Install log for 'r2sbml'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘r2sbml’ ...
** this is package ‘r2sbml’ version ‘0.1.0’
** package ‘r2sbml’ successfully unpacked and MD5 sums checked
** using staged installation
'config' variable 'CXX11FLAGS' is defunct
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++-16 -std=gnu++20 accepts -g... yes
checking for g++-16 -std=gnu++20 option to enable C++11 features... -std=gnu++11
checking how to run the C++ preprocessor... g++-16 -std=gnu++20 -std=gnu++11 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++-16 -std=gnu++20 -std=gnu++11 accepts -g... (cached) yes
checking for g++-16 -std=gnu++20 -std=gnu++11 option to enable C++11 features... (cached) -std=gnu++11
checking for pkg-config... yes
checking for cmake... /usr/bin/cmake
set CMAKE_BIN=/usr/bin/cmake
Extracting bundled libsbml-5.21.0 source...
set CC=gcc-16
set CC_LAUNCHER=
set CFLAGS=-I/usr/local/include -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native
set CXX_LAUNCHER=
set CXX=g++-16
set CXXFLAGS=-std=gnu++20 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native
set LDFLAGS=-Wl,-O1
-- The C compiler identification is GNU 16.2.0
-- The CXX compiler identification is GNU 16.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc-16 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++-16 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/gcc-16 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR) 
-- Found PkgConfig: /usr/bin/pkg-config (found version "2.5.1")
-- Looking for gzopen in /usr/lib/x86_64-linux-gnu/libz.so
-- Looking for gzopen in /usr/lib/x86_64-linux-gnu/libz.so - found
-- Looking for sin in m
-- Looking for sin in m - found
-- Performing Test LIBXML_LIBXML_TEST
-- Performing Test LIBXML_LIBXML_TEST - Success
-- LIBXML_LIBXML_TEST = 1
-- Found LIBXML: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.15.4")
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found BZ2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8")
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2")
-- Looking for include file check.h
-- Looking for include file check.h - not found
-- Looking for include file expat.h
-- Looking for include file expat.h - found
-- Looking for include file errno.h
-- Looking for include file errno.h - found
-- Looking for include file ieeefp.h
-- Looking for include file ieeefp.h - not found
-- Looking for include file math.h
-- Looking for include file math.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for include file float.h
-- Looking for include file float.h - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- 
----------------------------------------------------------------------
libSBML version 5.21.0
----------------------------------------------------------------------

   More information and the latest version are available online at
   https://sbml.org/software/libsbml/

   Please report problems using the issue tracker at
   https://github.com/sbmlteam/libsbml/issues

   To contact the developers directly, email libsbml-team@googlegroups.com

   Configured on host 'gimli2'
     host type                       = Linux
     host operating system           = Linux 7.2.12+deb14-amd64
     host CPU architecture           = x86_64

   General build flags:
     CC                              = /usr/bin/gcc-16
     CXX                             = /usr/bin/g++-16
     CPPFLAGS                        =  -DLINUX
     CFLAGS                          = -I/usr/local/include -fpic -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -Wno-format-truncation -Wno-format-overflow -Wno-stringop-overflow -Wno-old-style-definition -Wno-strict-prototypes -std=gnu17 -fno-strict-aliasing -fPIC
     CXXFLAGS                        = -std=gnu++20 -I/usr/local/include -fpic -O2 -Wall -pedantic -mtune=native -Wno-format-truncation -Wno-format-overflow -Wno-stringop-overflow -Wno-overloaded-virtual -Wno-reorder -Wno-parentheses -Wno-switch -Wno-array-bounds -fno-strict-aliasing -fPIC
     LDFLAGS                         = -Wl,-O1

   XML parser library configuration:
     XML library                     = libxml2
     CPPFLAGS for XML                = -I/usr/include/libxml2
     LIBS for XML                    = /usr/lib/x86_64-linux-gnu/libxml2.so

   Other libSBML configuration settings:
     Installation $prefix            = /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install
--      Value of $LD_LIBRARY_PATH       = /home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-25-openjdk-amd64/lib/server:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-25-openjdk-amd64/lib/server:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-25-openjdk-amd64/lib/server
--      Using SWIG                      = SWIG_EXECUTABLE-NOTFOUND (Version )
--      Using C++ namespace ('libsbml') = no
-- 
--      Build examples                  = no
-- 
-- 
--    Support for SBML Level 3 Packages: 
--      SBML 'arrays' package  = OFF
--      SBML 'comp' package    = OFF
--      SBML 'distrib' package  = OFF
--      SBML 'dyn' package     = OFF
--      SBML 'fbc' package     = OFF
--      SBML 'groups' package  = OFF
--      SBML 'l3v2extendedmath' package  = ON
--      SBML 'layout' package  = OFF
--      SBML 'multi' package   = OFF
--      SBML 'qual' package    = OFF
--      SBML 'render' package  = OFF
--      SBML 'req' package     = OFF
--      SBML 'spatial' package = OFF
-- 

-- Other potentially important settings:
--   Compression support is enabled for .zip and .gz files
--   Compression support is enabled for .bz2 files
-- 
----------------------------------------------------------------------
-- Configuring done (2.6s)
-- Generating done (0.1s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING


-- Build files have been written to: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-build
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[ 12%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLLevel1Version1Converter.cpp.o
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[ 14%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLReactionConverter.cpp.o
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp: In function 'void print_vectors(setCoeff)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp:64:18: warning: unused variable 'term' [-Wunused-variable]
   64 |         ASTNode* term = co.at(n).first;
      |                  ^~~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp: At global scope:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp:59:13: warning: 'void print_vectors(setCoeff)' defined but not used [-Wunused-function]
   59 | static void print_vectors(setCoeff co)
      |             ^~~~~~~~~~~~~
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/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/SBase.cpp: In member function 'virtual int SBase::setAnnotation(const XMLNode*)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/SBase.cpp:1398:8: warning: variable 'hasNestedTerms' set but not used [-Wunused-but-set-variable=]
 1398 |   bool hasNestedTerms = false;
      |        ^~~~~~~~~~~~~~
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/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp: In member function 'html2md::Converter* html2md::Converter::appendToMd(const char*)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp:230:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  230 |   for (auto i = 0; i < str_len; ++i) {
      |                    ~~^~~~~~~~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp: In member function 'bool html2md::Converter::ParseCharInTagContent(char)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp:582:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  582 |   if (chars_in_curr_line_ > option.softBreak && !is_in_table_ && !is_in_list_ &&
      |       ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp:588:36: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  588 |     } else if (chars_in_curr_line_ > option.hardBreak) {
      |                ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp: At global scope:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp:50:8: warning: 'size_t {anonymous}::ReplaceAll(std::string*, const std::string&, char)' defined but not used [-Wunused-function]
   50 | size_t ReplaceAll(string *haystack, const string &needle, const char c) {
      |        ^~~~~~~~~~
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/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/ASTNode.cpp: In member function 'void ASTNode::fillListOfNodesWithLevel(ASTNodePredicate, ASTNodeLevels&, unsigned int) const':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/ASTNode.cpp:1180:74: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare]
 1180 |         (vector_pairs.size() == 1 && vector_pairs.back().second == NULL) ||
      |                                                                          ^
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/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/DefinitionURLRegistry.cpp: In static member function 'static int DefinitionURLRegistry::addDefinitionURL(const std::string&, int)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/DefinitionURLRegistry.cpp:82:30: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   82 |   if (getNumDefinitionURLs() == n + 1)
      |       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/DefinitionURLRegistry.cpp: In static member function 'static std::string DefinitionURLRegistry::getDefinitionUrlByIndex(int)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/DefinitionURLRegistry.cpp:106:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  106 |     if (i == index)
      |         ~~^~~~~~~~
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L3Parser.cpp: In function 'void yy_stack_print(yy_state_t*, yy_state_t*)':
L3Parser.cpp:1113:11: warning: unused variable 'yybot' [-Wunused-variable]
L3Parser.cpp: In function 'void yy_reduce_print(yy_state_t*, SBML_YYSTYPE*, int)':
L3Parser.cpp:1133:7: warning: unused variable 'yylno' [-Wunused-variable]
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/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp: In function 'bool isValidCSymbol(SBMLNamespaces*, ASTNodeType_t)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp:404:18: warning: unused variable 'version' [-Wunused-variable]
  404 |     unsigned int version = sbmlns->getVersion();
      |                  ^~~~~~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp: In function 'void setTypeCI(ASTNode&, const XMLToken&, XMLInputStream&)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp:424:16: warning: unused variable 'n' [-Wunused-variable]
  424 |   unsigned int n = DefinitionURLRegistry::getInstance().getNumDefinitionURLs();
      |                ^
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp: In function 'ASTNode* readMathML(XMLInputStream&, std::string, bool)':
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp:2177:21: warning: unused variable 'name' [-Wunused-variable]
 2177 |       const string& name = element1.getName();
      |                     ^~~~
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLFunctionDefinitionConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLIdConverter.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLInitialAssignmentConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLLevel1Version1Converter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLLevelVersionConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLLocalParameterConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLRateOfConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLRateRuleConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLReactionConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLRuleConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLStripPackageConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLUnitsConverter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/ASTBasePlugin.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/ISBMLExtensionNamespaces.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLDocumentPlugin.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLDocumentPluginNotRequired.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLExtension.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLExtensionException.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLExtensionNamespaces.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLExtensionRegister.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBMLExtensionRegistry.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBaseExtensionPoint.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBasePlugin.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBasePluginCreator.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/SBasePluginCreatorBase.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/html2md/html2md.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/html2md/table.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/blockparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/breaklineparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/checklistparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/codeblockparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/emphasizedparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/headlineparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/horizontallineparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/htmlparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/imageparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/inlinecodeparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/italicparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/latexblockparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/lineparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/linkparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/orderedlistparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/paragraphparser.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/parserconfig.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/quoteparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/strikethroughparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/strongparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/tableparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/maddy/unorderedlistparser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/math/ASTNode.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/math/ASTNodeType.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/math/FormulaFormatter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/math/FormulaParser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/math/FormulaTokenizer.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/math/L3FormulaFormatter.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/units/UnitFormulaFormatter.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/util/IdList.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/util/IdentifierTransformer.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/util/MetaIdFilter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/util/PrefixTransformer.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/validator/ConsistencyValidator.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/validator/ConstraintMacros.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/validator/OverdeterminedValidator.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/validator/SBMLExternalValidator.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/validator/SBMLValidator.h
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-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLLogOverride.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLMemoryBuffer.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLNamespaces.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLNode.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLOutputStream.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLParser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLToken.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLTokenizer.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLTriple.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XercesAttributes.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XercesHandler.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XercesNamespaces.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XercesParser.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XercesTranscode.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/AlgebraicRule.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/AssignmentRule.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Compartment.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/CompartmentType.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Constraint.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Delay.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Event.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/EventAssignment.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/ExpectedAttributes.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/FunctionDefinition.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/InitialAssignment.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/KineticLaw.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/ListOf.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/LocalParameter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Model.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/ModifierSpeciesReference.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Parameter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Priority.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/RateRule.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Reaction.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Rule.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLConstructorException.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLError.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorTable.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLNamespaces.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLReader.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTransforms.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypeCodes.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLVisitor.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLWriter.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBO.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBase.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SimpleSpeciesReference.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Species.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SpeciesReference.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SpeciesType.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/StoichiometryMath.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SyntaxChecker.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Trigger.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/Unit.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/UnitDefinition.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/UnitKind.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/common/libsbml-config-common.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/common/libsbml-config-packages.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/common/libsbml-namespace.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/common/libsbml-package.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/common/libsbml-version.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/extension/RegisterExtensions.h
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-build/lib/libsbml-static.a
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/lib/cmake/sbml-static-targets.cmake
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/lib/cmake/sbml-static-targets-release.cmake
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/lib/cmake/sbml-static-config-version.cmake
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/lib/cmake/sbml-static-config.cmake
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/share/libsbml/COPYING.txt
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/share/libsbml/FUNDING.txt
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/share/libsbml/LICENSE.txt
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/share/libsbml/NEWS.txt
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/share/libsbml/README.md
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/share/libsbml/VERSION.txt
-- Installing: /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-build/lib/pkgconfig/libsbml.pc
Copied libsbml-static.a from build tree to install prefix.
configure: creating ./config.status
config.status: creating src/Makevars

Final src/Makevars
PKG_CPPFLAGS= -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2
PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -L/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/lib/ -lsbml-static -lxml2 -lbz2

# r2sbml.so statically links libsbml, so it inherits the debug info of every
# libsbml object the linker pulls in.  Removing it takes the installed shared
# object from ~65MB to ~6.6MB.  Global symbols are kept, so the R-level
# interface is unaffected; only DWARF is discarded.
#
# Guarded on uname because the flag spelling differs: GNU binutils uses
# --strip-debug, Apple's strip uses -S.  Anything else is left alone.
all: $(SHLIB) strippedLib

strippedLib: $(SHLIB)
	@if command -v strip >/dev/null 2>&1; then \
	  case `uname -s` in \
	    Linux)  strip --strip-debug $(SHLIB) || true ;; \
	    Darwin) strip -S $(SHLIB) || true ;; \
	  esac; \
	fi

.PHONY: all strippedLib
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c compartmentInfo.cpp -o compartmentInfo.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from compartmentInfo.cpp:5:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c convertReactions.cpp -o convertReactions.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from convertReactions.cpp:57:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c echoSBML.cpp -o echoSBML.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from echoSBML.cpp:3:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c getMath.cpp -o getMath.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from getMath.cpp:47:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c getModel.cpp -o getModel.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from getModel.cpp:3:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c getSpeciesNum.cpp -o getSpeciesNum.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from getSpeciesNum.cpp:3:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c paramInfo.cpp -o paramInfo.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from paramInfo.cpp:10:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c printSBML.cpp -o printSBML.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from printSBML.cpp:3:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c reactionInfo.cpp -o reactionInfo.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from reactionInfo.cpp:10:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c speciesInfo.cpp -o speciesInfo.o
In file included from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
                 from /home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
                 from speciesInfo.cpp:5:
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:200:16: warning: ‘virtual void XMLErrorLog::add(const std::__cxx11::list<XMLError>&)’ was hidden [-Woverloaded-virtual=]
  200 |   virtual void add (const std::list<XMLError>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/xml/XMLErrorLog.h:211:16: warning: ‘virtual void XMLErrorLog::add(const std::vector<XMLError*>&)’ was hidden [-Woverloaded-virtual=]
  211 |   virtual void add (const std::vector<XMLError*>& errors);
      |                ^~~
/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note:   by ‘void SBMLErrorLog::add(const SBMLError&)’
  298 |   void add (const SBMLError& error);
      |        ^~~
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o r2sbml.so RcppExports.o compartmentInfo.o convertReactions.o echoSBML.o getMath.o getModel.o getSpeciesNum.o paramInfo.o printSBML.o reactionInfo.o speciesInfo.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src/libsbml-install/lib/ -lsbml-static -lxml2 -lbz2 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGICaQ0/R.INSTALL32d9d7199ac46f/r2sbml/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-r2sbml/00new/r2sbml/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘r2sbml’
    finding HTML links ... done
    convertReactions                        html  
    echoSBML                                html  
    getCmtNames                             html  
    getCmtSizes                             html  
    getEventMath                            html  
    getFunctionDefinition                   html  
    getModel                                html  
    getNumSpecies                           html  
    getParameterTable                       html  
    getReactionMath                         html  
    getReactionTable                        html  
    getRuleMath                             html  
    getSpeciesIC                            html  
    getSpeciesNames                         html  
    getSpeciesTable                         html  
    printSBML                               html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (r2sbml)