* 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++ -std=gnu++20 accepts -g... yes
checking for g++ -std=gnu++20 option to enable C++11 features... -std=gnu++11
checking how to run the C++ preprocessor... g++ -std=gnu++20 -std=gnu++11 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++20 -std=gnu++11 accepts -g... (cached) yes
checking for g++ -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/sbin/cmake
set CMAKE_BIN=/usr/sbin/cmake
Extracting bundled libsbml-5.21.0 source...
set CC=gcc
set CC_LAUNCHER=
set CFLAGS=-I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes
set CXX_LAUNCHER=
set CXX=g++
set CXXFLAGS=-std=gnu++20 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection
set LDFLAGS=-L/usr/local/lib64
-- The C compiler identification is GNU 16.2.1
-- The CXX compiler identification is GNU 16.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/sbin/gcc - 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/sbin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/sbin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Found SWIG: /usr/sbin/swig (found version "4.4.1")
-- Found PkgConfig: /usr/sbin/pkg-config (found version "2.5.1")
-- Looking for gzopen in /lib64/libz.so
-- Looking for gzopen in /lib64/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/lib64/libxml2.so (found version "2.12.10")
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found
-- Found BZ2: /usr/lib64/libbz2.so (found version "1.0.8")
-- Found ZLIB: /lib64/libz.so (found version "1.3.1.zlib-ng")
-- Looking for include file check.h
-- Looking for include file check.h - 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 'gannet2.stats.ox.ac.uk'
host type = Linux
host operating system = Linux 7.2.14-200.fc44.x86_64
host CPU architecture = x86_64
General build flags:
CC = /usr/sbin/gcc
CXX = /usr/sbin/g++
CPPFLAGS = -DLINUX
CFLAGS = -I/usr/local/include -fpic -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -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-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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 = -L/usr/local/lib64
XML parser library configuration:
XML library = libxml2
CPPFLAGS for XML = -I/usr/include/libxml2
LIBS for XML = /usr/lib64/libxml2.so
Other libSBML configuration settings:
Installation $prefix = /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install
-- Value of $LD_LIBRARY_PATH = /data/localhost/ripley/R/R-devel/lib:/usr/local/lib64:/usr/lib/jvm/java-25/lib/server:/data/localhost/ripley/R/R-devel/lib:/usr/local/lib64:/usr/lib/jvm/java-25/lib/server:/data/localhost/ripley/R/R-devel/lib:/usr/local/lib64:/usr/lib/jvm/java-25/lib/server:/data/localhost/ripley/R/R-devel/lib:/usr/local/lib64:/usr/lib/jvm/java-25/lib/server::/usr/lib64/openmpi/lib
-- Using SWIG = /usr/sbin/swig (Version 4.4.1)
-- 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 (2.5s)
-- Generating done (0.1s)
CMake Warning:
Manually-specified variables were not used by the project:
BUILD_TESTING
-- Build files have been written to: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-build
gmake[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-build'
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[ 1%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.cpp.o
[ 1%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathMathMLConsistencyValidator.cpp.o
[ 2%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathUnitConsistencyValidator.cpp.o
[ 2%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathValidator.cpp.o
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[ 12%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLLevel1Version1Converter.cpp.o
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[ 13%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLLocalParameterConverter.cpp.o
[ 13%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLRateOfConverter.cpp.o
[ 14%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLRateRuleConverter.cpp.o
[ 14%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLReactionConverter.cpp.o
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp: In function 'void print_vectors(setCoeff)':
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp:64:18: warning: unused variable 'term' [-Wunused-variable]
64 | ASTNode* term = co.at(n).first;
| ^~~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/conversion/SBMLRateRuleConverter.cpp: At global scope:
/data/localhost/ripley/R/packages/tests-devel/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)
| ^~~~~~~~~~~~~
[ 15%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/conversion/SBMLRuleConverter.cpp.o
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[ 34%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/SBMLVisitor.cpp.o
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/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/SBase.cpp: In member function 'virtual int SBase::setAnnotation(const XMLNode*)':
/data/localhost/ripley/R/packages/tests-devel/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;
| ^~~~~~~~~~~~~~
[ 36%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/SimpleSpeciesReference.cpp.o
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/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp: In member function 'html2md::Converter* html2md::Converter::appendToMd(const char*)':
/data/localhost/ripley/R/packages/tests-devel/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) {
| ~~^~~~~~~~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp: In member function 'bool html2md::Converter::ParseCharInTagContent(char)':
/data/localhost/ripley/R/packages/tests-devel/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_ &&
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/packages/tests-devel/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) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/html2md/html2md.cpp: At global scope:
/data/localhost/ripley/R/packages/tests-devel/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) {
| ^~~~~~~~~~
[ 41%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/html2md/table.cpp.o
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/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/ASTNode.cpp: In member function 'void ASTNode::fillListOfNodesWithLevel(ASTNodePredicate, ASTNodeLevels&, unsigned int) const':
/data/localhost/ripley/R/packages/tests-devel/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) ||
| ^
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/DefinitionURLRegistry.cpp: In static member function 'static int DefinitionURLRegistry::addDefinitionURL(const std::string&, int)':
/data/localhost/ripley/R/packages/tests-devel/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)
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/DefinitionURLRegistry.cpp: In static member function 'static std::string DefinitionURLRegistry::getDefinitionUrlByIndex(int)':
/data/localhost/ripley/R/packages/tests-devel/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)
| ~~^~~~~~~~
[ 42%] Building CXX object src/CMakeFiles/sbml-static.dir/sbml/math/FormulaFormatter.cpp.o
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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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/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp: In function 'bool isValidCSymbol(SBMLNamespaces*, ASTNodeType_t)':
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp:404:18: warning: unused variable 'version' [-Wunused-variable]
404 | unsigned int version = sbmlns->getVersion();
| ^~~~~~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp: In function 'void setTypeCI(ASTNode&, const XMLToken&, XMLInputStream&)':
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp:424:16: warning: unused variable 'n' [-Wunused-variable]
424 | unsigned int n = DefinitionURLRegistry::getInstance().getNumDefinitionURLs();
| ^
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-src/src/sbml/math/MathML.cpp: In function 'ASTNode* readMathML(XMLInputStream&, std::string, bool)':
/data/localhost/ripley/R/packages/tests-devel/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: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLInitialAssignmentConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLLevel1Version1Converter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLLevelVersionConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLLocalParameterConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLRateOfConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLRateRuleConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLReactionConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLRuleConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLStripPackageConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/conversion/SBMLUnitsConverter.h
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/extension/ASTBasePlugin.h
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-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/lib/cmake/sbml-static-targets.cmake
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/lib/cmake/sbml-static-targets-release.cmake
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/lib/cmake/sbml-static-config-version.cmake
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/lib/cmake/sbml-static-config.cmake
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/share/libsbml/COPYING.txt
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/share/libsbml/FUNDING.txt
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/share/libsbml/LICENSE.txt
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/share/libsbml/NEWS.txt
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/share/libsbml/README.md
-- Installing: /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/share/libsbml/VERSION.txt
-- Installing: /data/localhost/ripley/R/packages/tests-devel/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/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2
PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -L/data/localhost/ripley/R/packages/tests-devel/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++ (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/r2sbml/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c compartmentInfo.cpp -o compartmentInfo.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c convertReactions.cpp -o convertReactions.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c echoSBML.cpp -o echoSBML.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c getMath.cpp -o getMath.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c getModel.cpp -o getModel.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c getSpeciesNum.cpp -o getSpeciesNum.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c paramInfo.cpp -o paramInfo.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c printSBML.cpp -o printSBML.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c reactionInfo.cpp -o reactionInfo.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/ -I/usr/include/libxml2 -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c speciesInfo.cpp -o speciesInfo.o
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from getSpeciesNum.cpp:3:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from printSBML.cpp:3:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from compartmentInfo.cpp:5:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from paramInfo.cpp:10:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from speciesInfo.cpp:5:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from getModel.cpp:3:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from echoSBML.cpp:3:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from getMath.cpp:47:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from reactionInfo.cpp:10:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
In file included from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:112,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLDocument.h:305,
from /data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLTypes.h:48,
from convertReactions.cpp:57:
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/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);
| ^~~
/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/include/sbml/SBMLErrorLog.h:298:8: note: by ‘void SBMLErrorLog::add(const SBMLError&)’
298 | void add (const SBMLError& error);
| ^~~
g++ -std=gnu++20 -shared -L/usr/local/lib64 -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/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/data/localhost/ripley/R/packages/tests-devel/r2sbml/src/libsbml-install/lib/ -lsbml-static -lxml2 -lbz2
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/r2sbml/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/r2sbml/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/r2sbml/src'
installing to /data/localhost/ripley/R/packages/tests-devel/r2sbml.Rcheck/00LOCK-r2sbml/00new/r2sbml/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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)