I am trying to install jellyfish using GNU bash, version 4.4.23(1)-release (x86_64-pc-msys). I have gcc and g++withversion 6.3.0 (MinGW.org GCC-6.3.0-1)`. When I run the configure file I get the error below:
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... configure: error: in `/c/Users/bjwil/Downloads/jellyfish-2.2.10':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
./configure: line 38: sort: No such file or directory
./configure: line 35: sed: No such file or directory
Then inside the config.log file I get starting with first error after COLLECT_GCC=C:\MinGW\bin\gcc.exe:
configure:3778: gcc -V >&5
gcc.exe: error: unrecognized command line option '-V'
gcc.exe: fatal error: no input files
compilation terminated.
configure:3789: $? = 1
configure:3778: gcc -qversion >&5
gcc.exe: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc.exe: fatal error: no input files
compilation terminated.
configure:3789: $? = 1
configure:3809: checking whether the C compiler works
configure:3831: gcc conftest.c >&5
configure:3835: $? = 0
configure:3883: result: yes
configure:3886: checking for C compiler default output file name
configure:3888: result: a.exe
configure:3894: checking for suffix of executables
configure:3901: gcc -o conftest.exe conftest.c >&5
configure:3905: $? = 0
configure:3927: result: .exe
configure:3949: checking whether we are cross compiling
configure:3957: gcc -o conftest.exe conftest.c >&5
configure:3961: $? = 0
configure:3968: ./conftest.exe
./configure: line 3970: ./conftest.exe: Permission denied
configure:3972: $? = 126
configure:3979: error: in `/c/Users/bjwil/Downloads/jellyfish-2.2.10':
configure:3981: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
Works fine in Ubuntu 64-bit.
Related
Can anyone help me with this issue?
In order to use dealii, I tried to install p4est using the command
./configure && make && make install
and
cmake .. -DP4EST_DIR=/usr/local -DDEAL_II_WITH_P4EST=ON -DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=/usr/local
under "build" folder, but some error occurs.
I also opened the file dealii-9.0.0/build/CMakeFiles/CMakeError.log, it says:
Source file was:
int main() { return 0; }
Performing C++ SOURCE FILE Test rt_LIBRARY failed with the following output:
Change Dir: /Users/chuxiaoyun/Downloads/dealii-9.0.0/build/CMakeFiles/CMakeScratch/TryCompile-Fscvq9
Run Build Command(s):/usr/bin/make -f Makefile cmTC_bc7f9/fast && /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/cmTC_bc7f9.dir/build.make CMakeFiles/cmTC_bc7f9.dir/build
Building CXX object CMakeFiles/cmTC_bc7f9.dir/src.cxx.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -Drt_LIBRARY -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -mmacosx-version-min=11.6 -MD -MT CMakeFiles/cmTC_bc7f9.dir/src.cxx.o -MF CMakeFiles/cmTC_bc7f9.dir/src.cxx.o.d -o CMakeFiles/cmTC_bc7f9.dir/src.cxx.o -c /Users/chuxiaoyun/Downloads/dealii-9.0.0/build/CMakeFiles/CMakeScratch/TryCompile-Fscvq9/src.cxx
Linking CXX executable cmTC_bc7f9
/opt/homebrew/Cellar/cmake/3.25.0/bin/cmake -E cmake_link_script CMakeFiles/cmTC_bc7f9.dir/link.txt --verbose=1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -mmacosx-version-min=11.6 -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_bc7f9.dir/src.cxx.o -o cmTC_bc7f9 -lrt
ld: library not found for -lrt
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [cmTC_bc7f9] Error 1
make: *** [cmTC_bc7f9/fast] Error 2
CMake Error at cmake/macros/macro_configure_feature.cmake:112 (MESSAGE):
Could not find the p4est library!
Insufficient p4est installation found!
p4est has to be configured with MPI enabled.
Please ensure that a suitable p4est library is installed on your computer.
If the library is not at a default location, either provide some hints for
autodetection,
$ P4EST_DIR="..." cmake <...>
$ cmake -DP4EST_DIR="..." <...>
or set the relevant variables by hand in ccmake.
Call Stack (most recent call first):
cmake/macros/macro_configure_feature.cmake:269 (FEATURE_ERROR_MESSAGE)
cmake/configure/configure_p4est.cmake:78 (CONFIGURE_FEATURE)
cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
CMakeLists.txt:124 (VERBOSE_INCLUDE)
I guess I haven't installed p4est correctly, so I configure it again.
# p4est-2.8 ./configure --enable-mpi.
( Here shows we are using MPI. I also tried p4est-2.8 ./configure --enable-mpi --prefix=/usr/local)
Then I tried to build and install p4est, but it gives me an error during installation:
# make
# ➜ p4est-2.8 make install
/Applications/Xcode.app/Contents/Developer/usr/bin/make install-recursive
Making install in sc
/Applications/Xcode.app/Contents/Developer/usr/bin/make install-am
build-aux/install-sh -c -d '/Users/xiaoyun/Downloads/p4est-2.8/local/lib'
/bin/sh ./libtool --mode=install /usr/bin/install -c src/libsc.la '/Users/xiaoyun/Downloads/p4est-2.8/local/lib'
libtool: install: /usr/bin/install -c src/.libs/libsc.0.dylib /Users/xiaoyun/Downloads/p4est-2.8/local/lib/libsc.0.dylib
install: /Users/xiaoyun/Downloads/p4est-2.8/local/lib/libsc.0.dylib: Permission denied
make[4]: *** [install-libLTLIBRARIES] Error 71
make[3]: *** [install-am] Error 2
make[2]: *** [install] Error 2
make[1]: *** [install-recursive] Error 1
I have no idea why the permission is denied, I also tried sudo make install:
objc[71909]: Class AMSupportURLConnectionDelegate is implemented in both /usr/lib/libauthinstall.dylib (0x20230f7e8) and /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x10c9082c8). One of the two will be used. Which one is undefined.
objc[71909]: Class AMSupportURLSession is implemented in both /usr/lib/libauthinstall.dylib (0x20230f838) and /System/Library/PrivateFrameworks/MobileDevice.framework/Versions/A/MobileDevice (0x10c908318). One of the two will be used. Which one is undefined.
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted
make: getcwd: Operation not permitted
make: Nothing to be done for `install'.
I am trying to run a makefile. I think the makefile is trying to access this path:
/home/s/miniconda3/lib/python3.7/site-packages/tensorflow/include/unsupported/Eigen
But when I run it, I get a No such file or directory error:
(base) s#s-VirtualBox:~/Downloads/3d-psrnet-master$ make
make: Circular utils/tf_ops/cd/tf_nndistance_g.cu <- utils/tf_ops/cd/tf_nndistance_g.cu.o dependency dropped.
/usr/local/cuda-10.1/bin/nvcc -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11 -c -o utils/tf_ops/cd/tf_nndistance_g.cu.o utils/tf_ops/cd/tf_nndistance_g.cu -I /home/s/miniconda3/lib/python3.7/site-packages -DGOOGLE_CUDA=1 -x cu -Xcompiler -fPIC -O2
utils/tf_ops/cd/tf_nndistance_g.cu:3:10: fatal error: include/unsupported/Eigen: No such file or directory
#include "include/unsupported/Eigen"
^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [makefile:12: utils/tf_ops/cd/tf_nndistance_g.cu.o] Error 1
I have it set like this at the top of makefile: tensorflow = /home/s/miniconda3/lib/python3.7/site-packages (which is the path that shows up if I type into Terminal pip show tensorflow)
And then in tf_nndistance_g.cu I have:
#include "include/unsupported/Eigen/"
What might be the reason that this makefile isn't working? I'm using Python 3.7 on a Virtual Machine (ubuntu Virtualbox). Thanks.
I installed tensorflow on the Raspberry Pi 3, running Jessie and did that in two ways, via the .whl file / pip install for Python 2.7.:
https://github.com/samjabrahams/tensorflow-on-raspberry-pi
as well as a full compile via:
https://github.com/tensorflow/tensorflow/tree/master/tensorflow/contrib/makefile
Both installs (I did them on different OS images) where successfull and went through without error.
Next, I wanted to compile the official Raspberry Pi examples from tensorflow's git repository:
https://github.com/tensorflow/tensorflow/tree/master/tensorflow/contrib/pi_examples
However, none of the examples does compile (neither the camera example nor the image recognition), both give the same error and Google doesn't tell me anything:
make -f tensorflow/contrib/pi_examples/camera/Makefile gcc --std=c++11
-O0 -I/usr/local/include -I. -I/home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/../../makefile/downloads
-I/home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/../../makefile/downloads/eigen/
-I/home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/../../makefile/gen/proto/
-I/home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/../../makefile/gen/proto_text/
-c tensorflow/contrib/pi_examples/camera/camera.cc -o /home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/gen/obj/tensorflow/contrib/pi_examples/camera/camera.o
In file included from ./tensorflow/core/platform/mutex.h:31:0,
from ./tensorflow/core/framework/variant.h:31,
from ./tensorflow/core/framework/allocator.h:26,
from ./tensorflow/core/framework/tensor.h:20,
from tensorflow/contrib/pi_examples/camera/camera.cc:33:
./tensorflow/core/platform/default/mutex.h:25:22: fatal error:
nsync_cv.h: No such file or directory #include "nsync_cv.h"
^ compilation terminated. tensorflow/contrib/pi_examples/camera/Makefile:80: recipe for target
'/home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/gen/obj/tensorflow/contrib/pi_examples/camera/camera.o'
failed make: ***
[/home/pi/tensorflow/tensorflow/contrib/pi_examples/camera/gen/obj/tensorflow/contrib/pi_examples/camera/camera.o]
Error 1
as well as:
make -f tensorflow/contrib/pi_examples/label_image/Makefile gcc
--std=c++11 -O0 -I/usr/local/include -I. -I/home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/../../makefile/downloads
-I/home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/../../makefile/downloads/eigen/
-I/home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/../../makefile/gen/proto/
-I/home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/../../makefile/gen/proto_text/
-c tensorflow/contrib/pi_examples/label_image/label_image.cc -o /home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/gen/obj/tensorflow/contrib/pi_examples/label_image/label_image.o
In file included from ./tensorflow/core/platform/mutex.h:31:0,
from ./tensorflow/core/framework/variant.h:31,
from ./tensorflow/core/framework/allocator.h:26,
from ./tensorflow/core/framework/tensor.h:20,
from tensorflow/contrib/pi_examples/label_image/label_image.cc:33:
./tensorflow/core/platform/default/mutex.h:25:22: fatal error:
nsync_cv.h: No such file or directory #include "nsync_cv.h"
^ compilation terminated. tensorflow/contrib/pi_examples/label_image/Makefile:79: recipe for
target
'/home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/gen/obj/tensorflow/contrib/pi_examples/label_image/label_image.o'
failed make: ***
[/home/pi/tensorflow/tensorflow/contrib/pi_examples/label_image/gen/obj/tensorflow/contrib/pi_examples/label_image/label_image.o]
Error 1
How can I locate / add / compile "nsync_cv.h"?
And btw:
export HOST_NSYNC_LIB=`tensorflow/contrib/makefile/compile_nsync.sh`
gives me:
g++ -M -std=c++11 -DNSYNC_USE_CPP11_TIMEPOINT -DNSYNC_ATOMIC_CPP11
-I../../platform/c++11 -I../../platform/gcc -I../../platform/posix -pthread -I../../public -I../../internal ../../internal/*.c ../../testing/*.c ../../platform/c++11/src/nsync_semaphore_mutex.cc
../../platform/c++11/src/per_thread_waiter.cc
../../platform/c++11/src/yield.cc
../../platform/c++11/src/time_rep_timespec.cc
../../platform/c++11/src/nsync_panic.cc \
../../platform/c++11/src/start_thread.cc > dependfile make: 'nsync.a' is up to date.
I once compiled tensorflow with the makefile on a nvidia Jetson TX1 and I could compile and run the examples by adding some lines to the Makefiles of the examples:
after line 18:
NSYNCLIBDIR := $(TFMAKEFILE_DIR)/downloads/nsync/builds/default.linux.c++11 !!!change folder default.linux.c++11 to where your libnsync.a is!!!
NSYNCLIBS := $(NSYNCLIBDIR)/libnsync.a
after line 26:
NSYNC := $(TFMAKEFILE_DIR)/downloads/nsync/public/
after line 36:
-L$(NSYNCLIBDIR) \
after line 43:
-I$(NSYNC) \
after line 51:
-lnsync \
change line 72 to:
$(EXECUTABLE_NAME): $(EXECUTABLE_OBJS) $(TFLIBS) $(NSYNCLIBS)
Hope it works with that changes, good luck :)
gcc: error: unrecognized command line option '-mfpu=neon-vfpv4' while building tensorflow from source. I have used bazel build -c opt --copt="-mfpu=neon-vfpv4" --copt="-funsafe-math-optimizations" --copt="-ftree-vectorize" --copt="-fomit-frame-pointer" --local_resources 1024,1.0,1.0 --verbose_failures tensorflow/tools/pip_package:build_pip_package to build it
Don't add --copt="-mfpu=neon-vfpv4" to your command line as this is not a flag gcc supports.
This flag is used on ARM architectures. If you are compiling under x86/amd64, just remove it.
$ gcc -mfpu=neon-vfpv4
gcc: error: unrecognized command line option '-mfpu=neon-vfpv4'
gcc: fatal error: no input files
compilation terminated.
$ arm-none-eabi-gcc -mfpu=neon-vfpv4
arm-none-eabi-gcc: fatal error: no input files
compilation terminated.
I'm trying to install SCIP on OSX mavericks. I've downloaded the tarball here, extracted it, and have tried to compile it using
make scipoptlib GMP=false ZLIB=false READLINE=false SHARED=true
This gives me error 1 below. My interpretation of error 1 is that /usr/local/lib/libisl.10.dylib does not exist. That's correct: I have isl.0.14.1, located at /usr/local/Cellar/isl/0.14.1. And in fact I can't install isl.0.10.1, because the compiler options it expects don't work with the current version of gcc (I think; see error 2 below).
Can I tell SCIP to use isl.0.14.1, and if so, how?
**error 1:**
** Extracting SoPlex archive "/Applications/scipoptsuite-3.2.0/soplex-2.2.0.tgz".
** Extracting ZIMPL archive "/Applications/scipoptsuite-3.2.0/zimpl-3.3.3.tgz".
** Extracting SCIP archive "/Applications/scipoptsuite-3.2.0/scip-3.2.0.tgz".
** compile libraries statically with compiler flag -fPIC
rm -rf obj/O.darwin.x86_64.gnu.normal.opt/* bin/zimpl-3.3.3.darwin.x86_64.gnu.normal.opt lib/libzimpl-3.3.3.darwin.x86_64.gnu.opt.a lib/libzimpl-3.3.3.darwin.x86_64.gnu.opt.dbl.a lib/libzimpl.darwin.x86_64.gnu.opt.a bin/zimpl.darwin.x86_64.gnu.opt bin/zimpl
** Creating directory "/Applications/scipoptsuite-3.2.0/scip-3.2.0/lib".
** Creating directory "/Applications/scipoptsuite-3.2.0/scip-3.2.0/lib/zimplinc".
** Building SoPlex library "/Applications/scipoptsuite-3.2.0/soplex-2.2.0/lib/libsoplex.darwin.x86_64.gnu.opt.a".
-> compiling obj/O.darwin.x86_64.gnu.opt/lib/changesoplex.o
dyld: Library not loaded: /usr/local/lib/libisl.10.dylib
Referenced from: /usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin13.2.0/4.9.1/cc1plus
Reason: image not found
g++: internal compiler error: Trace/BPT trap: 5 (program cc1plus)
make[4]: *** [obj/O.darwin.x86_64.gnu.opt/lib/changesoplex.o] Abort trap: 6
make[3]: [makelibfile] Error 2 (ignored)
-> compiling obj/O.darwin.x86_64.gnu.opt/lib/changesoplex.o
dyld: Library not loaded: /usr/local/lib/libisl.10.dylib
Referenced from: /usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin13.2.0/4.9.1/cc1plus
Reason: image not found
g++: internal compiler error: Trace/BPT trap: 5 (program cc1plus)
make[4]: *** [obj/O.darwin.x86_64.gnu.opt/lib/changesoplex.o] Abort trap: 6
make[3]: [all] Error 2 (ignored)
** ZIMPL support disabled.
** Creating necessary soft-links.
** Building SCIP libraries and executable.
-> generating necessary links
- Current settings: LPS=spx OSTYPE=darwin ARCH=x86_64 COMP=gnu SUFFIX= ZIMPL=false ZIMPLOPT=opt IPOPT=false IPOPTOPT=opt EXPRINT=cppad GAMS=false
* SCIP needs some softlinks to external programs, in particular, LP-solvers.
* Please insert the paths to the corresponding directories/libraries below.
* The links will be installed in the 'lib' directory.
* For more information and if you experience problems see the INSTALL file.
-> "spxinc" is the path to the SoPlex "src" directory, e.g., "../../soplex/src".
-> "libsoplex.*" is the path to the SoPlex library, e.g., "../../soplex/lib/libsoplex.darwin.x86_64.gnu.opt.a"
-> compiling obj/O.darwin.x86_64.gnu.opt/lib/scip/branch_allfullstrong.o
dyld: Library not loaded: /usr/local/lib/libisl.10.dylib
Referenced from: /usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin13.2.0/4.9.1/cc1
Reason: image not found
gcc: internal compiler error: Trace/BPT trap: 5 (program cc1)
make[4]: *** [obj/O.darwin.x86_64.gnu.opt/lib/scip/branch_allfullstrong.o] Abort trap: 6
make[3]: *** [makesciplibfile] Error 2
make[2]: *** [scipbinary] Error 2
make[1]: *** [scipbinary] Error 2
make: *** [scipoptlib] Error 2
error 2, produced by running ./configure in libisl.10 directory:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by isl configure 0.10, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ ./configure
## --------- ##
## Platform. ##
## --------- ##
hostname = dhcp-143-183.caltech.edu
uname -m = x86_64
uname -r = 13.4.0
uname -s = Darwin
uname -v = Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64
/usr/bin/uname -p = i386
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = Mach kernel version:
Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: i486 (Intel 80486)
Processors active: 0 1 2 3
Primary memory available: 16.00 gigabytes
Default processor set: 327 tasks, 1905 threads, 4 processors
Load average: 4.32, Mach factor: 0.47
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /Users/madeleine/anaconda/bin/
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/bin
PATH: /opt/X11/bin
PATH: /usr/local/go/bin
PATH: /usr/texbin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: /Applications/spark-0.9.1-bin-hadoop2/bin
PATH: /Applications/Julia-0.3.8.app/Contents/Resources/julia/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2762: checking for a BSD-compatible install
configure:2830: result: /usr/bin/install -c
configure:2841: checking whether build environment is sane
configure:2891: result: yes
configure:3032: checking for a thread-safe mkdir -p
configure:3071: result: ./install-sh -c -d
configure:3084: checking for gawk
configure:3114: result: no
configure:3084: checking for mawk
configure:3114: result: no
configure:3084: checking for nawk
configure:3114: result: no
configure:3084: checking for awk
configure:3100: found /usr/bin/awk
configure:3111: result: awk
configure:3122: checking whether make sets $(MAKE)
configure:3144: result: yes
configure:3287: checking for gcc
configure:3303: found /usr/local/bin/gcc
configure:3314: result: gcc
configure:3543: checking for C compiler version
configure:3552: gcc --version >&5
gcc (Homebrew gcc 4.9.1) 4.9.1
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3563: $? = 0
configure:3552: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin13.2.0/4.9.1/lto-wrapper
Target: x86_64-apple-darwin13.2.0
Configured with: ../configure --build=x86_64-apple-darwin13.2.0 --prefix=/usr/local/Cellar/gcc/4.9.1 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-4.9 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-cloog=/usr/local/opt/cloog --with-isl=/usr/local/opt/isl --with-system-zlib --enable-version-specific-runtime-libs --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --disable-werror --with-pkgversion='Homebrew gcc 4.9.1' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 4.9.1 (Homebrew gcc 4.9.1)
configure:3563: $? = 0
configure:3552: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3563: $? = 1
configure:3552: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:3563: $? = 1
configure:3583: checking whether the C compiler works
configure:3605: gcc conftest.c >&5
dyld: Library not loaded: /usr/local/lib/libisl.10.dylib
Referenced from: /usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin13.2.0/4.9.1/cc1
Reason: image not found
gcc: internal compiler error: Trace/BPT trap: 5 (program cc1)
./configure: line 3607: 9063 Abort trap: 6 $CC $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS 1>&5
I can't see where or why the SCIP Optimization Suite would be using isl. To be precise, in your case not SCIP fails to compile but SoPlex. Have you checked whether you can compile SoPlex alone? Just go into the subdirectory and type make or make SHARED=true GMP=false ZLIB=false to match the original command.
Have you compiled some other code with your compiler? It may also be that your gcc itself is broken.
I have the impression that the C++ compiler itself is broken:
dyld: Library not loaded: /usr/local/lib/libisl.10.dylib
Referenced from: /usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin13.2.0/4.9.1/cc1plus
Maybe try a simple (hello-world) C++ program first to test that the compiler itself is ok.