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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lpsymphony
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘lpsymphony’ ...
** using staged installation
* Defaulting to clang/clang++
configure: loading site script /Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... i386-apple-darwin18.7.0
checking whether we want to compile in debug mode... no
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ANSI C... none needed
configure: C compiler options are: -w -g -O2  
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++17 accepts -g... yes
rm: conftest.dSYM: is a directory
checking whether C++ compiler clang++ -mmacosx-version-min=10.13 -std=gnu++17 works... yes
configure: C++ compiler options are: -w -g -O2  
configure: Trying to determine Fortran compiler name
checking for xlf_r... no
checking for fort77... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
configure: Fortran compiler options are: -O3 -pipe  
checking for egrep... grep -E
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... none
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++17... none
checking whether to enable maintainer-specific portions of Makefiles... no
checking host system type... i386-apple-darwin18.7.0
checking for a sed that does not truncate output... /usr/bin/sed
checking for ld used by clang -mmacosx-version-min=10.13... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++17 -E
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... rm: conftest.dSYM: is a directory
yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common works... rm: conftest.dSYM: is a directory
yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... rm: conftest.dSYM: is a directory
no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking for ld used by clang++ -mmacosx-version-min=10.13 -std=gnu++17... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++17 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++17 option to produce PIC... -fno-common
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++17 PIC flag -fno-common works... rm: conftest.dSYM: is a directory
yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++17 static flag -static works... rm: conftest.dSYM: is a directory
no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++17 supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++17 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fno-common
checking if gfortran PIC flag -fno-common works... rm: conftest.dSYM: is a directory
yes
checking if gfortran static flag -static works... rm: conftest.dSYM: is a directory
no
checking if gfortran supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the gfortran linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
configure: Build is "i386-apple-darwin18.7.0".
configure: Applying patches to libtool for Darwin
checking if library version is set... no
checking whether source of project Blas is available and should be compiled... no, source file ./ThirdParty/Blas/daxpy.f not available
checking whether source of project Lapack is available and should be compiled... no, source file ./ThirdParty/Lapack/LAPACK/SRC/dlarf.f not available
checking whether source of project Glpk is available and should be compiled... no, source file ./ThirdParty/Glpk/glpk/src/glplpx01.c not available
checking whether source of project Sample is available and should be compiled... no
checking whether source of project miblib3 is available and should be compiled... no
checking whether source of project CoinUtils is available and should be compiled... yes, source in CoinUtils
checking whether source of project Osi is available and should be compiled... yes, source in Osi
checking whether source of project Clp is available and should be compiled... yes, source in Clp
checking whether source of project Cgl is available and should be compiled... yes, source in Cgl
checking whether source of project DyLP is available and should be compiled... no
checking whether source of project Vol is available and should be compiled... no
checking whether source of project SYMPHONY is available and should be compiled... yes, source in SYMPHONY
checking whether Clp is required... yes
checking which command should be used to link input files... ln -s
configure: creating ./config.status
config.status: creating Makefile
config.status: executing depfiles commands
configure: configuring in CoinUtils
configure: running /bin/sh './configure' --prefix=/Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++17' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-openmp' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CPPFLAGS=-I/usr/local/include' 'LDFLAGS=-L/usr/local/lib' --cache-file=/dev/null --srcdir=.
configure: loading site script /Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... i386-apple-darwin18.7.0
checking for svnversion... yes
checking whether we want to compile in debug mode... no
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ANSI C... none needed
configure: C compiler options are: -w -g -O2   -DCOINUTILS_BUILD
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++17 accepts -g... yes
rm: conftest.dSYM: is a directory
checking whether C++ compiler clang++ -mmacosx-version-min=10.13 -std=gnu++17 works... yes
configure: C++ compiler options are: -w -g -O2   -DCOINUTILS_BUILD
configure: Trying to determine Fortran compiler name
checking for xlf_r... no
checking for fort77... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
configure: Fortran compiler options are: -O3 -pipe  
checking how to get verbose linking output from gfortran... rm: conftest.dSYM: is a directory
-v
checking for Fortran libraries of gfortran... rm: conftest.dSYM: is a directory
 -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0/../../.. -lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm
configure: Corrected Fortran libraries:  -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0/../../.. -lgfortran -lSystem -lquadmath -lm
checking for dummy main to link with Fortran libraries... rm: conftest.dSYM: is a directory
none
checking for Fortran name-mangling scheme... rm: conftest.dSYM: is a directory
lower case, underscore, no extra underscore
checking for egrep... grep -E
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... none
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++17... none
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Using libtool script in directory ..
checking if library version is set... 13:6:10
checking cmath usability... yes
checking cmath presence... yes
checking for cmath... yes
checking cfloat usability... yes
checking cfloat presence... yes
checking for cfloat... yes
checking cieeefp usability... no
checking cieeefp presence... no
checking for cieeefp... no
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking whether isfinite is declared... no
checking whether finite is declared... yes
checking for cmath... (cached) yes
checking for cfloat... (cached) yes
checking for cieeefp... (cached) no
checking for ieeefp.h... (cached) no
checking whether isnan is declared... no
checking whether std::isnan(42.42) is declared... yes
checking cinttypes usability... yes
checking cinttypes presence... yes
checking for cinttypes... yes
checking cstdint usability... yes
checking cstdint presence... yes
checking for cstdint... yes
checking for int64_t... yes
checking for intptr_t... yes
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking endian.h usability... no
checking endian.h presence... no
checking for endian.h... no
checking for pkg-config... pkg-config
checking pkg-config is at least version 0.16.0... yes
checking for BLAS in Veclib... yes: -framework Accelerate
checking whether LAPACK is already available with BLAS library... yes: -framework Accelerate
checking for COIN-OR package Glpk... not given: No package 'coinglpk' found
checking for COIN-OR package Sample... not given: No package 'coindatasample' found
checking for COIN-OR package Netlib... not given: No package 'coindatanetlib' found
checking whether this is a VPATH configuration... no
configure: configuring doxygen documentation options
checking for doxygen... no
checking for latex... yes
checking for dot... NO
checking which command should be used to link input files... ln -s
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating coinutils.pc
config.status: creating coinutils-uninstalled.pc
config.status: creating doxydoc/doxygen.conf
config.status: creating src/config.h
config.status: creating src/config_coinutils.h
config.status: executing depfiles commands
configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting
configure: Configuration of CoinUtils successful
configure: configuring in Osi
configure: running /bin/sh './configure' --prefix=/Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++17' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-openmp' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CPPFLAGS=-I/usr/local/include' 'LDFLAGS=-L/usr/local/lib' --cache-file=/dev/null --srcdir=.
configure: loading site script /Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... i386-apple-darwin18.7.0
checking for svnversion... yes
checking whether we want to compile in debug mode... no
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ANSI C... none needed
configure: C compiler options are: -w -g -O2   -DOSI_BUILD
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++17 accepts -g... yes
rm: conftest.dSYM: is a directory
checking whether C++ compiler clang++ -mmacosx-version-min=10.13 -std=gnu++17 works... yes
configure: C++ compiler options are: -w -g -O2   -DOSI_BUILD
checking for egrep... grep -E
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... none
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++17... none
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Using libtool script in directory ..
checking if library version is set... 13:4:12
checking for pkg-config... pkg-config
checking pkg-config is at least version 0.16.0... yes
checking for COIN-OR package CoinUtils... yes: 2.10.6 
checking for COIN-OR package Glpk... not given: No package 'coinglpk' found
checking for COIN-OR package SoPlex... not given: No package 'coinsoplex' found
checking for COIN-OR package Sample... not given: No package 'coindatasample' found
checking for COIN-OR package Netlib... not given: No package 'coindatanetlib' found
checking if user provides library for Cplex... no
checking if user provides library for Mosek... no
checking if user provides library for Xpress... no
checking if user provides library for Gurobi... no
configure: WARNING: No solver available, examples will not work.
configure: configuring doxygen documentation options
checking for doxygen... no
checking for latex... yes
checking for dot... NO
checking for doxygen doc'n for CoinUtils ... ../CoinUtils/doxydoc (tag)
checking cmath usability... yes
checking cmath presence... yes
checking for cmath... yes
checking cfloat usability... yes
checking cfloat presence... yes
checking for cfloat... yes
checking cieeefp usability... no
checking cieeefp presence... no
checking for cieeefp... no
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking which command should be used to link input files... ln -s
configure: creating ./config.status
config.status: creating Makefile
config.status: creating examples/Makefile
config.status: creating src/Osi/Makefile
config.status: creating src/OsiCpx/Makefile
config.status: creating src/OsiGlpk/Makefile
config.status: creating src/OsiMsk/Makefile
config.status: creating src/OsiXpr/Makefile
config.status: creating src/OsiGrb/Makefile
config.status: creating src/OsiSpx/Makefile
config.status: creating src/OsiCommonTest/Makefile
config.status: creating test/Makefile
config.status: creating osi.pc
config.status: creating osi-uninstalled.pc
config.status: creating osi-unittests.pc
config.status: creating osi-unittests-uninstalled.pc
config.status: creating doxydoc/doxygen.conf
config.status: creating src/Osi/config.h
config.status: creating src/Osi/config_osi.h
config.status: executing depfiles commands
configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting
configure: Configuration of Osi successful
configure: configuring in Clp
configure: running /bin/sh './configure' --prefix=/Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++17' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-openmp' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CPPFLAGS=-I/usr/local/include' 'LDFLAGS=-L/usr/local/lib' --cache-file=/dev/null --srcdir=.
configure: loading site script /Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... i386-apple-darwin18.7.0
checking for svnversion... yes
checking whether we want to compile in debug mode... no
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ANSI C... none needed
configure: C compiler options are: -w -g -O2   -DCLP_BUILD
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++17 accepts -g... yes
rm: conftest.dSYM: is a directory
checking whether C++ compiler clang++ -mmacosx-version-min=10.13 -std=gnu++17 works... yes
configure: C++ compiler options are: -w -g -O2   -DCLP_BUILD
checking for egrep... grep -E
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... none
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++17... none
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Using libtool script in directory ..
checking if library version is set... 14:6:13
checking for pkg-config... pkg-config
checking pkg-config is at least version 0.16.0... yes
checking for COIN-OR package CoinUtils... yes: 2.10.6 
checking for COIN-OR package Osi... yes: 0.107.4 
checking for COIN-OR package OsiTests... yes: 0.107.4 
checking for COIN-OR package Sample... not given: No package 'coindatasample' found
checking for COIN-OR package Netlib... not given: No package 'coindatanetlib' found
checking if user provides library for AMD... no
checking if user provides library for CHOLMOD... no
checking for COIN-OR package Glpk... not given: No package 'coinglpk' found
checking for COIN-OR package Mumps... not given: No package 'coinmumps' found
checking for COIN-OR package ASL... not given: No package 'coinasl' found
checking cmath usability... yes
checking cmath presence... yes
checking for cmath... yes
checking cfloat usability... yes
checking cfloat presence... yes
checking for cfloat... yes
checking cieeefp usability... no
checking cieeefp presence... no
checking for cieeefp... no
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking whether this is a VPATH configuration... no
configure: configuring doxygen documentation options
checking for doxygen... no
checking for latex... yes
checking for dot... NO
checking for doxygen doc'n for CoinUtils ... ../CoinUtils/doxydoc (tag)
checking for doxygen doc'n for Osi ... ../Osi/doxydoc (tag)
checking which command should be used to link input files... ln -s
configure: creating ./config.status
config.status: creating Makefile
config.status: creating examples/Makefile
config.status: creating src/Makefile
config.status: creating src/OsiClp/Makefile
config.status: creating test/Makefile
config.status: creating clp.pc
config.status: creating clp-uninstalled.pc
config.status: creating osi-clp.pc
config.status: creating osi-clp-uninstalled.pc
config.status: creating doxydoc/doxygen.conf
config.status: creating src/config.h
config.status: creating src/config_clp.h
config.status: executing depfiles commands
configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting
configure: Configuration of Clp successful
configure: configuring in Cgl
configure: running /bin/sh './configure' --prefix=/Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++17' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-openmp' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CPPFLAGS=-I/usr/local/include' 'LDFLAGS=-L/usr/local/lib' --cache-file=/dev/null --srcdir=.
configure: loading site script /Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... i386-apple-darwin18.7.0
checking for svnversion... yes
checking whether we want to compile in debug mode... no
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ANSI C... none needed
configure: C compiler options are: -w -g -O2   -DCGL_BUILD
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++17 accepts -g... yes
rm: conftest.dSYM: is a directory
checking whether C++ compiler clang++ -mmacosx-version-min=10.13 -std=gnu++17 works... yes
configure: C++ compiler options are: -w -g -O2   -DCGL_BUILD
checking for egrep... grep -E
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... none
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++17... none
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Using libtool script in directory ..
checking if library version is set... 10:4:9
checking for pkg-config... pkg-config
checking pkg-config is at least version 0.16.0... yes
checking for COIN-OR package CoinUtils... yes: 2.10.6 
checking for COIN-OR package Osi... yes: 0.107.4 
checking for COIN-OR package Sample... not given: No package 'coindatasample' found
checking for COIN-OR package OsiClp... yes: 1.16.6 
checking for COIN-OR package OsiCpx... not given: No package 'osi-cplex' found
checking for COIN-OR package OsiGlpk... not given: No package 'osi-glpk' found
checking for COIN-OR package OsiMsk... not given: No package 'osi-mosek' found
checking for COIN-OR package OsiXpr... not given: No package 'osi-xpress' found
checking for COIN-OR package OsiVol... not given: No package 'osi-vol' found
checking for COIN-OR package OsiDyLP... not given: No package 'osi-dylp' found
checking cmath usability... yes
checking cmath presence... yes
checking for cmath... yes
checking cfloat usability... yes
checking cfloat presence... yes
checking for cfloat... yes
checking cieeefp usability... no
checking cieeefp presence... no
checking for cieeefp... no
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
configure: configuring doxygen documentation options
checking for doxygen... no
checking for latex... yes
checking for dot... NO
checking for doxygen doc'n for CoinUtils ... ../CoinUtils/doxydoc (tag)
checking whether this is a VPATH configuration... no
checking which command should be used to link input files... ln -s
configure: creating ./config.status
config.status: creating Makefile
config.status: creating examples/Makefile
config.status: creating src/Makefile
config.status: creating src/CglAllDifferent/Makefile
config.status: creating src/CglClique/Makefile
config.status: creating src/CglDuplicateRow/Makefile
config.status: creating src/CglFlowCover/Makefile
config.status: creating src/CglGMI/Makefile
config.status: creating src/CglGomory/Makefile
config.status: creating src/CglKnapsackCover/Makefile
config.status: creating src/CglLandP/Makefile
config.status: creating src/CglLiftAndProject/Makefile
config.status: creating src/CglMixedIntegerRounding/Makefile
config.status: creating src/CglMixedIntegerRounding2/Makefile
config.status: creating src/CglOddHole/Makefile
config.status: creating src/CglPreProcess/Makefile
config.status: creating src/CglProbing/Makefile
config.status: creating src/CglRedSplit/Makefile
config.status: creating src/CglRedSplit2/Makefile
config.status: creating src/CglResidualCapacity/Makefile
config.status: creating src/CglSimpleRounding/Makefile
config.status: creating src/CglTwomir/Makefile
config.status: creating src/CglZeroHalf/Makefile
config.status: creating test/Makefile
config.status: creating cgl.pc
config.status: creating cgl-uninstalled.pc
config.status: creating doxydoc/doxygen.conf
config.status: creating src/config.h
config.status: creating src/config_cgl.h
config.status: executing depfiles commands
configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting
configure: Configuration of Cgl successful
configure: configuring in SYMPHONY
configure: running /bin/sh './configure' --prefix=/Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++17' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-openmp' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CPPFLAGS=-I/usr/local/include' 'LDFLAGS=-L/usr/local/lib' --cache-file=/dev/null --srcdir=.
configure: loading site script /Users/biocbuild/bbs-3.17-bioc/meat/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... i386-apple-darwin18.7.0
checking for svnversion... yes
checking whether we want to compile in debug mode... no
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ANSI C... none needed
configure: C compiler options are: -w -g -O2   -DSYMPHONY_BUILD
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++17 accepts -g... yes
rm: conftest.dSYM: is a directory
checking whether C++ compiler clang++ -mmacosx-version-min=10.13 -std=gnu++17 works... yes
configure: C++ compiler options are: -w -g -O2   -DSYMPHONY_BUILD
checking for egrep... grep -E
checking whether ln -s works... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... none
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++17... none
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Using libtool script in directory ..
checking if library version is set... 9:10:6
checking for pkg-config... pkg-config
checking pkg-config is at least version 0.16.0... yes
checking for COIN-OR package CoinDepend... yes: 2.10.6 0.107.4 
checking for COIN-OR package Clp... yes: 1.16.6 
checking for COIN-OR package DyLP... not given: No package 'osi-dylp' found
checking for COIN-OR package Vol... not given: No package 'osi-vol' found
checking for COIN-OR package Cgl... yes: 0.59.4 
checking for COIN-OR package OsiTests... yes: 0.107.4 
checking for COIN-OR package Sample... not given: No package 'coindatasample' found
checking for COIN-OR package Netlib... not given: No package 'coindatanetlib' found
checking for COIN-OR package Miplib3... not given: No package 'coindatamiplib3' found
checking for COIN-OR package Cpx... not given: No package 'osi-cplex' found
checking for COIN-OR package Glpk... not given: No package 'osi-glpk' found
checking for COIN-OR package Msk... not given: No package 'osi-mosek' found
checking for COIN-OR package Xpr... not given: No package 'osi-xpress' found
checking for SYMPHONY default solver... Clp
checking whether to compile with gmpl... no
checking whether to compile application library... no
checking if user provides library for Pvm... no
checking whether this is a VPATH configuration... no
checking which command should be used to link input files... ln -s
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/OsiSym/Makefile
config.status: creating test/Makefile
config.status: creating Examples/Makefile
config.status: creating Applications/Makefile.Applications
config.status: creating Applications/CNRP/Makefile
config.status: creating Applications/MATCH/Makefile
config.status: creating Applications/MCKP/Makefile
config.status: creating Applications/MPP/Makefile
config.status: creating Applications/SPP/Makefile
config.status: creating Applications/SPP+CUTS/Makefile
config.status: creating Applications/USER/Makefile
config.status: creating Applications/VRP/Makefile
config.status: creating symphony.pc
config.status: creating symphony-app.pc
config.status: creating symphony-uninstalled.pc
config.status: creating osi-sym.pc
config.status: creating osi-sym-uninstalled.pc
config.status: creating include/config.h
config.status: creating include/config_sym.h
config.status: executing depfiles commands
configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting
configure: Configuration of SYMPHONY successful
configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting
configure: Main configuration of SYMPHONY successful
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using SDK: ‘’
Making all in CoinUtils
Making all in src
make  all-am
/bin/sh ../../libtool --tag=CXX --mode=compile clang++ -mmacosx-version-min=10.13 -std=gnu++17 -DHAVE_CONFIG_H -I. -I`echo .`   -I/usr/local/include  -w -g -O2   -DCOINUTILS_BUILD -c -o CoinAlloc.lo CoinAlloc.cpp
 clang++ -mmacosx-version-min=10.13 -std=gnu++17 -DHAVE_CONFIG_H -I. -I. -I/usr/local/include -w -g -O2 -DCOINUTILS_BUILD -c CoinAlloc.cpp  -fno-common -DPIC -o CoinAlloc.o
/bin/sh ../../libtool --tag=CXX --mode=compile clang++ -mmacosx-version-min=10.13 -std=gnu++17 -DHAVE_CONFIG_H -I. -I`echo .`   -I/usr/local/include  -w -g -O2   -DCOINUTILS_BUILD -c -o CoinBuild.lo CoinBuild.cpp
 clang++ -mmacosx-version-min=10.13 -std=gnu++17 -DHAVE_CONFIG_H -I. -I. -I/usr/local/include -w -g -O2 -DCOINUTILS_BUILD -c CoinBuild.cpp  -fno-common -DPIC -o CoinBuild.o
In file included from CoinBuild.cpp:18:
./CoinHelperFunctions.hpp:44:11: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinCopyN(register const T* from, const int size, register T* to)
          ^~~~~~~~~
./CoinHelperFunctions.hpp:44:51: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinCopyN(register const T* from, const int size, register T* to)
                                                  ^~~~~~~~~
./CoinHelperFunctions.hpp:55:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int n = (size + 7) / 8;
    ^~~~~~~~~
./CoinHelperFunctions.hpp:57:2: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
        register const T* downfrom = from + size;
        ^~~~~~~~~
./CoinHelperFunctions.hpp:58:2: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
        register T* downto = to + size;
        ^~~~~~~~~
./CoinHelperFunctions.hpp:102:10: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinCopy(register const T* first, register const T* last, register T* to)
         ^~~~~~~~~
./CoinHelperFunctions.hpp:102:35: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinCopy(register const T* first, register const T* last, register T* to)
                                  ^~~~~~~~~
./CoinHelperFunctions.hpp:102:59: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinCopy(register const T* first, register const T* last, register T* to)
                                                          ^~~~~~~~~
./CoinHelperFunctions.hpp:117:19: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinDisjointCopyN(register const T* from, const int size, register T* to)
                  ^~~~~~~~~
./CoinHelperFunctions.hpp:117:59: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinDisjointCopyN(register const T* from, const int size, register T* to)
                                                          ^~~~~~~~~
./CoinHelperFunctions.hpp:138:10: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    for (register int n = size / 8; n > 0; --n, from += 8, to += 8) {
         ^~~~~~~~~
./CoinHelperFunctions.hpp:170:18: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinDisjointCopy(register const T* first, register const T* last,
                 ^~~~~~~~~
./CoinHelperFunctions.hpp:170:43: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinDisjointCopy(register const T* first, register const T* last,
                                          ^~~~~~~~~
./CoinHelperFunctions.hpp:171:4: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
                 register T* to)
                 ^~~~~~~~~
./CoinHelperFunctions.hpp:259:13: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinMemcpyN(register const T* from, const int size, register T* to)
            ^~~~~~~~~
./CoinHelperFunctions.hpp:259:53: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinMemcpyN(register const T* from, const int size, register T* to)
                                                    ^~~~~~~~~
./CoinHelperFunctions.hpp:299:10: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    for (register int n = size / 8; n > 0; --n, from += 8, to += 8) {
         ^~~~~~~~~
./CoinHelperFunctions.hpp:346:12: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinMemcpy(register const T* first, register const T* last,
           ^~~~~~~~~
./CoinHelperFunctions.hpp:346:37: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
CoinMemcpy(register const T* first, register const T* last,
                                    ^~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[4]: *** [CoinBuild.lo] Error 1
make[3]: *** [all] Error 2
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/lpsymphony’