3172): undefined reference to `log'
collect2: error: ld returned 1 exit status

In this particular example I used the official installation tar-ball, not the AUR package. I built the library in /home/olenellus/Local_programs/ViennaRNA-2.6.3, the default installation paths are: /usr/local/lib for the libRNA.a and /usr/local/include for the directory ViennaRNA with the header files.

As you can see, for some reason the information on the initial source location is somehow retained. There is also a problem with the standard math library. The addition of the -lm flag removes the math related errors but does not help overall. Here is the output of

> gcc fold_compound_md.c -lRNA -lm -ofold_compound_md

/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:294:(.text+0x117c): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::Kernel(int, svm_node* const*, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x129b): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:284:(.text+0x12d6): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_values._omp_fn.0':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x15b2): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x15c3): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x1619): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_values._omp_fn.1':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x16ca): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x16d3): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x1709): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x1aaa): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x1ac6): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x1ae2): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:525:(.text+0x1b19): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:532:(.text+0x1b95): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:540: more undefined references to `operator new[](unsigned long)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:780:(.text+0x21f9): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:781:(.text+0x2207): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:782:(.text+0x2215): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:783:(.text+0x2223): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:784:(.text+0x2231): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:785: more undefined references to `operator delete[](void*)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:532:(.text+0x25b8): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:540:(.text+0x25ca): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:541:(.text+0x25d5): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1616:(.text+0x2c60): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svr':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1617:(.text+0x2c6b): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1618: more undefined references to `operator new[](unsigned long)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text+0x2df2): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text+0x2e00): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text+0x2e0e): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text+0x2e1c): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text+0x2e2a): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text+0x2e38): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1643: more undefined references to `operator delete[](void*)' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1577:(.text+0x2ff9): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_epsilon_svr':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1578:(.text+0x3004): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1579:(.text+0x3013): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text+0x3170): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text+0x317e): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text+0x318c): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text+0x319a): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text+0x31a8): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text+0x31b6): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1455:(.text+0x3265): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_c_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1456:(.text+0x3274): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x3342): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text+0x3361): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text+0x33a1): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text+0x3476): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text+0x3497): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text+0x34a8): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_c_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1481:(.text+0x3577): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1482:(.text+0x357f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1493:(.text+0x35a2): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1516:(.text+0x3671): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text+0x36f9): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text+0x3718): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text+0x3758): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text+0x3838): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text+0x3869): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text+0x388a): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1536:(.text+0x3965): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1537:(.text+0x3971): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_train_one(svm_problem const*, svm_parameter const*, double, double)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1545:(.text+0x3995): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_one_class':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1546:(.text+0x39a0): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::ONE_CLASS_Q(svm_problem const&, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1329:(.text+0x3b0e): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1330:(.text+0x3b4e): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1361:(.text+0x3c26): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1362:(.text+0x3c37): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_one_class':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1568:(.text+0x3c4b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1569:(.text+0x3c53): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_nu_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1516:(.text+0x3cee): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `svm_predict_values':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x3ec8): undefined reference to `GOMP_parallel'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x3f6a): undefined reference to `GOMP_parallel'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:295:(.text+0x118b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:296:(.text+0x11b3): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::Solve(int, QMatrix const&, double const*, signed char const*, double*, double, double, double, Solver::SolutionInfo*, int)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:786:(.text+0x2276): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver::~Solver()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:400:(.text._ZN6SolverD0Ev[_ZN6SolverD5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Solver_NU::~Solver_NU()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1013:(.text._ZN9Solver_NUD0Ev[_ZN9Solver_NUD5Ev]+0x6): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::get_Q(int, int) const [clone ._omp_fn.0]':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x4d): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x56): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x8a): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::get_Q(int, int) const [clone ._omp_fn.0]':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1290:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0x50): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1293:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0xdd): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1293:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0xea): undefined reference to `GOMP_loop_end_nowait'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::get_Q(int, int) const':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii[_ZNK5SVR_Q5get_QEii]+0x120): undefined reference to `GOMP_parallel'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::get_Q(int, int) const':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1290:(.text._ZNK5SVC_Q5get_QEii[_ZNK5SVC_Q5get_QEii]+0x87): undefined reference to `GOMP_parallel'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text._ZN5SVC_QD2Ev[_ZN5SVC_QD5Ev]+0x21): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text._ZN5SVC_QD2Ev[_ZN5SVC_QD5Ev]+0x3f): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text._ZN5SVC_QD2Ev[_ZN5SVC_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1361:(.text._ZN11ONE_CLASS_QD2Ev[_ZN11ONE_CLASS_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1362:(.text._ZN11ONE_CLASS_QD2Ev[_ZN11ONE_CLASS_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x5b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x69): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text._ZN5SVR_QD2Ev[_ZN5SVR_QD5Ev]+0x77): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1361:(.text._ZN11ONE_CLASS_QD0Ev[_ZN11ONE_CLASS_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1362:(.text._ZN11ONE_CLASS_QD0Ev[_ZN11ONE_CLASS_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::~ONE_CLASS_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1363:(.text._ZN11ONE_CLASS_QD0Ev[_ZN11ONE_CLASS_QD5Ev]+0x5a): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1313:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x21): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1314:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x3f): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1315:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::~SVC_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1316:(.text._ZN5SVC_QD0Ev[_ZN5SVC_QD5Ev]+0x68): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1430:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x31): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1431:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x3f): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1432:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x4d): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1433:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x5b): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1434:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x69): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1435:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x77): undefined reference to `operator delete[](void*)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::~SVR_Q()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1436:(.text._ZN5SVR_QD0Ev[_ZN5SVR_QD5Ev]+0x92): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `clone<svm_node* const, const svm_node*>':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text.unlikely+0x1): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `clone<double const, double>':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:27:(.text.unlikely+0x21): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text.unlikely+0x3a): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `solve_c_svc':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1455:(.text.unlikely+0x7a): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1278:(.text.unlikely+0x93): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1330: more undefined references to `__cxa_throw_bad_array_new_length' follow
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVC_Q::SVC_Q(svm_problem const&, svm_parameter const&, signed char const*)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text.unlikely+0xea): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1277:(.text.unlikely+0x124): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `ONE_CLASS_Q::ONE_CLASS_Q(svm_problem const&, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1329:(.text.unlikely+0x15e): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `SVR_Q::SVR_Q(svm_problem const&, svm_parameter const&)':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1376:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x3b): undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1377:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x80): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1378:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x92): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1379:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0xbb): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1389:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x169): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1390:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x18e): undefined reference to `operator new[](unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1390:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1ae): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1376:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1bb): undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1389:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1d0): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1379:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1d5): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:1377:(.text._ZN5SVR_QC2ERK11svm_problemRK13svm_parameter[_ZN5SVR_QC5ERK11svm_problemRK13svm_parameter]+0x1da): undefined reference to `__cxa_throw_bad_array_new_length'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI7QMatrix[_ZTI7QMatrix]+0x0): undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI6Kernel[_ZTI6Kernel]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI6Solver[_ZTI6Solver]+0x0): undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI9Solver_NU[_ZTI9Solver_NU]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI5SVC_Q[_ZTI5SVC_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI11ONE_CLASS_Q[_ZTI11ONE_CLASS_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.ro._ZTI5SVR_Q[_ZTI5SVR_Q]+0x0): undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o):(.data.rel.local.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0'
collect2: error: ld returned 1 exit status

I really do not know how to start to understand what is going on and how to fix it. Any suggestion is welcome.

Last edited by olenellus (2024-06-24 17:33:27)

256 · 2024-05-27 16:40:35

My first thought (well, other than "what changed just before it broke?") is that this is a mismatch between C and C++. You're compiling a C program and the linker is complaining that libRNA.a can't reference parts of what I assume would be libgcc (the internal library used by GCC) that GCC uses for its C++ object code. Try renaming fold_compound_md.c to fold_compound_md.c++ to see what happens. I'm doubtful that this would fix the problem though, it might be more complicated. (I'm not even sure GCC needs to know if an object file was generated by C or C++. Does anyone know?)

I don't know much about how GCC links heterogenous C/C++ programs together. All I know is that "__cxxabiv1" being missing is very conspicuous; looking it up, this is meant to be provided by GCC.

Also, as of version 2.6.0 (released 2023-06-09, AUR updated the next day), ViennaRNA requires C++17. Maybe try passing "-std=c++17" as an option to the compiler? Depending on how often you update, maybe this is the cause. Also, are you sure your example could compile succesfully before?

The more I think about this the less sense it makes. I've realised I don't know as much about linking as I thought I did. Another avenue of exploration is looking at Ofront+'s changelogs, assuming it was updated.

olenellus · 2024-05-27 17:46:42

Thank you for your reply!

No, Ofront+ has nothing to do with the actual problem. The example above is one of the examples supplied together with ViennaRNA.

The compilation and linking worked as late as April 26 2024. I update weekly. There has been a renewal of something important in the system that resulted in a failure of a compilation with Ofront+ (I have not saved the error message and I don't remember details) and a dysfunction of yay. The latter I discovered by an attempt to recompile ViennaRNA.

The current problem may in theory come from two sources: either the linking step, or the building of ViennaRNA. The retention of the source paths in the error messages, perhaps, suggests the latter.

During the building process there were some warnings concerning C++17. I guess, that were C++11 features.

The actually recommended by the developers flags to compile the example above are the following

-L/usr/lib -lRNA -flto -fopenmp

see https://viennarna.readthedocs.io/en/latest/linking.html

They also recommend to add -I/usr/include flag. But the addition of neither -I/usr/include -I/usr/local/include -L/usr/lib -L/usr/local/lib nor of any of their combinations helps (because, as far as I understand, these are already among the standard locations). The same errors are indicated in attempt to compile the example.

The web site also mentions that the C++11 support can be disabled. Maybe I need to try this, too.

Last edited by olenellus (2024-05-27 17:48:35)

256 · 2024-05-27 19:08:36

I just did a quick test with gcc, and the inclusion of full original filepaths is not a bug. If an object file is compiled with the -g option, then the linker errors will contain the full original filepath used to reach the source file that it came from, with line number; else, the filename with a non-human-readable offset. I think you're barking up the wrong tree there.

I'm tempted to say that there are deeper problems with your system. Have you confirmed that C/C++ code that doesn't depend on ViennaRNA can still compile just fine? (I'm trying to use deductive reasoning here, as I usually do with difficult bugs.)

Lone_Wolf · 2024-05-28 09:26:49

from man ld

Note---if the linker is being invoked indirectly, via a compiler driver (e.g. gcc) then all the linker command-line options should be prefixed by -Wl, (or whatever is appropriate for the particular compiler driver) like this:

gcc -Wl,--start-group foo.o bar.o -Wl,--end-group

Try adding -Wl .

Also ld defaults to looking for dynamic libraries when using -lsomelibraryname .
you may want/need to add -static (man ld for details) .

olenellus · 2024-05-28 14:49:02

At least some C code that doesn't depend on ViennaRNA can be compiled without problems. I have just rebuilt anew the Ofront+ translator and its static library. I can still translate my Oberon programs into .c-files and .oh-files and then to compile them with gcc (linking to the newly compiled libOfront.a) without any problem.

If it's important, the command that I used for this compilation was

> gcc RK.c MutualLigationContT.c -s -Os -fno-exceptions -I../../../Mod/Lib -I../Lib/Obj -L../Lib -oMutualLigationContT -lOfront

Here RK.c and MutualLigationContT.c are C-files that are the result of a translation of my Oberon modules to C, libOfront.a is located in ../Lib, ../Lib/Obj and ../../../Mod/Lib contains C-files and header files for additional modules that I use in my programs. The resulting binary is working properly.

I have tried adding -Wl in the following manner

> gcc fold_compound_md.c -Wl,--start-group -lRNA -static -Wl,--end-group -ofold_compound_md
> gcc fold_compound_md.c -Wl,-lRNA -static -ofold_compound_md
> gcc fold_compound_md.c -lRNA -static -ofold_compound_md

All variants result in the same list of error messages as the simple -lRNA

The following variant gives a different result

> gcc fold_compound_md.c -Wl,-lRNA -Wl,-static -ofold_compound_md
/usr/bin/ld: cannot find -lgcc_s: No such file or directory
/usr/bin/ld: cannot find -lgcc_s: No such file or directory
collect2: error: ld returned 1 exit status

I guess, it is the only variant that does enforce the -static flag, and the compilation fails because in my system libgcc_s only exists as a dynamic library

> ls -l /usr/lib | grep gcc
drwxr-xr-x   3 root       root            4096 May 20  2021 gcc
lrwxrwxrwx   1 root       root              17 Feb  4 11:30 libgccpp.so -> libgccpp.so.1.5.0
lrwxrwxrwx   1 root       root              17 Feb  4 11:30 libgccpp.so.1 -> libgccpp.so.1.5.0
-rwxr-xr-x   1 root       root           14144 Feb  4 11:30 libgccpp.so.1.5.0
-rw-r--r--   1 root       root             132 May 22 14:09 libgcc_s.so
-rw-r--r--   1 root       root          911792 May 22 14:09 libgcc_s.so.1

olenellus · 2024-06-24 15:42:03

The problem is solved.

It consisted in the absence of libsvm in the system. And the solution was sticking out the linker errors right in the beginning:

/usr/bin/ld: /usr/local/lib/libRNA.a(svm.o): in function `Kernel::~Kernel()':
/home/olenellus/Local_programs/ViennaRNA-2.6.3/src/ViennaRNA/../libsvm-3.31/svm.cpp:294:(.text+0x117c): undefined reference to `operator delete[](void*)'

but is was not obvious for me, as the report complains against an undefined construct rather than about the lack of a library.

After installation of the libsvm package I can now correctly link my program with libRNA using

gcc fold_compound_md.c -lsvm -lm -lRNA -flto -fopenmp -o fold_compound_md

Why and how libsvm has disappeared from my system and why it is not included into the requirements of the viennarna package stays mysterious to me.

Last edited by olenellus (2024-06-24 15:43:14)

Arch Linux

#1 2024-05-27 14:08:57

[SOLVED] No linking against a static library after an update

#2 2024-05-27 16:40:35

Re: [SOLVED] No linking against a static library after an update

#3 2024-05-27 17:46:42

Re: [SOLVED] No linking against a static library after an update

#4 2024-05-27 19:08:36

Re: [SOLVED] No linking against a static library after an update

#5 2024-05-28 09:26:49

Re: [SOLVED] No linking against a static library after an update

#6 2024-05-28 14:49:02

Re: [SOLVED] No linking against a static library after an update

#7 2024-06-24 15:42:03

Re: [SOLVED] No linking against a static library after an update

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