############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NetPathMiner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘NetPathMiner’ ... ** using staged installation 'config' variable 'CPP' is defunct checking for gcc... gcc 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for xmlParseFile in -lxml2... yes checking for readSBML in -lsbml... yes untarring boost include tree... libSBML found, finding configuration... pkg-config tool found libsbml.pc found. Using pkg-config to extract it. checking for xml2-config... /usr/bin/xml2-config configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c PathRanker.cpp -o PathRanker.o In file included from ./boost/mpl/aux_/na_assert.hpp:23, from ./boost/mpl/arg.hpp:25, from ./boost/mpl/placeholders.hpp:24, from ./boost/iterator/iterator_categories.hpp:17, from ./boost/graph/graph_traits.hpp:25, from ./boost/graph/graph_utility.hpp:29, from PathRanker.cpp:27: ./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 188 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ ./boost/mpl/assert.hpp:187:21: note: remove parentheses 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 188 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ | - ./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ ./boost/mpl/assert.hpp:192:21: note: remove parentheses 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ | - gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c handlesegfault.c -o handlesegfault.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c hme3m.c -o hme3m.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c kgml_interface.cpp -o kgml_interface.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c methods.cpp -o methods.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c pathScope.cpp -o pathScope.o In file included from ./boost/mpl/aux_/na_assert.hpp:23, from ./boost/mpl/arg.hpp:25, from ./boost/mpl/placeholders.hpp:24, from ./boost/iterator/iterator_categories.hpp:17, from ./boost/graph/graph_traits.hpp:25, from ./boost/graph/graph_utility.hpp:29, from pathScope.cpp:34: ./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 188 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ ./boost/mpl/assert.hpp:187:21: note: remove parentheses 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 188 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ | - ./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ ./boost/mpl/assert.hpp:192:21: note: remove parentheses 192 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ | - g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I. -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -c sbml_interface.cpp -o sbml_interface.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lsbml -lxml2 -lxml2 -lsbml -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-NetPathMiner/00new/NetPathMiner/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (NetPathMiner)