Problem compiling neuron in cygwin for Windows
Posted: Tue Jan 13, 2015 2:13 pm
I am having difficulty compiling neuron in cygwin for Windows 7. I am trying to follow the instructions found here: http://www.neuron.yale.edu/neuron/downl ... pile_mswin
I have installed neuron using the .exe file, and have downloaded and installed cygwin. I have downloaded both iv and nrn using mercurial
hg clone http://www.neuron.yale.edu/hg/neuron/iv/
hg clone http://www.neuron.yale.edu/hg/neuron/nrn/
I have run build.sh, ./configure, make, and make install in iv without problems.
After switching to the nrn directory, build and ./configure worked. However, upon attempting to make, I get the following error:
make all-recursive
make[1]: Entering directory '/home/Grado/neuron/nrn'
Making all in src
make[2]: Entering directory '/home/Grado/neuron/nrn/src'
Making all in readline
make[3]: Entering directory '/home/Grado/neuron/nrn/src/readline'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/readline'
Making all in memacs
make[3]: Entering directory '/home/Grado/neuron/nrn/src/memacs'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/memacs'
Making all in e_editor
make[3]: Entering directory '/home/Grado/neuron/nrn/src/e_editor'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/e_editor'
Making all in modlunit
make[3]: Entering directory '/home/Grado/neuron/nrn/src/modlunit'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/modlunit'
Making all in nmodl
make[3]: Entering directory '/home/Grado/neuron/nrn/src/nmodl'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/nmodl'
Making all in sparse
make[3]: Entering directory '/home/Grado/neuron/nrn/src/sparse'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/sparse'
Making all in sparse13
make[3]: Entering directory '/home/Grado/neuron/nrn/src/sparse13'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/sparse13'
Making all in scopmath
make[3]: Entering directory '/home/Grado/neuron/nrn/src/scopmath'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/scopmath'
Making all in Random123
make[3]: Entering directory '/home/Grado/neuron/nrn/src/Random123'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/Random123'
Making all in nrnmpi
make[3]: Entering directory '/home/Grado/neuron/nrn/src/nrnmpi'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/nrnmpi'
Making all in oc
make[3]: Entering directory '/home/Grado/neuron/nrn/src/oc'
make all-am
make[4]: Entering directory '/home/Grado/neuron/nrn/src/oc'
/bin/sh ../../libtool --tag=CC --mode=link gcc -g -O2 -Wl,--enable-auto-import -o oc.exe ocmain.o ocnoiv.o nocable.o modlreg.o ockludge.o libocxt.la liboc.la ../nrnmpi/libnrnmpi.la ../memacs/libmemacs.la ../readline/libreadline.la -lncurses
libtool: link: gcc -g -O2 -Wl,--enable-auto-import -o .libs/oc.exe ocmain.o ocnoiv.o nocable.o modlreg.o ockludge.o ./.libs/libocxt.a ./.libs/liboc.a ../nrnmpi/.libs/libnrnmpi.a ../memacs/.libs/libmemacs.a ../readline/.libs/libreadline.a -lncurses
./.libs/liboc.a(cygwinprt.o): In function `hoc_Plt':
/home/Grado/neuron/nrn/src/oc/mswinprt.c:363: multiple definition of `hoc_Plt'
./.libs/liboc.a(plt.o):/home/Grado/neuron/nrn/src/oc/plt.c:11: first defined here
./.libs/liboc.a(cygwinprt.o): In function `hoc_Setcolor':
/home/Grado/neuron/nrn/src/oc/mswinprt.c:364: multiple definition of `hoc_Setcolor'
./.libs/liboc.a(plt.o):/home/Grado/neuron/nrn/src/oc/plt.c:36: first defined here
./.libs/liboc.a(cygwinprt.o): In function `hoc_Lw':
/home/Grado/neuron/nrn/src/oc/mswinprt.c:365: multiple definition of `hoc_Lw'
./.libs/liboc.a(plt.o):/home/Grado/neuron/nrn/src/oc/plt.c:44: first defined here
collect2: error: ld returned 1 exit status
Makefile:661: recipe for target 'oc.exe' failed
make[4]: *** [oc.exe] Error 1
make[4]: Leaving directory '/home/Grado/neuron/nrn/src/oc'
Makefile:505: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/oc'
Makefile:487: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/Grado/neuron/nrn/src'
Makefile:624: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/Grado/neuron/nrn'
Makefile:481: recipe for targe
There seems to be a problem with oc.exe. How do I fix this?
Thanks!
I have installed neuron using the .exe file, and have downloaded and installed cygwin. I have downloaded both iv and nrn using mercurial
hg clone http://www.neuron.yale.edu/hg/neuron/iv/
hg clone http://www.neuron.yale.edu/hg/neuron/nrn/
I have run build.sh, ./configure, make, and make install in iv without problems.
After switching to the nrn directory, build and ./configure worked. However, upon attempting to make, I get the following error:
make all-recursive
make[1]: Entering directory '/home/Grado/neuron/nrn'
Making all in src
make[2]: Entering directory '/home/Grado/neuron/nrn/src'
Making all in readline
make[3]: Entering directory '/home/Grado/neuron/nrn/src/readline'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/readline'
Making all in memacs
make[3]: Entering directory '/home/Grado/neuron/nrn/src/memacs'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/memacs'
Making all in e_editor
make[3]: Entering directory '/home/Grado/neuron/nrn/src/e_editor'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/e_editor'
Making all in modlunit
make[3]: Entering directory '/home/Grado/neuron/nrn/src/modlunit'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/modlunit'
Making all in nmodl
make[3]: Entering directory '/home/Grado/neuron/nrn/src/nmodl'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/nmodl'
Making all in sparse
make[3]: Entering directory '/home/Grado/neuron/nrn/src/sparse'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/sparse'
Making all in sparse13
make[3]: Entering directory '/home/Grado/neuron/nrn/src/sparse13'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/sparse13'
Making all in scopmath
make[3]: Entering directory '/home/Grado/neuron/nrn/src/scopmath'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/scopmath'
Making all in Random123
make[3]: Entering directory '/home/Grado/neuron/nrn/src/Random123'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/Random123'
Making all in nrnmpi
make[3]: Entering directory '/home/Grado/neuron/nrn/src/nrnmpi'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/nrnmpi'
Making all in oc
make[3]: Entering directory '/home/Grado/neuron/nrn/src/oc'
make all-am
make[4]: Entering directory '/home/Grado/neuron/nrn/src/oc'
/bin/sh ../../libtool --tag=CC --mode=link gcc -g -O2 -Wl,--enable-auto-import -o oc.exe ocmain.o ocnoiv.o nocable.o modlreg.o ockludge.o libocxt.la liboc.la ../nrnmpi/libnrnmpi.la ../memacs/libmemacs.la ../readline/libreadline.la -lncurses
libtool: link: gcc -g -O2 -Wl,--enable-auto-import -o .libs/oc.exe ocmain.o ocnoiv.o nocable.o modlreg.o ockludge.o ./.libs/libocxt.a ./.libs/liboc.a ../nrnmpi/.libs/libnrnmpi.a ../memacs/.libs/libmemacs.a ../readline/.libs/libreadline.a -lncurses
./.libs/liboc.a(cygwinprt.o): In function `hoc_Plt':
/home/Grado/neuron/nrn/src/oc/mswinprt.c:363: multiple definition of `hoc_Plt'
./.libs/liboc.a(plt.o):/home/Grado/neuron/nrn/src/oc/plt.c:11: first defined here
./.libs/liboc.a(cygwinprt.o): In function `hoc_Setcolor':
/home/Grado/neuron/nrn/src/oc/mswinprt.c:364: multiple definition of `hoc_Setcolor'
./.libs/liboc.a(plt.o):/home/Grado/neuron/nrn/src/oc/plt.c:36: first defined here
./.libs/liboc.a(cygwinprt.o): In function `hoc_Lw':
/home/Grado/neuron/nrn/src/oc/mswinprt.c:365: multiple definition of `hoc_Lw'
./.libs/liboc.a(plt.o):/home/Grado/neuron/nrn/src/oc/plt.c:44: first defined here
collect2: error: ld returned 1 exit status
Makefile:661: recipe for target 'oc.exe' failed
make[4]: *** [oc.exe] Error 1
make[4]: Leaving directory '/home/Grado/neuron/nrn/src/oc'
Makefile:505: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory '/home/Grado/neuron/nrn/src/oc'
Makefile:487: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/Grado/neuron/nrn/src'
Makefile:624: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/Grado/neuron/nrn'
Makefile:481: recipe for targe
There seems to be a problem with oc.exe. How do I fix this?
Thanks!