Temporary header file '/tmp/82Zk4_TBrb/dump1.h' with the following content will be compiled to create GCC translation unit dump:

  // add defines
  #define __STDC_VERSION__ 201710L
#define _GXX_NULLPTR_T
#define CLUTTER_ENABLE_COMPOSITOR_API 1
#define _REGEX_NELTS(n)
#define _Atomic
#define PACKED
#define getaddrinfo_a(a,b,c,d)

  // add includes
  #include "/usr/include/clustalo/clustal/hhalign_wrapper.h"
  #include "/usr/include/clustalo/clustal/ktuple_pair.h"
  #include "/usr/include/clustalo/clustal/log.h"
  #include "/usr/include/clustalo/clustal/mbed.h"
  #include "/usr/include/clustalo/clustal/muscle_tree.h"
  #include "/usr/include/clustalo/clustal/pair_dist.h"
  #include "/usr/include/clustalo/clustal/progress.h"
  #include "/usr/include/clustalo/clustal/seq.h"
  #include "/usr/include/clustalo/clustal/symmatrix.h"
  #include "/usr/include/clustalo/clustal/tree.h"
  #include "/usr/include/clustalo/clustal/util.h"
  #include "/usr/include/clustalo/clustal/weights.h"
  #include "/usr/include/clustalo/clustal-omega-config.h"
  #include "/usr/include/clustalo/clustal-omega.h"
  #include "/usr/include/clustalo/hhalign/general.h"
  #include "/usr/include/clustalo/hhalign/hhfunc.h"
  #include "/usr/include/clustalo/squid/gki.h"
  #include "/usr/include/clustalo/squid/gsi64.h"
  #include "/usr/include/clustalo/squid/msa.h"
  #include "/usr/include/clustalo/squid/rk.h"
  #include "/usr/include/clustalo/squid/sqfuncs.h"
  #include "/usr/include/clustalo/squid/squid.h"
  #include "/usr/include/clustalo/squid/sre_random.h"
  #include "/usr/include/clustalo/squid/ssi.h"
  #include "/usr/include/clustalo/squid/stockholm.h"
  #include "/usr/include/clustalo/squid/stopwatch.h"
  #include "/usr/include/clustalo/squid/vectorops.h"
  #include "/usr/include/clustalo/squid/version.h"

  // add classes
  ReadSeqVars* tmp_add_class_0;
  _G_fpos64_t* tmp_add_class_1;
  _G_fpos_t* tmp_add_class_2;
  _IO_cookie_io_functions_t* tmp_add_class_3;
  aliinfo_s* tmp_add_class_4;
  gki_elem* tmp_add_class_5;
  intstack_s* tmp_add_class_6;
  iupactype* tmp_add_class_7;
  msa_struct* tmp_add_class_8;
  msafile_struct* tmp_add_class_9;
  opt_s* tmp_add_class_10;
  phylo_s* tmp_add_class_11;
  seqinfo_s* tmp_add_class_12;
  sqd_regexp* tmp_add_class_13;
  ssifile_s* tmp_add_class_14;
  ssiindex_s* tmp_add_class_15;
  ssioffset_s* tmp_add_class_16;
  ssipkey_s* tmp_add_class_17;
  ssiskey_s* tmp_add_class_18;
  stopwatch_s* tmp_add_class_19;
  tms* tmp_add_class_20;

The GCC parameters:
  gcc -fdump-lang-raw -fkeep-inline-functions -c -x c++ -fpermissive -w "/tmp/82Zk4_TBrb/dump1.h"  -I/usr/include/clustalo

In file included from /tmp/82Zk4_TBrb/dump1.h:12:
/usr/include/clustalo/clustal/hhalign_wrapper.h:20:1: error: variable or field ‘SetDefaultHhalignPara’ declared void
   20 | SetDefaultHhalignPara(hhalign_para *prHhalignPara);
      | ^~~~~~~~~~~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:20:23: error: ‘hhalign_para’ was not declared in this scope
   20 | SetDefaultHhalignPara(hhalign_para *prHhalignPara);
      |                       ^~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:20:37: error: ‘prHhalignPara’ was not declared in this scope
   20 | SetDefaultHhalignPara(hhalign_para *prHhalignPara);
      |                                     ^~~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:24: error: ‘mseq_t’ was not declared in this scope
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      |                        ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:32: error: ‘prMSeq’ was not declared in this scope
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      |                                ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:40: error: ‘hmm_light’ was not declared in this scope
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      |                                        ^~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:65: error: ‘hhalign_para’ was not declared in this scope
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      |                                                                 ^~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:92: error: expected primary-expression before ‘char’
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      |                                                                                            ^~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:26:8: error: ‘mseq_t’ was not declared in this scope
   26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
      |        ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:26:16: error: ‘prMSeq’ was not declared in this scope
   26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
      |                ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:26:24: error: ‘hhalign_para’ was not declared in this scope
   26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
      |                        ^~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:26:51: error: expected primary-expression before ‘int’
   26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
      |                                                   ^~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:29:16: error: ‘mseq_t’ was not declared in this scope
   29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR,
      |                ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:29:24: error: ‘mseq’ was not declared in this scope
   29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR,
      |                        ^~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:29:30: error: expected primary-expression before ‘int’
   29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR,
      |                              ^~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:30:16: error: expected primary-expression before ‘double’
   30 |                double *pdSeqWeights, int iNodeCount,
      |                ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:30:38: error: expected primary-expression before ‘int’
   30 |                double *pdSeqWeights, int iNodeCount,
      |                                      ^~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:31:16: error: ‘hmm_light’ was not declared in this scope
   31 |                hmm_light *prHMMList, int iHMMCount,
      |                ^~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:31:27: error: ‘prHMMList’ was not declared in this scope
   31 |                hmm_light *prHMMList, int iHMMCount,
      |                           ^~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:31:38: error: expected primary-expression before ‘int’
   31 |                hmm_light *prHMMList, int iHMMCount,
      |                                      ^~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:32:16: error: expected primary-expression before ‘int’
   32 |                int iProfProfSeparator, hhalign_para rHhalignPara);
      |                ^~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:32:40: error: ‘hhalign_para’ was not declared in this scope
   32 |                int iProfProfSeparator, hhalign_para rHhalignPara);
      |                                        ^~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:34:1: error: variable or field ‘SanitiseUnknown’ declared void
   34 | SanitiseUnknown(mseq_t *mseq);
      | ^~~~~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:34:17: error: ‘mseq_t’ was not declared in this scope
   34 | SanitiseUnknown(mseq_t *mseq);
      |                 ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:34:25: error: ‘mseq’ was not declared in this scope
   34 | SanitiseUnknown(mseq_t *mseq);
      |                         ^~~~
In file included from /usr/include/clustalo/clustal-omega.h:51,
                 from /tmp/82Zk4_TBrb/dump1.h:25:
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:113: error: ‘int PosteriorProbabilities(mseq_t*, hmm_light, hhalign_para, char*)’ redeclared as different kind of entity
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      |                                                                                                                 ^
/usr/include/clustalo/clustal/hhalign_wrapper.h:23:1: note: previous declaration ‘int PosteriorProbabilities’
   23 | PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
      | ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:26:67: error: ‘double PileUp(mseq_t*, hhalign_para, int)’ redeclared as different kind of entity
   26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
      |                                                                   ^
/usr/include/clustalo/clustal/hhalign_wrapper.h:26:1: note: previous declaration ‘double PileUp’
   26 | PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
      | ^~~~~~
/usr/include/clustalo/clustal/hhalign_wrapper.h:32:65: error: ‘double HHalignWrapper(mseq_t*, int*, double*, int, hmm_light*, int, int, hhalign_para)’ redeclared as different kind of entity
   32 |                int iProfProfSeparator, hhalign_para rHhalignPara);
      |                                                                 ^
/usr/include/clustalo/clustal/hhalign_wrapper.h:29:1: note: previous declaration ‘double HHalignWrapper’
   29 | HHalignWrapper(mseq_t *mseq, int *piOrderLR,
      | ^~~~~~~~~~~~~~

