nrniv.dll missing after build with cygwin under 64 bit win 8

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Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

nrniv.dll missing after build with cygwin under 64 bit win 8

Post by Keivan » Sat Feb 01, 2014 7:00 am

For some reason nrniv.dll is missing in my mswin-i686 (with cygwin i686, under 64bit version of windows 8.1) build of neuron. Could you please help me to make my own nrniv.dll.

PS: currently, gcc-3 is completely removed from the cygwin repositories that causes some errors in compiling nrn. I have bypassed the error with making a shortcut for gcc-4.5 and rename it to gcc-3. Some function of gcc-4.5 is removed from gcc-4.7 and gcc-4.8 and therefore it is impossible to use them instead.

hines
Site Admin
Posts: 1510
Joined: Wed May 18, 2005 3:32 pm

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by hines » Sun Feb 02, 2014 8:16 pm

Are there any error messages if you go to nrn/src and type
make

hines
Site Admin
Posts: 1510
Joined: Wed May 18, 2005 3:32 pm

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by hines » Sun Feb 02, 2014 8:16 pm

I forgot to ask. What configure statement did you use?

Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by Keivan » Mon Feb 03, 2014 12:54 am

This is my .bashrc:

Code: Select all

export HOME=/home/keivan
export IV="$HOME/neuron/iv"
export N="$HOME/neuron/nrn"
export CPU="i686"
export host_cpu=$CPU
export PATH="$HOME:$PATH:/bin:/usr/bin:/usr/sbin"
export PATH="$IV/$CPU/bin:$N/$CPU/bin:$PATH"

export CPATH="$CPATH:/usr/include"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/lib"
export CC="gcc"
export CXX="g++"
export AR="ar"
export RANLIB="ranlib"
export CFLAGS="-march=native -fexcess-precision=fast -ffast-math -O2 -static -pipe"
export CXXFLAGS="$CFLAGS"
export LDFLAGS="-Wl,--enable-auto-import"
export WANT_AUTOMAKE=1.11
cd
this is my build script:

Code: Select all

#! /bin/bash
rm -r ./iv &&
hg clone http://www.neuron.yale.edu/hg/neuron/iv &&
cd iv &&
./build.sh &&
./configure --prefix=`pwd` &&
make -j 9 &&
make install
cd .. &&
rm -r ./nrn &&
hg clone http://www.neuron.yale.edu/hg/neuron/nrn &&
cd nrn &&
./build.sh &&
./configure --prefix=`pwd` --with-iv=$IV &&
make -j 9 &&
make mswin &&
cd ..
There were some errors:

Code: Select all

make[3]: Entering directory '/home/keivan/neuron/nrn/src/nrniv'
if test "i686"="x86_64" ; then \
x86_64-w64-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../src/mswin/extra/mos2nrn.cpp ;\
fi
In file included from /usr/include/sys/cdefs.h:45:0,
                 from /usr/include/string.h:12,
                 from /usr/x86_64-w64-mingw32/sys-root/mingw/include/guiddef.h:148,
                 from /usr/x86_64-w64-mingw32/sys-root/mingw/include/winnt.h:602,
                 from /usr/x86_64-w64-mingw32/sys-root/mingw/include/minwindef.h:146,
                 from /usr/x86_64-w64-mingw32/sys-root/mingw/include/windef.h:8,
                 from /usr/x86_64-w64-mingw32/sys-root/mingw/include/windows.h:69,
                 from ../../src/mswin/extra/mos2nrn.cpp:4:
/usr/include/stdint.h:97:23: error: conflicting declaration ‘typedef long unsigned int uintptr_t’
 typedef unsigned long uintptr_t;
                       ^
In file included from /usr/x86_64-w64-mingw32/sys-root/mingw/include/windows.h:9:0,
                 from ../../src/mswin/extra/mos2nrn.cpp:4:
/usr/x86_64-w64-mingw32/sys-root/mingw/include/_mingw.h:412:44: error: ‘uintptr_t’ has a previous declaration as ‘typedef long long unsigned int uintptr_t’
 __MINGW_EXTENSION typedef unsigned __int64 uintptr_t;
                                            ^
In file included from /usr/x86_64-w64-mingw32/sys-root/mingw/include/windows.h:114:0,
                 from ../../src/mswin/extra/mos2nrn.cpp:4:
/usr/x86_64-w64-mingw32/sys-root/mingw/include/stralign.h: In function ‘int ua_wcsicmp(LPCUWSTR, LPCUWSTR)’:
/usr/x86_64-w64-mingw32/sys-root/mingw/include/stralign.h:155:56: error: ‘_wcsicmp’ was not declared in this scope
       return _wcsicmp((LPCWSTR)String1,(LPCWSTR)String2);
                                                        ^
In file included from /usr/include/stdio.h:47:0,
                 from ../../src/mswin/extra/mos2nrn.cpp:5:
/usr/include/sys/types.h: At global scope:
/usr/include/sys/types.h:122:18: error: conflicting declaration ‘typedef long int time_t’
 typedef _TIME_T_ time_t;
                  ^
In file included from /usr/x86_64-w64-mingw32/sys-root/mingw/include/windows.h:9:0,
                 from ../../src/mswin/extra/mos2nrn.cpp:4:
/usr/x86_64-w64-mingw32/sys-root/mingw/include/_mingw.h:481:20: error: ‘time_t’ has a previous declaration as ‘typedef __time64_t time_t’
 typedef __time64_t time_t;
                    ^
Makefile:973: recipe for target 'mos2nrn.exe' failed
make[3]: *** [mos2nrn.exe] Error 1
make[3]: Leaving directory '/home/keivan/neuron/nrn/src/nrniv'
Makefile:426: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/keivan/neuron/nrn/src'
Makefile:559: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/keivan/neuron/nrn'
Makefile:416: recipe for target 'all' failed
make: *** [all] Error 2
I thought I had fixed the problem by changing one of the makefile.am files, but I have undone them now by cloning a fresh copy of source and this is the error I see.

hines
Site Admin
Posts: 1510
Joined: Wed May 18, 2005 3:32 pm

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by hines » Mon Feb 03, 2014 6:51 am

The problem seems to be a failure in building the mos2nrn.exe file but that is surrounded by so many bizarre puzzles I hardly know what to make of it.
First, it is a puzzle why if test "i686"="x86_64" is true. That is, the body of the statement is being processed despite i686 being manifestly not the same
as x86_64. Second, why isn't there an alternative to the test value so that mos2nrn.exe is built using $(CXX32WIN)? (That is a rhetorical question).
Anyway, since you are building from the repository sources, try the work around of editing nrn/src/nrniv/Makefile.am and replacing the
$(CXX64WIN) tokens in the mos2nrn.exe and neuron.exe rules with $(CXX32WIN) and meanwhile I'll review more closely what was intended vs what
is actually there. Since mos2nrn.exe and neuron.exe are conceptually irrelevant to libnrniv it might appear puzzling that a failure there prevents libnrniv
from being built. However, $(cygexe) was added to the nrniv_DEPENDENCIES so that they would be built as a side effect in those situations where
it made sense to do so.

Looking at changsets 925, 926, and 979 for that Makefile.am, it seems that the proper rules for mos2nrn.exe and neuron.exe should be:

Code: Select all

mos2nrn.exe: $(nsrc)/mswin/extra/mos2nrn.cpp
        if test "$(host_cpu)"="x86_64" ; then \
        $(CXX64WIN) -g -O2 -DCYGWIN -o mos2nrn.exe $(nsrc)/mswin/extra/mos2nrn.cpp ;\
        else \
        $(CXX32WIN) -g -O2 -DCYGWIN -o mos2nrn.exe $(nsrc)/mswin/extra/mos2nrn.cpp ;\
        fi

neuron.exe: $(nsrc)/mswin/extra/neuron.cpp
        echo "id ICON \"$(nsrc)/mswin/nrniv10.ico\"" > nrnicon.rc
        windres nrnicon.rc -O coff -o nrnicon.res
        if test "$(host_cpu)"="x86_64" ; then \
        $(CXX64WIN) -g -O2 -DCYGWIN -o neuron.exe $(nsrc)/mswin/extra/neuron.cpp nrnicon.res ;\
        else \
        $(CXX32WIN) -g -O2 -DCYGWIN -o neuron.exe $(nsrc)/mswin/extra/neuron.cpp nrnicon.res ;\
        fi
But I'm a bit worried about it in your case since the if statement didn't seem to work.
Anyway, I will test this on my i686 and x86_64 mswin 7 virtualboxes

Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by Keivan » Mon Feb 03, 2014 11:39 am

for some reason your modification of makefile.am do not work even after re-executing the ./build.sh script and re-configuring. I mean still the x86_64 version of mingw tries to compile the code.
I changed the makefile to test the i686 version. Still this error appears
nrn/src/nrniv/makefile:

Code: Select all

mos2nrn.exe: $(nsrc)/mswin/extra/mos2nrn.cpp
		# if test "$(host_cpu)"="x86_64" ; then \
		# $(CXX64WIN) -g -O2 -DCYGWIN -o mos2nrn.exe $(nsrc)/mswin/extra/mos2nrn.cpp ;\
		# else \
		$(CXX32WIN) -g -O2 -DCYGWIN -o mos2nrn.exe $(nsrc)/mswin/extra/mos2nrn.cpp ;\
		# fi

neuron.exe: $(nsrc)/mswin/extra/neuron.cpp
		echo "id ICON \"$(nsrc)/mswin/nrniv10.ico\"" > nrnicon.rc
		windres nrnicon.rc -O coff -o nrnicon.res
		# if test "$(host_cpu)"="x86_64" ; then \
		# $(CXX64WIN) -g -O2 -DCYGWIN -o neuron.exe $(nsrc)/mswin/extra/neuron.cpp nrnicon.res ;\
		# else \
		$(CXX32WIN) -g -O2 -DCYGWIN -o neuron.exe $(nsrc)/mswin/extra/neuron.cpp nrnicon.res ;\
		# fi
error:
make[3]: Entering directory '/home/keivan/neuron/nrn/src/nrniv'
# if test "i686"="x86_64" ; then \
# x86_64-w64-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../src/mswin/ extra/mos2nrn.cpp ;\
# else \
i686-pc-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../src/mswin/extra /mos2nrn.cpp ;\
# fi
/tmp/ccCvXDJB.o: In function `Z20hoc_dos2cygdrivepathPKci':
/home/keivan/neuron/nrn/src/nrniv/../../src/mswin/extra/d2upath.c:23: undefined reference to `__assert_func'
collect2: error: ld returned 1 exit status
Makefile:973: recipe for target 'mos2nrn.exe' failed
make[3]: *** [mos2nrn.exe] Error 1
make[3]: Leaving directory '/home/keivan/neuron/nrn/src/nrniv'
Makefile:426: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/keivan/neuron/nrn/src'
Makefile:559: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/keivan/neuron/nrn'
Makefile:416: recipe for target 'all' failed
make: *** [all] Error 2
Is it possible to use previous command instead?

Code: Select all

mos2nrn.exe: $(nsrc)/mswin/extra/mos2nrn.cpp
	$(CXX) -g -O2 -DMINGW -o mos2nrn.exe $(nsrc)/mswin/extra/mos2nrn.cpp

neuron.exe: $(nsrc)/mswin/extra/neuron.cpp
	$(CXX) -g -O2 -DMINGW -o neuron.exe $(nsrc)/mswin/extra/neuron.cpp
I have tried that and build was successful, but there was no nrniv.dll.

another question: Is it necessary to remove the CFLAGS in this part?

PS: "make clean" behaves strangely. It starts to re-configure and then ends with an error.

Code: Select all

$ make clean
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /home/keivan/neuron/nrn/missing --                                                                                                                                                                                               run aclocal-1.11 -I m4
configure.in:247: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in                                                                                                                                                                                                body
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:2678: AC_LINK_IFELSE is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/m4suga                                                                                                                                                                                               r/m4sh.m4:639: AS_IF is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:1481: AC_ARG_WITH is expanded from...
m4/withmpi.m4:136: AC_NRN_WITH_METIS is expanded from...
configure.in:247: the top level
 cd . && /bin/sh /home/keivan/neuron/nrn/missing --run automake-1.11 --foreign
configure.in:247: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in                                                                                                                                                                                                body
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:2678: AC_LINK_IFELSE is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/m4suga                                                                                                                                                                                               r/m4sh.m4:639: AS_IF is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:1481: AC_ARG_WITH is expanded from...
m4/withmpi.m4:136: AC_NRN_WITH_METIS is expanded from...
configure.in:247: the top level
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /home/keivan/neuron/nrn/missing --                                                                                                                                                                                               run autoconf
configure.in:247: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in                                                                                                                                                                                                body
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:2678: AC_LINK_IFELSE is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/m4suga                                                                                                                                                                                               r/m4sh.m4:639: AS_IF is expanded from...
/usr/src/packages/autoconf/26/32/autoconf2.5-2.69-2/src/autoconf-2.69/lib/autoco                                                                                                                                                                                               nf/general.m4:1481: AC_ARG_WITH is expanded from...
m4/withmpi.m4:136: AC_NRN_WITH_METIS is expanded from...
configure.in:247: the top level
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --prefix=/home/keivan/neuron/nr                                                                                                                                                                                               n --with-iv=/home/keivan/neuron/iv CXX=g++ CXXFLAGS=-march=native -fexcess-preci                                                                                                                                                                                               sion=fast -ffast-math -O2 -static -pipe LDFLAGS=-Wl,--enable-auto-import CC=gcc                                                                                                                                                                                                CFLAGS=-march=native -fexcess-precision=fast -ffast-math -O2 -static -pipe --no-                                                                                                                                                                                               create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
CYGWIN=yes
MINGW=no
checking for style of include used by make... GNU
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... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
Not trying to build rpms for your system (use --enable-rpm-rules to override)
checking for gcc... gcc
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 dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for gawk... (cached) gawk
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking whether ln -s works... yes
checking for cython... echo
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/i686-pc-cygwin/bin/ld.exe
checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 8192
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert i686-pc-cygwin file names to i686-pc-cygwin format... func_convert_file_noop
checking how to convert i686-pc-cygwin file names to toolchain format... func_convert_file_noop
checking for /usr/i686-pc-cygwin/bin/ld.exe option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL
checking for dlltool... dlltool
checking how to associate runtime and link libraries... func_cygming_dll_for_implib
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if gcc PIC flag -DDLL_EXPORT -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking whether -lc should be explicitly linked in... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/i686-pc-cygwin/bin/ld.exe
checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld... yes
checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking for g++ option to produce PIC... -DDLL_EXPORT -DPIC
checking if g++ PIC flag -DDLL_EXPORT -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
configure: Use the default unix style for "special" (not NRNMECH_DLL_STYLE)
checking for tgetent in -lncurses... yes
checking which library has the termcap functions... using libncurses
build our own version of libreadline
Do not compile neosim specific code.
Not building the nrnjava interface
 CYGWIN and no X11 so make MSWwin version
configure: 'make mswin' will marshal for building the installer in the marshall_dir = /cygdrive/c/marshalnrn
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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checking limits.h usability... yes
checking limits.h presence... yes
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checking malloc.h usability... yes
checking malloc.h presence... yes
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checking sgtty.h usability... no
checking sgtty.h presence... no
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checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
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checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
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checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking termio.h usability... yes
checking termio.h presence... yes
checking for termio.h... yes
checking for unistd.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking varargs.h usability... no
checking varargs.h presence... no
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checking stropts.h usability... no
checking stropts.h presence... no
checking for stropts.h... no
checking sys/conf.h usability... no
checking sys/conf.h presence... no
checking for sys/conf.h... no
checking locale.h usability... yes
checking locale.h presence... yes
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checking fenv.h usability... yes
checking fenv.h presence... yes
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checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
configure: Using pthreads.
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
configure: successful.
PTHREAD_LIBS=
PTHREAD_CFLAGS=
PTHREAD_CC=gcc
checking float.h usability... yes
checking float.h presence... yes
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checking math.h usability... yes
checking math.h presence... yes
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checking stream.h usability... no
checking stream.h presence... no
checking for stream.h... no
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether byte ordering is bigendian... no
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for working alloca.h... yes
checking for alloca... yes
checking for working memcmp... yes
checking return type of signal handlers... void
checking for vprintf... yes
checking for _doprnt... no
checking for ftime... yes
checking for getcwd... yes
checking for getpw... no
checking for gethostname... yes
checking for gettimeofday... yes
checking for mkdir... yes
checking for putenv... yes
checking for setenv... yes
checking for select... yes
checking for strdup... yes
checking for strstr... yes
checking for index... yes
checking for bzero... yes
checking for bcopy... yes
checking for stty... no
checking for lockf... yes
checking for isatty... yes
checking for mkstemp... yes
checking for setitimer... yes
checking for sigaction... yes
checking for fesetround... yes
checking for posix_memalign... yes
checking for mallinfo... yes
checking if SIGBUS defined in signal.h... yes
checking if SIGSEGV defined in signal.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking _G_config.h usability... no
checking _G_config.h presence... no
checking for _G_config.h... no
checking whether the compiler implements namespaces... yes
checking whether the compiler has stringstream... yes
checking compilation with interviews... ok
checking if InterViews is up to date with respect to nrn-7.3 and later... ok
The signal function does not need a cast for the handler
checking /include/pvm3.h usability... no
checking /include/pvm3.h presence... no
checking for /include/pvm3.h... no

do SIGPOLL and I_GETSIG work: no
 But see config.log to see why it failed.
checking whether the compiler supports Standard Template Library... yes
NRNOC_X11 = 0
configure: creating ./config.status
 /bin/sh ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/e_editor/Makefile
config.status: creating src/modlunit/Makefile
config.status: creating src/nmodl/Makefile
config.status: creating nrnrpm.spec
config.status: creating src/sundials/Makefile
config.status: creating src/sundials/shared/Makefile
config.status: creating src/sundials/cvodes/Makefile
config.status: creating src/sundials/ida/Makefile
config.status: creating src/sparse/Makefile
config.status: creating src/memacs/Makefile
config.status: creating src/readline/Makefile
config.status: creating src/sparse13/Makefile
config.status: creating src/Random123/Makefile
config.status: creating src/oc/Makefile
config.status: creating src/scopmath/Makefile
config.status: creating src/nrnoc/Makefile
config.status: creating src/gnu/Makefile
config.status: creating src/uxnrnbbs/Makefile
config.status: creating src/mesch/Makefile
config.status: creating src/uxnrnbbs/mos2nrn.h
config.status: creating src/nrnmpi/Makefile
config.status: creating src/ivoc/Makefile
config.status: creating src/nrncvode/Makefile
config.status: creating src/parallel/Makefile
config.status: creating src/nrniv/Makefile
config.status: creating src/ivos/Makefile
config.status: creating src/ivos/InterViews/Makefile
config.status: creating src/ivos/OS/Makefile
config.status: creating src/nrnjava/Makefile
config.status: creating src/nrnjava/nrnccmb/Makefile
config.status: creating src/nrnjava/neuron/Makefile
config.status: creating src/nrnpython/Makefile
config.status: creating src/ni_pci_6229/Makefile
config.status: creating src/mac/Makefile
config.status: creating src/mswin/Makefile
config.status: creating src/mswin/batch/Makefile
config.status: creating src/mswin/nrnsetup.nsi
config.status: creating src/mswin/nrncygso.sh
config.status: creating src/mswin/lib/mknrndll.mak
config.status: creating src/mswin/nrnsetupmingw.nsi
config.status: creating src/mswin/extra/Makefile
config.status: creating src/mswin/rdln/Makefile
config.status: creating src/mswin/windll/Makefile
config.status: creating src/mswin/wnrnbbs/Makefile
config.status: creating src/mswin/lib/Makefile
config.status: creating src/mswin/bin/Makefile
config.status: creating src/neuronmusic/Makefile
config.status: creating src/neuronmusic/setup.py
config.status: creating share/Makefile
config.status: creating bin/nrnoc_makefile
config.status: WARNING:  'bin/nrnoc_makefile.in' seems to ignore the --datarootdir setting
config.status: creating bin/nrniv_makefile
config.status: WARNING:  'bin/nrniv_makefile.in' seems to ignore the --datarootdir setting
config.status: creating bin/nrnmech_makefile
config.status: creating share/lib/Makefile
config.status: creating share/lib/hoc/Makefile
config.status: creating share/lib/python/Makefile
config.status: creating share/lib/hoc/celbild/Makefile
config.status: creating share/lib/hoc/mulfit/Makefile
config.status: creating share/lib/hoc/netbild/Makefile
config.status: creating share/lib/hoc/lincir/Makefile
config.status: creating share/lib/hoc/mview/Makefile
config.status: creating share/lib/hoc/chanbild/Makefile
config.status: creating share/lib/hoc/import3d/Makefile
config.status: creating share/lib/auditscripts/Makefile
config.status: creating share/lib/nrn.defaults
config.status: creating bin/Makefile
config.status: creating bin/nrnocmodl
config.status: creating bin/nrnivmodl
config.status: creating bin/neurondemo
config.status: creating bin/nrngui
config.status: creating bin/bbswork.sh
config.status: creating bin/mos2nrn2.sh
config.status: creating bin/hel2mos1.sh
config.status: creating share/examples/Makefile
config.status: creating share/examples/ivoc/Makefile
config.status: creating share/examples/nrniv/Makefile
config.status: creating share/examples/nrniv/cable/Makefile
config.status: creating share/examples/nrniv/kkin/Makefile
config.status: creating share/examples/nrniv/netcon/Makefile
config.status: creating share/examples/nrniv/netsyn/Makefile
config.status: creating share/examples/nrniv/nmodl/Makefile
config.status: creating share/examples/nrniv/nrnoc/Makefile
config.status: creating share/examples/nrniv/randomsyn/Makefile
config.status: creating share/examples/nrniv/soma/Makefile
config.status: creating share/examples/nrniv/vrecorder/Makefile
config.status: creating share/examples/nrniv/xmech/Makefile
config.status: creating share/demo/Makefile
config.status: creating share/demo/release/Makefile
config.status: creating share/demo/dend3/Makefile
config.status: creating share/demo/sync/Makefile
config.status: creating src/nrnpython/setup.py
config.status: creating config.h
config.status: config.h is unchanged
config.status: creating nmodlconf.h
config.status: nmodlconf.h is unchanged
config.status: creating nrnconf.h
config.status: nrnconf.h is unchanged
config.status: creating src/nrnoc/nrnconfigargs.h
config.status: src/nrnoc/nrnconfigargs.h is unchanged
config.status: creating src/oc/nrnmpiuse.h
config.status: src/oc/nrnmpiuse.h is unchanged
config.status: creating src/oc/nrnrtuse.h
config.status: src/oc/nrnrtuse.h is unchanged
config.status: creating src/oc/nrnpthread.h
config.status: src/oc/nrnpthread.h is unchanged
config.status: creating src/parallel/bbsconf.h
config.status: src/parallel/bbsconf.h is unchanged
config.status: creating src/nrnjava/njconf.h
config.status: src/nrnjava/njconf.h is unchanged
config.status: creating src/nrncvode/nrnneosm.h
config.status: src/nrncvode/nrnneosm.h is unchanged
config.status: creating src/ivos/ivstream.h
config.status: src/ivos/ivstream.h is unchanged
config.status: creating src/sundials/sundials_config.h
config.status: src/sundials/sundials_config.h is unchanged
config.status: creating src/nrnpython/nrnpython_config.h
config.status: src/nrnpython/nrnpython_config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
Making clean in share
make[1]: Entering directory '/home/keivan/neuron/nrn/share'
Making clean in demo
make[2]: Entering directory '/home/keivan/neuron/nrn/share/demo'
Making clean in sync
make[3]: Entering directory '/home/keivan/neuron/nrn/share/demo/sync'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/demo/sync'
Making clean in dend3
make[3]: Entering directory '/home/keivan/neuron/nrn/share/demo/dend3'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/demo/dend3'
Making clean in release
make[3]: Entering directory '/home/keivan/neuron/nrn/share/demo/release'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/demo/release'
Making clean in .
make[3]: Entering directory '/home/keivan/neuron/nrn/share/demo'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/demo'
make[2]: Leaving directory '/home/keivan/neuron/nrn/share/demo'
Making clean in examples
make[2]: Entering directory '/home/keivan/neuron/nrn/share/examples'
Making clean in nrniv
make[3]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv'
Making clean in xmech
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/xmech'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/xmech'
Making clean in vrecorder
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/vrecorder'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/vrecorder'
Making clean in soma
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/soma'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/soma'
Making clean in randomsyn
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/randomsyn'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/randomsyn'
Making clean in nrnoc
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/nrnoc'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/nrnoc'
Making clean in nmodl
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/nmodl'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/nmodl'
Making clean in netsyn
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/netsyn'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/netsyn'
Making clean in netcon
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/netcon'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/netcon'
Making clean in kkin
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/kkin'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/kkin'
Making clean in cable
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv/cable'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv/cable'
Making clean in .
make[4]: Entering directory '/home/keivan/neuron/nrn/share/examples/nrniv'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv'
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/examples/nrniv'
Making clean in ivoc
make[3]: Entering directory '/home/keivan/neuron/nrn/share/examples/ivoc'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/examples/ivoc'
Making clean in .
make[3]: Entering directory '/home/keivan/neuron/nrn/share/examples'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/examples'
make[2]: Leaving directory '/home/keivan/neuron/nrn/share/examples'
Making clean in lib
make[2]: Entering directory '/home/keivan/neuron/nrn/share/lib'
Making clean in python
make[3]: Entering directory '/home/keivan/neuron/nrn/share/lib/python'
rm -rf .libs _libs
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make[3]: Leaving directory '/home/keivan/neuron/nrn/share/lib/python'
Making clean in hoc
make[3]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc'
Making clean in import3d
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/import3d'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/import3d'
Making clean in chanbild
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/chanbild'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/chanbild'
Making clean in mview
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/mview'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/mview'
Making clean in lincir
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/lincir'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/lincir'
Making clean in netbild
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/netbild'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/netbild'
Making clean in mulfit
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/mulfit'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/mulfit'
Making clean in celbild
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc/celbild'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc/celbild'
Making clean in .
make[4]: Entering directory '/home/keivan/neuron/nrn/share/lib/hoc'
rm -rf .libs _libs
rm -f *.lo
make[4]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc'
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/lib/hoc'
Making clean in auditscripts
make[3]: Entering directory '/home/keivan/neuron/nrn/share/lib/auditscripts'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/lib/auditscripts'
Making clean in .
make[3]: Entering directory '/home/keivan/neuron/nrn/share/lib'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/share/lib'
make[2]: Leaving directory '/home/keivan/neuron/nrn/share/lib'
Making clean in .
make[2]: Entering directory '/home/keivan/neuron/nrn/share'
rm -rf .libs _libs
rm -f *.lo
make[2]: Leaving directory '/home/keivan/neuron/nrn/share'
make[1]: Leaving directory '/home/keivan/neuron/nrn/share'
Making clean in bin
make[1]: Entering directory '/home/keivan/neuron/nrn/bin'
rm -rf .libs _libs
rm -f *.lo
make[1]: Leaving directory '/home/keivan/neuron/nrn/bin'
Making clean in src
make[1]: Entering directory '/home/keivan/neuron/nrn/src'
Making clean in mswin
make[2]: Entering directory '/home/keivan/neuron/nrn/src/mswin'
Making clean in .
make[3]: Entering directory '/home/keivan/neuron/nrn/src/mswin'
rm -rf .libs _libs
rm -f *.lo
make[3]: Leaving directory '/home/keivan/neuron/nrn/src/mswin'
make[2]: Leaving directory '/home/keivan/neuron/nrn/src/mswin'
Making clean in mac
make[2]: Entering directory '/home/keivan/neuron/nrn/src/mac'
rm -rf .libs _libs
rm -f *.lo
make[2]: Leaving directory '/home/keivan/neuron/nrn/src/mac'
Making clean in nrniv
make[2]: Entering directory '/home/keivan/neuron/nrn/src/nrniv'
Makefile:975: *** missing separator.  Stop.
make[2]: Leaving directory '/home/keivan/neuron/nrn/src/nrniv'
Makefile:453: recipe for target 'clean-recursive' failed
make[1]: *** [clean-recursive] Error 1
make[1]: Leaving directory '/home/keivan/neuron/nrn/src'
Makefile:586: recipe for target 'clean-recursive' failed
make: *** [clean-recursive] Error 1

hines
Site Admin
Posts: 1510
Joined: Wed May 18, 2005 3:32 pm

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by hines » Mon Feb 03, 2014 1:10 pm

The Makefile.am is fixed and works for i686 cygwin32 and x86_64 cygwin64 mswin 7. See
http://www.neuron.yale.edu/hg/neuron/nr ... 42bf32c155
The problem with the if is that in a shell if test statment the = must be surrounded by spaces.
I didn't see the problem with mosinit.exe and neuron.exe until I removed them because those files existed from an earlier build.

Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by Keivan » Mon Feb 03, 2014 4:03 pm

Thank you for fixing that problem. I have cloned the source again and recompiled the code. This is the error:

Code: Select all

if test "i686" = "x86_64" ; then \
x86_64-w64-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../src/mswin/extra/mos2nrn.cpp ;\
else \
i686-pc-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../src/mswin/extra/mos2nrn.cpp ;\
fi
mv -f .deps/netpar.Tpo .deps/netpar.Plo
mv -f .deps/partrans.Tpo .deps/partrans.Plo
echo "id ICON \"../../src/mswin/nrniv10.ico\"" > nrnicon.rc
mv -f .deps/matrixmap.Tpo .deps/matrixmap.Plo
windres nrnicon.rc -O coff -o nrnicon.res
mv -f .deps/kschan.Tpo .deps/kschan.Plo
mv -f .deps/geometry3d.Tpo .deps/geometry3d.Plo
mv -f .deps/netcvode.Tpo .deps/netcvode.Plo
if test "i686" = "x86_64" ; then \
x86_64-w64-mingw32-g++ -g -O2 -DCYGWIN -o neuron.exe ../../src/mswin/extra/neuron.cpp nrnicon.res ;\
else \
i686-pc-mingw32-g++ -g -O2 -DCYGWIN -o neuron.exe ../../src/mswin/extra/neuron.cpp nrnicon.res ;\
fi
mv -f .deps/nvkludge.Tpo .deps/nvkludge.Po
mv -f .deps/multisplit.Tpo .deps/multisplit.Plo
/bin/sh ../../libtool --tag=CXX   --mode=link g++  -march=native -fexcess-precision=fast -ffast-math -O2 -static -pipe  -Wl,--enable-auto-import -o libnrniv.la -rpath /home/keivan/neuron/nrn/nrn/i686/lib nrnmenu.lo shape.lo classreg.lo rotate3d.lo datapath.lo symdir.lo spaceplt.lo shapeplt.lo ppshape.lo secbrows.lo ndatclas.lo impedanc.lo savstate.lo hocmech.lo ocjump.lo vrecord.lo cvodestb.lo occvode.lo cvodeobj.lo cvtrset.lo tqueue.lo netcvode.lo singlech.lo nrndaspk.lo glinerec.lo cxprop.lo ocbbs.lo bbs.lo bbslocal.lo bbslsrv.lo bbsrcli.lo bbsdirect.lo bbslsrv2.lo bbssrv.lo linmod.lo linmod1.lo cachevec.lo kschan.lo kssingle.lo nonlinz.lo finithnd.lo nrnste.lo nrnrtime.lo nvector_nrnthread.lo nrnpy.lo nvector_nrnthread_ld.lo nvector_nrnserial_ld.lo  bgpmeminfo.lo netpar.lo partrans.lo splitcell.lo multisplit.lo nrndae.lo matrixmap.lo geometry3d.lo
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared libraries
libtool: link: ar cru .libs/libnrniv.a  nrnmenu.o shape.o classreg.o rotate3d.o datapath.o symdir.o spaceplt.o shapeplt.o ppshape.o secbrows.o ndatclas.o impedanc.o savstate.o hocmech.o ocjump.o vrecord.o cvodestb.o occvode.o cvodeobj.o cvtrset.o tqueue.o netcvode.o singlech.o nrndaspk.o glinerec.o cxprop.o ocbbs.o bbs.o bbslocal.o bbslsrv.o bbsrcli.o bbsdirect.o bbslsrv2.o bbssrv.o linmod.o linmod1.o cachevec.o kschan.o kssingle.o nonlinz.o finithnd.o nrnste.o nrnrtime.o nvector_nrnthread.o nrnpy.o nvector_nrnthread_ld.o nvector_nrnserial_ld.o bgpmeminfo.o netpar.o partrans.o splitcell.o multisplit.o nrndae.o matrixmap.o geometry3d.o
libtool: link: ranlib .libs/libnrniv.a
libtool: link: ( cd ".libs" && rm -f "libnrniv.la" && ln -s "../libnrniv.la" "libnrniv.la" )
/tmp/ccprq5N4.o: In function `Z20hoc_dos2cygdrivepathPKci':
/home/keivan/neuron/nrn/nrn/src/nrniv/../../src/mswin/extra/d2upath.c:23: undefined reference to `__assert_func'
collect2: error: ld returned 1 exit status
Makefile:973: recipe for target 'mos2nrn.exe' failed
make[3]: *** [mos2nrn.exe] Error 1
make[3]: *** Waiting for unfinished jobs....
/tmp/ccdNT5et.o: In function `Z20hoc_dos2cygdrivepathPKci':
/home/keivan/neuron/nrn/nrn/src/nrniv/../../src/mswin/extra/d2upath.c:23: undefined reference to `__assert_func'
collect2: error: ld returned 1 exit status
Makefile:980: recipe for target 'neuron.exe' failed
make[3]: *** [neuron.exe] Error 1
make[3]: Leaving directory '/home/keivan/neuron/nrn/nrn/src/nrniv'
Makefile:426: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/keivan/neuron/nrn/nrn/src'
Makefile:559: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/keivan/neuron/nrn/nrn'
Makefile:416: recipe for target 'all' failed
make: *** [all] Error 2
It seems there is no change in the error.
I hope you don't think that I am spamming. I want to give you my feedback but I am not sure you need it.

hines
Site Admin
Posts: 1510
Joined: Wed May 18, 2005 3:32 pm

Re: nrniv.dll missing after build with cygwin under 64 bit w

Post by hines » Mon Feb 03, 2014 5:06 pm

because of the parallel make the output is interleaved and therefore a bit confusing to interpret. can you do another make and send the lines that are in the neighborhood of the error.
We might as well take this to email. You can send to michael.hines@yale.edu

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