############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL NetPathMiner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 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 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c handlesegfault.c -o handlesegfault.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c hme3m.c -o hme3m.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c kgml_interface.cpp -o kgml_interface.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c methods.cpp -o methods.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/include/libxml2 -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c sbml_interface.cpp -o sbml_interface.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lsbml -lxml2 -lxml2 -lsbml -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-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)