MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
I ran into errors when trying to set up minpath for use. Thank you in advance for any advice to help fix this problem. Below are the details:
$ cd /MinPath-math-master/glpk-4.6/
$ ./configure
$ make
here it returns:
cd . && automake --gnu Makefile
cd . && autoconf
/bin/sh ./config.status --recheck
running /bin/sh ./configure --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/missing: Unknown --run' option Try/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/missing --help' for more information
configure: WARNING: missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc 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 ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking for sqrt in -lm... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes configure: creating ./config.status cd . \ && CONFIG_FILES=Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating Makefile config.status: executing depfiles commands Making all in include make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include'
cd .. \
&& CONFIG_FILES=include/Makefile CONFIG_HEADERS= /bin/sh ./config.status
config.status: creating include/Makefile
config.status: WARNING: 'include/Makefile.in' seems to ignore the --datarootdir setting
config.status: executing depfiles commands
make[1]: Leaving directory /project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include' make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include'
make[1]: Nothing to be done for all'. make[1]: Leaving directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include'
Making all in src
make[1]: Entering directory /project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src' cd .. \ && CONFIG_FILES=src/Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating src/Makefile config.status: WARNING: 'src/Makefile.in' seems to ignore the --datarootdir setting config.status: executing depfiles commands make[1]: Leaving directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src'
make[1]: Entering directory `/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src'
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpavl.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpchol.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpdmp.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpiet.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpinv.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpios1.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpios2.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpios3.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpipm.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib1a.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib1b.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib2.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib3.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpp1.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpp2.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpt.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx1.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx2.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx3.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx4.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx5.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6a.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6b.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6c.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6d.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx7.c
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx8a.c
glplpx8a.c: In function ‘glp_lpx_write_bas’:
glplpx8a.c:938:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs]
dir == LPX_MAX ? "(MAXimum)" : "(???)");
glplpx8a.c: In function ‘glp_lpx_print_sol’:
glplpx8a.c:1282:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs]
dir == LPX_MAX ? "(MAXimum)" : "(???)");
glplpx8a.c: In function ‘glp_lpx_print_ips’:
glplpx8a.c:1539:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs]
dir == LPX_MAX ? "(MAXimum)" : "(???)");
glplpx8a.c: In function ‘glp_lpx_print_mip’:
glplpx8a.c:1696:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs]
dir == LPX_MAX ? "(MAXimum)" : "(???)", lp_obj);
Hello,
I ran into errors when trying to set up minpath for use. Thank you in advance for any advice to help fix this problem. Below are the details:
$ cd /MinPath-math-master/glpk-4.6/ $ ./configure $ make
here it returns:
cd . && automake --gnu Makefile cd . && autoconf /bin/sh ./config.status --recheck running /bin/sh ./configure --no-create --no-recursion checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/missing: Unknown
--run' option Try/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/missing --help' for more information configure: WARNING:missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc 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 ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking for sqrt in -lm... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes configure: creating ./config.status cd . \ && CONFIG_FILES=Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating Makefile config.status: executing depfiles commands Making all in include make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include' cd .. \ && CONFIG_FILES=include/Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating include/Makefile config.status: WARNING: 'include/Makefile.in' seems to ignore the --datarootdir setting config.status: executing depfiles commands make[1]: Leaving directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include' make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include' make[1]: Nothing to be done forall'. make[1]: Leaving directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/include' Making all in src make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src' cd .. \ && CONFIG_FILES=src/Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating src/Makefile config.status: WARNING: 'src/Makefile.in' seems to ignore the --datarootdir setting config.status: executing depfiles commands make[1]: Leaving directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src' make[1]: Entering directory `/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpavl.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpchol.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpdmp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpiet.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpinv.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpios1.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpios2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpios3.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpipm.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib1a.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib1b.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplib3.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpp1.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpp2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpt.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx1.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx3.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx4.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx5.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6a.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6b.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6c.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx6d.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx7.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx8a.c glplpx8a.c: In function ‘glp_lpx_write_bas’: glplpx8a.c:938:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] dir == LPX_MAX ? "(MAXimum)" : "(???)");glplpx8a.c: In function ‘glp_lpx_print_sol’: glplpx8a.c:1282:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] dir == LPX_MAX ? "(MAXimum)" : "(???)");
glplpx8a.c: In function ‘glp_lpx_print_ips’: glplpx8a.c:1539:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] dir == LPX_MAX ? "(MAXimum)" : "(???)");
glplpx8a.c: In function ‘glp_lpx_print_mip’: glplpx8a.c:1696:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] dir == LPX_MAX ? "(MAXimum)" : "(???)", lp_obj);
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx8b.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx8c.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx8d.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glplpx8e.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpluf.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmat.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmip1.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmip2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmpl1.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmpl2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmpl3.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmpl4.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpmps.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpqmd.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpspx1.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpspx2.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpstr.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glptsp.c rm -f libglpk.a ar cru libglpk.a glpavl.o glpchol.o glpdmp.o glpiet.o glpinv.o glpios1.o glpios2.o glpios3.o glpipm.o glplib1a.o glplib1b.o glplib2.o glplib3.o glplpp1.o glplpp2.o glplpt.o glplpx1.o glplpx2.o glplpx3.o glplpx4.o glplpx5.o glplpx6a.o glplpx6b.o glplpx6c.o glplpx6d.o glplpx7.o glplpx8a.o glplpx8b.o glplpx8c.o glplpx8d.o glplpx8e.o glpluf.o glpmat.o glpmip1.o glpmip2.o glpmpl1.o glpmpl2.o glpmpl3.o glpmpl4.o glpmps.o glpqmd.o glprng.o glpspx1.o glpspx2.o glpstr.o glptsp.o ranlib libglpk.a make[1]: Leaving directory
/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/src' Making all in examples make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/examples' cd .. \ && CONFIG_FILES=examples/Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating examples/Makefile config.status: WARNING: 'examples/Makefile.in' seems to ignore the --datarootdir setting config.status: executing depfiles commands make[1]: Leaving directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/examples' make[1]: Entering directory/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/examples' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"GLPK\" -DVERSION=\"4.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -I. -I. -I../include -g -O2 -c glpsol.c gcc -g -O2 -o glpsol glpsol.o ../src/libglpk.a -lm ../src/libglpk.a: could not read symbols: File in wrong format collect2: error: ld returned 1 exit status make[1]: [glpsol] Error 1 make[1]: Leaving directory `/project/uma_david_sela/Shuqi_Li/Ezgi_BioreactorShotgun_SL/MinPath-master/glpk-4.6/examples' make: [all-recursive] Error 1when I check the ../src/libglpk.a file, it says
$ less src/libglpk.a "src/libglpk.a" may be a binary file. See it anyway?
I paused here since I dont know how to fix this. Could someone give any help?