############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rsbml ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘rsbml’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBSBML... yes configure: === Begin local SOSLib build === checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... config/config.guess: unable to guess system type This script, last modified 2008-01-23, has failed to recognize the operating system you are using. It is advised that you download the most up to date version of the config scripts from http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD and http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD If the version you run (config/config.guess) is already up to date, please send the following data and any information you think might be pertinent to in order to provide the needed information to handle your system. config.guess timestamp = 2008-01-23 uname -m = aarch64 uname -r = 5.10.0-136.85.0.166.oe2203sp1.aarch64 uname -s = Linux uname -v = #1 SMP Wed Jul 17 17:20:17 CST 2024 /usr/bin/uname -p = aarch64 /bin/uname -X = hostinfo = /bin/universe = /usr/bin/arch -k = /bin/arch = aarch64 /usr/bin/oslevel = /usr/convex/getsysinfo = UNAME_MACHINE = aarch64 UNAME_RELEASE = 5.10.0-136.85.0.166.oe2203sp1.aarch64 UNAME_SYSTEM = Linux UNAME_VERSION = #1 SMP Wed Jul 17 17:20:17 CST 2024 configure: error: cannot guess build type; you must specify one configure: === End local SOSLib build === configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c StringMap.c -o StringMap.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c check.c -o check.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c doc.c -o doc.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c dom.c -o dom.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c graph.c -o graph.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c io.c -o io.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c layoutWrappers.cpp -o layoutWrappers.o In file included from /home/biocbuild/libsbml-from-git/include/sbml/SBMLErrorLog.h:112, from /home/biocbuild/libsbml-from-git/include/sbml/SBMLDocument.h:305, from /home/biocbuild/libsbml-from-git/include/sbml/SBMLTypes.h:48, from rsbml.h:1, from layoutWrappers.cpp:1: /home/biocbuild/libsbml-from-git/include/sbml/xml/XMLErrorLog.h:211:16: warning: 'virtual void XMLErrorLog::add(const std::vector&)' was hidden [-Woverloaded-virtual=] 211 | virtual void add (const std::vector& errors); | ^~~ /home/biocbuild/libsbml-from-git/include/sbml/SBMLErrorLog.h:326:8: note: by 'SBMLErrorLog::add' 326 | void add (const std::vector& errors); | ^~~ /home/biocbuild/libsbml-from-git/include/sbml/xml/XMLErrorLog.h:200:16: warning: 'virtual void XMLErrorLog::add(const std::__cxx11::list&)' was hidden [-Woverloaded-virtual=] 200 | virtual void add (const std::list& errors); | ^~~ /home/biocbuild/libsbml-from-git/include/sbml/SBMLErrorLog.h:326:8: note: by 'SBMLErrorLog::add' 326 | void add (const std::vector& errors); | ^~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c mathml.c -o mathml.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -c simulate.c -o simulate.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -L/home/biocbuild/libsbml-from-git/lib -lsbml -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-rsbml/00new/rsbml/libs ** R ** 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 Error: package or namespace load failed for ‘rsbml’: .onLoad failed in loadNamespace() for 'rsbml', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/home/biocbuild/R/R-4.4.1/site-library/00LOCK-rsbml/00new/rsbml/libs/rsbml.so': /home/biocbuild/libsbml-from-git/lib/libsbml.so.5: undefined symbol: _ZTI13ElementFilter Error: loading failed Execution halted ERROR: loading failed * removing ‘/home/biocbuild/R/R-4.4.1/site-library/rsbml’