vladchimescu/lpsymphony

lpsymphony's Issues

Error while compiling lpsymphony

Hi!

I tried to install this package as a dependency for another one. I am struggling to do so. I have tried with Bioconductor, install.packages from source, from this github - it always fails with the same error.
Before failing it calls MatLab library v617 installation - which I already have installed. Once installation is done (twice) the following errors appear:
<Making install in CoinUtils
make[2]: Entering directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils'
Making install in src
make[3]: Entering directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[4]: Entering directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils/src'
/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils/install-sh -c -m 644 config_coinutils.h /tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/include/coin/CoinUtilsConfig.h
test -z "/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64" || mkdir -p -- "/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64"
/bin/sh ../../libtool --mode=install /home/kselav/bin/install -c 'libCoinUtils.la' '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64/libCoinUtils.la'
/home/kselav/bin/install -c .libs/libCoinUtils.lai /tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64/libCoinUtils.la
Preparing installation files ...
Installing ...
Finished
/home/kselav/bin/install -c .libs/libCoinUtils.a /tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64/libCoinUtils.a
Preparing installation files ...
Installing ...
Finished
chmod 644 /tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64/libCoinUtils.a
chmod: cannot access '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/lib64/libCoinUtils.a': No such file or directory
make[4]: *** [Makefile:569: install-libLTLIBRARIES] Error 1
make[4]: Leaving directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[3]: *** [Makefile:796: install-am] Error 2
make[3]: Leaving directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[2]: *** [Makefile:436: install-recursive] Error 1
make[2]: Leaving directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY/CoinUtils'
make[1]: *** [Makefile:324: install-recursive] Error 1
make[1]: Leaving directory '/tmp/RtmpwyWaDV/R.INSTALL1be31a14ed34/lpsymphony/src/SYMPHONY'
make: *** [Makevars:13: SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’

Could you advise how I can solve it (on a server with no root rights, installing to my local user).
Thanks you in advance for any tips.

Unequal constraints

Hi,

I'm experiencing the following problems when using this software.

Error in lpsymphony_solve_LP(obj = f.obj, mat = f.con, dir = f.dir, rhs = f.rhs, : Argument 'dir' must be one of '<', '<=', '>', '>=', or '=='.

But the help document showed that this software supports unequal operation !=.

Arguments  |

obj | a vector with the objective coefficients
mat | a vector or a matrix of the constraint coefficients
dir | a character vector with the directions of the constraints. Each element must be one of "<", "<=", ">", ">=", "==" or "!=".

Meng

Problem building lpsymphony on macos

Hi Vlad,

I'm experiencing the following error when installing lpsymphony on macos:

/usr/local/opt/llvm/bin/clang++ -std=gnu++11 -w -g -O2 -DSYMPHONY_BUILD -TP -o symphony symphony-main.o -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -framework Accelerate -Wl,-bind_at_load  ./.libs/libSym.a /private/var/folders/fg/g7fr2fs50l3frgx731lv3mjw0000gn/T/RtmpGQLusa/R.INSTALLfd4c6326cd64/lpsymphony/src/SYMPHONY/Cgl/src/.libs/libCgl.a /private/var/folders/fg/g7fr2fs50l3frgx731lv3mjw0000gn/T/RtmpGQLusa/R.INSTALLfd4c6326cd64/lpsymphony/src/SYMPHONY/Clp/src/OsiClp/.libs/libOsiClp.a /private/var/folders/fg/g7fr2fs50l3frgx731lv3mjw0000gn/T/RtmpGQLusa/R.INSTALLfd4c6326cd64/lpsymphony/src/SYMPHONY/Clp/src/.libs/libClpSolver.a /private/var/folders/fg/g7fr2fs50l3frgx731lv3mjw0000gn/T/RtmpGQLusa/R.INSTALLfd4c6326cd64/lpsymphony/src/SYMPHONY/Clp/src/.libs/libClp.a /private/var/folders/fg/g7fr2fs50l3frgx731lv3mjw0000gn/T/RtmpGQLusa/R.INSTALLfd4c6326cd64/lpsymphony/src/SYMPHONY/Osi/src/Osi/.libs/libOsi.a /private/var/folders/fg/g7fr2fs50l3frgx731lv3mjw0000gn/T/RtmpGQLusa/R.INSTALLfd4c6326cd64/lpsymphony/src/SYMPHONY/CoinUtils/src/.libs/libCoinUtils.a
ld: unknown option: -T
clang-8: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [symphony] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’

have you any idea how to solve this or could you give me some hint where I could start digging into it?

BTW my R:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.1

And the compiler I'm using:

clang version 8.0.0 (tags/RELEASE_800/final)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin

configure: error: linking to Fortran libraries from C fails

* installing *source* package ‘lpsymphony’ ...
** using staged installation
configure: loading site script /tmp/RtmpDCNb50/R.INSTALL12889754599a5/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... x86_64-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 x86_64-conda_cos6-linux-gnu-gcc accepts -g... yes
checking for x86_64-conda_cos6-linux-gnu-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 /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ accepts -g... yes
checking whether C++ compiler /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ 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 /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran accepts -g... yes
configure: Fortran compiler options are: -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/include
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 x86_64-conda_cos6-linux-gnu-gcc... none
checking dependency style of /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++... none
checking whether to enable maintainer-specific portions of Makefiles... no
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /usr/bin/sed
checking for ld used by x86_64-conda_cos6-linux-gnu-gcc... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld
checking if the linker (/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld) is GNU ld... yes
checking for /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld option to reload object files... -r
checking for BSD-compatible nm... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-nm
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-cpp
checking for ANSI C header files... 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... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ -E
checking the maximum length of command line arguments... 32768
checking command to parse /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-nm output from x86_64-conda_cos6-linux-gnu-gcc object... ok
checking for objdir... .libs
checking for ar... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ar
checking for ranlib... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ranlib
checking for strip... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-strip
checking if x86_64-conda_cos6-linux-gnu-gcc supports -fno-rtti -fno-exceptions... yes
checking for x86_64-conda_cos6-linux-gnu-gcc option to produce PIC... -fPIC
checking if x86_64-conda_cos6-linux-gnu-gcc PIC flag -fPIC works... yes
hecking if x86_64-conda_cos6-linux-gnu-gcc supports -c -o file.o... yes
checking whether the x86_64-conda_cos6-linux-gnu-gcc linker (/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld -m elf_x86_64) 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 /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++... /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld -m elf_x86_64
checking if the linker (/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld -m elf_x86_64) is GNU ld... yes
checking whether the /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ linker (/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes
checking for /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ option to produce PIC... -fPIC
checking if /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ PIC flag -fPIC works... yes
checking if /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ static flag -static works... yes
checking if /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ supports -c -o file.o... yes
checking whether the /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ linker (/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld -m elf_x86_64) 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 /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran option to produce PIC... -fPIC
checking if /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran PIC flag -fPIC works... yes
checking if /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran static flag -static works... no
checking if /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran supports -c -o file.o... yes
checking whether the /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran linker (/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: Build is "x86_64-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=/tmp/RtmpDCNb50/R.INSTALL12889754599a5/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=x86_64-conda_cos6-linux-gnu-gcc' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/include' 'CPP=/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-cpp' 'CXX=/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++' 'F77=/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran' 'FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/include' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/lib -Wl,-rpath-link,/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/lib' --cache-file=/dev/null --srcdir=.
configure: loading site script /tmp/RtmpDCNb50/R.INSTALL12889754599a5/lpsymphony/src/SYMPHONY/share/config.site
checking build system type... x86_64-unknown-linux-gnu
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 x86_64-conda_cos6-linux-gnu-gcc accepts -g... yes
checking for x86_64-conda_cos6-linux-gnu-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 /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ accepts -g... yes
checking whether C++ compiler /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-c++ 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 /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran accepts -g... yes
configure: Fortran compiler options are: -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/include
checking how to get verbose linking output from /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran... -v
checking for Fortran libraries of /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/x86_64-conda_cos6-linux-gnu-gfortran...  -lm' -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib -lgfortran -lm -lgomp -lgcc_s -lquadmath -lpthread
configure: Corrected Fortran libraries:  -lm' -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib -L/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib -lgfortran -lm -lgomp -lquadmath -lpthread
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
make[1]: Entering directory '/tmp/RtmpDCNb50/R.INSTALL12889754599a5/lpsymphony/src/SYMPHONY'
Making all in CoinUtils
make[2]: Entering directory '/tmp/RtmpDCNb50/R.INSTALL12889754599a5/lpsymphony/src/SYMPHONY/CoinUtils'
make[2]: *** No rule to make target 'all'.  Stop.
make[2]: Leaving directory '/tmp/RtmpDCNb50/R.INSTALL12889754599a5/lpsymphony/src/SYMPHONY/CoinUtils'
make[1]: *** [Makefile:324: all-recursive] Error 1
make[1]: Leaving directory '/tmp/RtmpDCNb50/R.INSTALL12889754599a5/lpsymphony/src/SYMPHONY'
make: *** [Makevars:13: SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
* removing ‘/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/R/4.0/lib64/R/site-library/lpsymphony’

Specify number of threads

Thank you very much for developing this package! I am interested in running some benchmarks comparing SMYPHONY to some other solvers. To help with this, it would be really useful to specify the maximum number of threads used by SYMPHONY when attempting to solve problems. Do you think this functionality would be useful? I would be happy to look into creating a PR to add this functionality if that would be helpful?

build error

• R: 4.1.2
• OS: ArchLinux
• g++: 11.2.0

I've installed packages including CoinPragma.hpp, but it reports so, in the installed dependencies, it's under /usr/include/coin/ Code should be placed in three backticks as shown below

 CoinIndexedVector.o CoinLpIO.o CoinMessage.o CoinMessageHandler.o CoinModel.o CoinStructuredModel.o CoinModelUseful.o CoinModelUseful2.o CoinMpsIO.o CoinPackedMatrix.o CoinPackedVector.o CoinPackedVectorBase.o CoinParam.o CoinParamUtils.o CoinPostsolveMatrix.o CoinPrePostsolveMatrix.o CoinPresolveDoubleton.o CoinPresolveDual.o CoinPresolveDupcol.o CoinPresolveEmpty.o CoinPresolveFixed.o CoinPresolveForcing.o CoinPresolveHelperFunctions.o CoinPresolveImpliedFree.o CoinPresolveIsolated.o CoinPresolveMatrix.o CoinPresolvePsdebug.o CoinPresolveMonitor.o CoinPresolveSingleton.o CoinPresolveSubst.o CoinPresolveTighten.o CoinPresolveTripleton.o CoinPresolveUseless.o CoinPresolveZeros.o CoinRational.o CoinSearchTree.o CoinShallowPackedVector.o CoinSnapshot.o CoinWarmStartBasis.o CoinWarmStartVector.o CoinWarmStartDual.o CoinWarmStartPrimalDual.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib .libs/libCoinUtils.a
creating libCoinUtils.la
(cd .libs && rm -f libCoinUtils.la && ln -s ../libCoinUtils.la libCoinUtils.la)
make[4]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[3]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[3]: Entering directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/CoinUtils'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/CoinUtils'
make[2]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/CoinUtils'
Making all in Osi
make[2]: Entering directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/Osi'
Making all in src/Osi
make[3]: Entering directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/Osi/src/Osi'
make  all-am
make[4]: Entering directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/Osi/src/Osi'
/bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`  -I/tmp/RtmprwBDNn/Rbuild12daa92b38f71c/lpsymphony/src/SYMPHONY/include/coin  -D_FORTIFY_SOURCE=2  -w -g -O2   -DOSI_BUILD -c -o OsiAuxInfo.lo OsiAuxInfo.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -I/tmp/RtmprwBDNn/Rbuild12daa92b38f71c/lpsymphony/src/SYMPHONY/include/coin -D_FORTIFY_SOURCE=2 -w -g -O2 -DOSI_BUILD -c OsiAuxInfo.cpp  -fPIC -DPIC -o OsiAuxInfo.o
OsiAuxInfo.cpp:10:10: fatal error: CoinPragma.hpp: No such file or directory
   10 | #include "CoinPragma.hpp"
      |          ^~~~~~~~~~~~~~~~
compilation terminated.
make[4]: *** [Makefile:535: OsiAuxInfo.lo] Error 1
make[4]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/Osi/src/Osi'
make[3]: *** [Makefile:407: all] Error 2
make[3]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/Osi/src/Osi'
make[2]: *** [Makefile:532: all-recursive] Error 1
make[2]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY/Osi'
make[1]: *** [Makefile:324: all-recursive] Error 1
make[1]: Leaving directory '/tmp/Rtmp5DxR9W/R.INSTALL42134b7bec9/lpsymphony/src/SYMPHONY'
make: *** [Makevars:13: SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
* removing ‘/build/r-lpsymphony/src/lpsymphony’
* restoring previous ‘/build/r-lpsymphony/src/lpsymphony’

Upgrade SYMPHONY to support linux aarch64/arm64?

We are going to support Bioconductor on linux aarch64 https://stat.ethz.ch/pipermail/bioc-devel/2023-January/019398.html .

We hit a issue on lpsymphony:

checking build system type... ./config.guess: unable to guess system type

This script, last modified 2007-05-17, 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://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
and
  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <[email protected]> in order to provide the needed
information to handle your system.

config.guess timestamp = 2007-05-17

• Upstream SYMPHONY already fix this issue by upgrade the config.guess in coin-or/SYMPHONY@f14fc9a .

We should upgrade the SYMPHONY to latest to include the patch?

[1] Related: Yikun/BBS#13
[2] [Bioc-devel] Support for Linux ARM64: https://stat.ethz.ch/pipermail/bioc-devel/2023-January/019398.html