############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data lpsymphony ### ############################################################################## ############################################################################## * checking for file ‘lpsymphony/DESCRIPTION’ ... OK * preparing ‘lpsymphony’: * checking DESCRIPTION meta-information ... OK * cleaning src * running ‘cleanup’ * installing the package to build vignettes ----------------------------------- * installing *source* package ‘lpsymphony’ ... ** using staged installation Running on Linux CXX is g++ -std=gnu++17 CXX is g++ -std=gnu++14 checking build system type... aarch64-unknown-linux-gnu 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 gcc accepts -g... yes checking for gcc 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 g++ -std=gnu++17 accepts -g... yes checking whether C++ compiler g++ -std=gnu++17 works... yes configure: C++ compiler options are: -w -g -O2 configure: Trying to determine Fortran compiler name 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... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking dependency style of g++ -std=gnu++17... none checking whether to enable maintainer-specific portions of Makefiles... no checking host system type... aarch64-unknown-linux-gnu checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by gcc... /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld checking if the linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) is GNU ld... yes checking for /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/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... gcc -E checking for ANSI C header files... no 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... g++ -std=gnu++17 -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so 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 checking for ld used by g++ -std=gnu++17... /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld checking if the linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) is GNU ld... yes checking whether the g++ -std=gnu++17 linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) supports shared libraries... yes checking for g++ -std=gnu++17 option to produce PIC... -fPIC checking if g++ -std=gnu++17 PIC flag -fPIC works... yes checking if g++ -std=gnu++17 static flag -static works... yes checking if g++ -std=gnu++17 supports -c -o file.o... yes checking whether the g++ -std=gnu++17 linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate appending configuration tag "F77" to libtool 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... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking whether the gfortran linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate configure: Build is "aarch64-unknown-linux-gnu". 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=/home/biocbuild/tmp/Rtmp5G5UN4/Rbuild24ddb05c6eed5/lpsymphony/src/SYMPHONY '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' 'CC=gcc' 'CXX=g++ -std=gnu++17' 'F77=gfortran' 'FLIBS=-L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm' 'CPPFLAGS=-I/usr/local/include' 'LDFLAGS=-L/usr/local/lib' --cache-file=/dev/null --srcdir=. checking build system type... aarch64-unknown-linux-gnu checking for svnversion... no 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 gcc accepts -g... yes checking for gcc 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 g++ -std=gnu++17 accepts -g... yes checking whether C++ compiler g++ -std=gnu++17 works... yes configure: C++ compiler options are: -w -g -O2 -DCOINUTILS_BUILD configure: Trying to determine Fortran compiler name 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... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm checking for dummy main to link with Fortran libraries... unknown configure: error: linking to Fortran libraries from C fails See `config.log' for more details. configure: error: /bin/sh './configure' failed for CoinUtils ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/biocbuild/tmp/Rtmp5G5UN4/Rbuild24ddb05c6eed5/lpsymphony/src/SYMPHONY' Making all in CoinUtils make[2]: Entering directory '/home/biocbuild/tmp/Rtmp5G5UN4/Rbuild24ddb05c6eed5/lpsymphony/src/SYMPHONY/CoinUtils' make[2]: *** No rule to make target 'all'. Stop. make[2]: Leaving directory '/home/biocbuild/tmp/Rtmp5G5UN4/Rbuild24ddb05c6eed5/lpsymphony/src/SYMPHONY/CoinUtils' make[1]: *** [Makefile:324: all-recursive] Error 1 make[1]: Leaving directory '/home/biocbuild/tmp/Rtmp5G5UN4/Rbuild24ddb05c6eed5/lpsymphony/src/SYMPHONY' make: *** [Makevars:14: SYMPHONY.ts] Error 2 ERROR: compilation failed for package ‘lpsymphony’ * removing ‘/home/biocbuild/tmp/Rtmp5G5UN4/Rinst24ddb0431221b3/lpsymphony’ ----------------------------------- ERROR: package installation failed