diff --git a/.travis.yml b/.travis.yml
index b69295819b7..1675a70c44d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -72,7 +72,7 @@ jobs:
       script:
         - echo $PATH
         - doxygen --version
-        - scripts/travis_doxygen.sh
+        - scripts/run_doxygen.sh
       before_cache:
       after_success:
         # Google Cloud Integration
diff --git a/scripts/expected_doxygen_warnings.txt b/scripts/expected_doxygen_warnings.txt
index 18310b2d691..e92e7ca493b 100644
--- a/scripts/expected_doxygen_warnings.txt
+++ b/scripts/expected_doxygen_warnings.txt
@@ -20,7 +20,7 @@
 /cbmc/src/solvers/refinement/string_refinement.cpp:1511: warning: argument 'stream' of command @param is not found in the argument list of compute_inverse_function(const exprt &qvar, const exprt &val, const exprt &f)
 /cbmc/src/solvers/refinement/string_refinement.cpp:239: warning: Invalid list item found
 /cbmc/src/solvers/refinement/string_refinement.cpp:1823: warning: argument 'stream' of command @param is not found in the argument list of instantiate(const string_constraintt &axiom, const exprt &str, const exprt &val)
-/cbmc/src/solvers/refinement/string_refinement.cpp:112: warning: The following parameters of instantiate(const string_not_contains_constraintt &axiom, const index_set_pairt &index_set, const string_constraint_generatort &generator, const std::map< string_not_contains_constraintt, symbol_exprt > &witnesses) are not documented:
+/cbmc/src/solvers/refinement/string_refinement.cpp:112: warning: The following parameters of instantiate(const string_not_contains_constraintt &axiom, const index_set_pairt &index_set, const string_constraint_generatort &generator, const std::unordered_map< string_not_contains_constraintt, symbol_exprt > &witnesses) are not documented:
   parameter 'witnesses'
 /cbmc/src/solvers/refinement/string_refinement.cpp:1052: warning: The following parameters of substitute_array_access(const with_exprt &expr, const exprt &index, const bool left_propagate) are not documented:
   parameter 'left_propagate'
@@ -95,9 +95,6 @@
 /cbmc/src/goto-programs/goto_program.cpp:21: warning: argument 'instruction' of command @param is not found in the argument list of goto_programt::output_instruction(const namespacet &ns, const irep_idt &identifier, std::ostream &out, const instructionst::value_type &it) const
 /cbmc/src/goto-programs/goto_program.h:560: warning: The following parameters of goto_programt::output_instruction(const namespacet &ns, const irep_idt &identifier, std::ostream &out, const instructionst::value_type &it) const are not documented:
   parameter 'it'
-/cbmc/src/goto-symex/goto_symex.h:179: warning: argument 'goto_functions' of command @param is not found in the argument list of goto_symext::initialize_entry_point(statet &state, const get_goto_functiont &get_goto_function, goto_programt::const_targett pc, goto_programt::const_targett limit)
-/cbmc/src/goto-symex/goto_symex.h:185: warning: The following parameters of goto_symext::initialize_entry_point(statet &state, const get_goto_functiont &get_goto_function, goto_programt::const_targett pc, goto_programt::const_targett limit) are not documented:
-  parameter 'get_goto_function'
 /cbmc/src/goto-instrument/wmm/goto2graph.h:260: warning: The following parameters of instrumentert::cfg_visitort::visit_cfg_function(value_setst &value_sets, memory_modelt model, bool no_dependencies, loop_strategyt duplicate_body, const irep_idt &function, std::set< nodet > &ending_vertex) are not documented:
   parameter 'model'
   parameter 'no_dependencies'
@@ -171,3 +168,5 @@
 /cbmc/src/pointer-analysis/dereference.h:26: warning: argument '_options' of command @param is not found in the argument list of dereferencet::dereferencet(const namespacet &_ns)
 /cbmc/src/pointer-analysis/dereference.h:26: warning: argument '_dereference_callback' of command @param is not found in the argument list of dereferencet::dereferencet(const namespacet &_ns)
 /cbmc/src/goto-programs/rebuild_goto_start_function.cpp:22: warning: argument '_message_handler' of command @param is not found in the argument list of rebuild_goto_start_function_baset< maybe_lazy_goto_modelt >::rebuild_goto_start_function_baset(const optionst &options, maybe_lazy_goto_modelt &goto_model, message_handlert &message_handler)
+/cbmc/src/solvers/README.md:4: warning: @copydetails or @copydoc target 'check_axioms(const string_axiomst &axioms, string_constraint_generatort &generator, const std::function<exprt(const exprt &)> &get, messaget::mstreamt &stream, const namespacet &ns, bool use_counter_example, const union_find_replacet &symbol_resolve, const std::map<string_not_contains_constraintt, symbol_exprt> &not_contain_witnesses)' not found
+/cbmc/src/solvers/README.md:428: warning: unable to resolve link to `check_axioms(const string_axiomst &axioms, string_constraint_generatort &generator, const std::function<exprt(const exprt &)> &get, messaget::mstreamt &stream, const namespacet &ns, bool use_counter_example, const union_find_replacet &symbol_resolve, const std::map<string_not_contains_constraintt, symbol_exprt> &not_contain_witnesses)' for \link command
diff --git a/scripts/run_diff.sh b/scripts/run_diff.sh
index dd0aa5c2f08..85f3c3f66e9 100755
--- a/scripts/run_diff.sh
+++ b/scripts/run_diff.sh
@@ -5,7 +5,7 @@ set -e
 script_folder=$(dirname "$0")
 absolute_repository_root=$(git rev-parse --show-toplevel)
 mode=$1
-modes="CPPLINT | DOXYGEN"
+modes="CPPLINT"
 
 if [[ "$#" -gt 3 ]]
 then
@@ -39,23 +39,6 @@ then
   else
     cmd='${script_folder}/cpplint.py --filter=-whitespace/operators,-readability/identifier_spacing $file 2>&1 >/dev/null'
   fi
-elif [[ "$mode" == "DOXYGEN" ]]
-then
-  doxygen=doxygen
-  doxygenlogdir="doc/html"
-  doxygenlog="$doxygenlogdir/doxygen.log"
-  suppress_warnings=(
-    "warning: Included by graph for .* not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES.")
-  if ! $doxygen --version &>/dev/null
-  then
-    echo "Doxygen is not installed on this PC"
-    echo "Please install before running this script"
-    exit 1
-  else
-    mkdir -p $doxygenlogdir && cd src && $doxygen &> ../$doxygenlog && cd ..
-    suppress_warnings_regex=$(IFS="|" ; echo "${suppress_warnings[*]}")
-    cmd='grep -Ev "$suppress_warnings_regex" $doxygenlog'
-  fi
 else
   echo "Mode $mode not recognized"
   echo "Possible values: $modes"
diff --git a/scripts/travis_doxygen.sh b/scripts/travis_doxygen.sh
deleted file mode 100755
index 359de72ff60..00000000000
--- a/scripts/travis_doxygen.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-set -e
-
-script_folder=`dirname $0`
-pip install --user unidiff
-
-if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
-  $script_folder/run_diff.sh DOXYGEN HEAD~1 # Check for errors introduced in last commit
-else
-  TMP_HEAD=$(git rev-parse HEAD)
-  git config remote.origin.fetch +refs/heads/$TRAVIS_BRANCH:refs/remotes/origin/$TRAVIS_BRANCH
-  git fetch --unshallow
-  git checkout $TMP_HEAD
-  $script_folder/run_diff.sh DOXYGEN origin/$TRAVIS_BRANCH # Check for errors compared to merge target
-fi