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- dan ~/pkgbuilds/neuron $ makepkg -s
- ==> Making package: neuron 7.4-1 (Thu Jun 9 23:17:04 CDT 2016)
- ==> Checking runtime dependencies...
- ==> Checking buildtime dependencies...
- ==> Retrieving sources...
- -> Found nrn-7.4.tar.gz
- ==> Validating source files with md5sums...
- nrn-7.4.tar.gz ... Passed
- ==> Extracting sources...
- -> Extracting nrn-7.4.tar.gz with bsdtar
- ==> Removing existing $pkgdir/ directory...
- ==> Starting build()...
- 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 whether make supports nested variables... yes
- checking build system type... x86_64-unknown-linux-gnu
- checking host system type... x86_64-unknown-linux-gnu
- CYGWIN=no
- MINGW=no
- checking for style of include used by make... GNU
- checking for g++... g++
- checking whether the C++ compiler works... yes
- checking for C++ compiler default output file name... a.out
- checking for suffix of executables...
- 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 whether gcc understands -c and -o together... yes
- 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 cos in -lm... yes
- Python binary found (/home/dan/.pyenv/shims/python)
- checking nrnpython configuration... get_python_version() '3.5'
- sys.version_info[0] '3'
- get_python_inc(0) '/usr/include/python3.5m'
- get_config_var('LIBS') '-lpthread -ldl -lutil'
- get_config_var('LIBRARY') 'libpython3.5m.a'
- get_config_var('LIBDIR') '/usr/lib'
- get_config_var('LIBS') '-lpthread -ldl -lutil'
- checking if python include files and libraries work... yes
- checking for python... python
- checking for cython... no
- checking for cython... cython
- checking for mpicc... mpicc
- checking for MPI_Init... yes
- checking for mpi.h... yes
- checking for mpic++... mpic++
- checking for mpi.h... yes
- 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 mpicc... /usr/lib/hardening-wrapper/bin/ld
- checking if the linker (/usr/lib/hardening-wrapper/bin/ld) 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... 1572864
- checking whether the shell understands some XSI constructs... yes
- checking whether the shell understands "+="... yes
- checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
- checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
- checking for /usr/lib/hardening-wrapper/bin/ld option to reload object files... -r
- checking for objdump... objdump
- checking how to recognize dependent libraries... pass_all
- checking for dlltool... no
- checking how to associate runtime and link libraries... printf %s\n
- checking for ar... ar
- checking for archiver @FILE support... @
- checking for strip... strip
- checking for ranlib... ranlib
- checking command to parse /usr/bin/nm -B output from mpicc 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 mpicc supports -fno-rtti -fno-exceptions... no
- checking for mpicc option to produce PIC... -fPIC -DPIC
- checking if mpicc PIC flag -fPIC -DPIC works... yes
- checking if mpicc static flag -static works... no
- checking if mpicc supports -c -o file.o... yes
- checking if mpicc supports -c -o file.o... (cached) yes
- checking whether the mpicc linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) supports shared libraries... yes
- checking whether -lc should be explicitly linked in... no
- checking dynamic linker characteristics... GNU/Linux ld.so
- checking how to hardcode library paths into programs... immediate
- checking for shl_load... no
- checking for shl_load in -ldld... no
- checking for dlopen... no
- checking for dlopen in -ldl... yes
- 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... mpic++ -E
- checking for ld used by mpic++... /usr/lib/hardening-wrapper/bin/ld -m elf_x86_64
- checking if the linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) is GNU ld... yes
- checking whether the mpic++ linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) supports shared libraries... yes
- checking for mpic++ option to produce PIC... -fPIC -DPIC
- checking if mpic++ PIC flag -fPIC -DPIC works... yes
- checking if mpic++ static flag -static works... no
- checking if mpic++ supports -c -o file.o... yes
- checking if mpic++ supports -c -o file.o... (cached) yes
- checking whether the mpic++ linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) supports shared libraries... yes
- checking dynamic linker characteristics... (cached) GNU/Linux ld.so
- checking how to hardcode library paths into programs... immediate
- configure: Use the NRNMECH_DLL_STYLE for "special"
- checking for tgetent in -lncurses... yes
- checking which library has the termcap functions... using libncurses
- checking checking compilation with -lreadline... ok
- Do not compile neosim specific code.
- Not building the nrnjava interface
- checking for X... libraries , headers
- checking for gethostbyname... yes
- checking for connect... yes
- checking for remove... yes
- checking for shmat... yes
- checking for IceConnectionNumber in -lICE... yes
- 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
- checking for fcntl.h... yes
- checking limits.h usability... yes
- checking limits.h presence... yes
- checking for limits.h... yes
- checking malloc.h usability... yes
- checking malloc.h presence... yes
- checking for malloc.h... yes
- checking sgtty.h usability... yes
- checking sgtty.h presence... yes
- checking for sgtty.h... yes
- checking for strings.h... (cached) yes
- checking sys/file.h usability... yes
- checking sys/file.h presence... yes
- checking for sys/file.h... yes
- checking sys/ioctl.h usability... yes
- checking sys/ioctl.h presence... yes
- checking for sys/ioctl.h... yes
- 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
- checking for varargs.h... no
- checking stropts.h usability... yes
- checking stropts.h presence... yes
- checking for stropts.h... yes
- 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
- checking for locale.h... yes
- checking fenv.h usability... yes
- checking fenv.h presence... yes
- checking for fenv.h... yes
- 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=mpicc
- checking float.h usability... yes
- checking float.h presence... yes
- checking for float.h... yes
- checking math.h usability... yes
- checking math.h presence... yes
- checking for math.h... yes
- 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 for int64_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... yes
- 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 mpic++ accepts -g... (cached) yes
- checking dependency style of mpic++... (cached) gcc3
- checking _G_config.h usability... yes
- checking _G_config.h presence... yes
- checking for _G_config.h... yes
- checking whether the compiler implements namespaces... yes
- checking whether the compiler has stringstream... yes
- Not compiling with interviews.
- Building nrniv only with classes that do not depend on InterViews.
- The signal function does not need a cast for the handler
- 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 = 1
- checking that generated files are newer than configure... done
- configure: creating ./config.status
- config.status: creating Makefile
- config.status: creating src/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/EnvVarUpdate.nsh
- 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 share/lib/python/neuron/rxd/geometry3d/Makefile
- config.status: creating share/lib/python/neuron/Makefile
- config.status: creating share/lib/python/neuron/rxd/Makefile
- config.status: creating src/nrnpython/setup.py
- RefactoringTool: Skipping optional fixer: buffer
- RefactoringTool: Skipping optional fixer: idioms
- RefactoringTool: Skipping optional fixer: set_literal
- RefactoringTool: Skipping optional fixer: ws_comma
- RefactoringTool: Refactored src/nrnpython/setup.py
- --- src/nrnpython/setup.py (original)
- +++ src/nrnpython/setup.py (refactored)
- @@ -24,10 +24,10 @@
- nrn_srcdir = '../../' + nrn_srcdir
- if nrnpython_pyver!=get_python_version():
- - print "Error:"
- - print "NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver
- - print "Python presently executing setup.py: "+sys.executable+" "+ get_python_version()
- - print "These do not match, and they should!"
- + print("Error:")
- + print("NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver)
- + print("Python presently executing setup.py: "+sys.executable+" "+ get_python_version())
- + print("These do not match, and they should!")
- sys.exit(1)
- @@ -94,7 +94,7 @@
- # specify that the data_files paths are relative to same place as python files
- # from http://stackoverflow.com/questions/1612733/including-non-python-files-with-setup-py
- from distutils.command.install import INSTALL_SCHEMES
- -for scheme in INSTALL_SCHEMES.values():
- +for scheme in list(INSTALL_SCHEMES.values()):
- scheme['data'] = scheme['purelib']
- ext_modules = [hoc_module]
- RefactoringTool: Files that were modified:
- RefactoringTool: src/nrnpython/setup.py
- RefactoringTool: Skipping optional fixer: buffer
- RefactoringTool: Skipping optional fixer: idioms
- RefactoringTool: Skipping optional fixer: set_literal
- RefactoringTool: Skipping optional fixer: ws_comma
- RefactoringTool: No changes to share/lib/python/neuron/rxd/geometry3d/setup.py
- RefactoringTool: Files that need to be modified:
- RefactoringTool: share/lib/python/neuron/rxd/geometry3d/setup.py
- config.status: creating share/lib/python/neuron/rxd/geometry3d/setup.py
- RefactoringTool: Skipping optional fixer: buffer
- RefactoringTool: Skipping optional fixer: idioms
- RefactoringTool: Skipping optional fixer: set_literal
- RefactoringTool: Skipping optional fixer: ws_comma
- RefactoringTool: Refactored src/nrnpython/setup.py
- --- src/nrnpython/setup.py (original)
- +++ src/nrnpython/setup.py (refactored)
- @@ -25,8 +25,8 @@
- if nrnpython_pyver!=get_python_version():
- print("Error:")
- - print("NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver)
- - print("Python presently executing setup.py: "+sys.executable+" "+ get_python_version())
- + print(("NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver))
- + print(("Python presently executing setup.py: "+sys.executable+" "+ get_python_version()))
- print("These do not match, and they should!")
- sys.exit(1)
- RefactoringTool: Files that were modified:
- RefactoringTool: src/nrnpython/setup.py
- RefactoringTool: Skipping optional fixer: buffer
- RefactoringTool: Skipping optional fixer: idioms
- RefactoringTool: Skipping optional fixer: set_literal
- RefactoringTool: Skipping optional fixer: ws_comma
- RefactoringTool: No changes to share/lib/python/neuron/rxd/geometry3d/setup.py
- RefactoringTool: Files that need to be modified:
- RefactoringTool: share/lib/python/neuron/rxd/geometry3d/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
- make all-recursive
- make[1]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4'
- Making all in src
- make[2]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src'
- Making all in memacs
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/memacs'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/memacs'
- Making all in modlunit
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/modlunit'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/modlunit'
- Making all in nmodl
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nmodl'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nmodl'
- Making all in sparse
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/sparse'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/sparse'
- Making all in sparse13
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/sparse13'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/sparse13'
- Making all in scopmath
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/scopmath'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/scopmath'
- Making all in Random123
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/Random123'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/Random123'
- Making all in nrnmpi
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnmpi'
- make[3]: Nothing to be done for 'all'.
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnmpi'
- Making all in oc
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/oc'
- make all-am
- make[4]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/oc'
- make[4]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/oc'
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/oc'
- Making all in nrnoc
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnoc'
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./hh )
- Translating ./hh.mod into ./hh.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./hh.c > hh.tmp
- mv hh.tmp ./hh.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./feature )
- Translating ./feature.mod into ./feature.c
- Notice: VERBATIM blocks are not thread safe
- sed "s/_reg()/_reg_()/" ./feature.c > feature.tmp
- mv feature.tmp ./feature.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./passive )
- Translating ./passive.mod into ./passive.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./passive.c > passive.tmp
- mv passive.tmp ./passive.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./stim )
- Translating ./stim.mod into ./stim.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./stim.c > stim.tmp
- mv stim.tmp ./stim.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./syn )
- Translating ./syn.mod into ./syn.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./syn.c > syn.tmp
- mv syn.tmp ./syn.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./vclmp )
- Translating ./vclmp.mod into ./vclmp.c
- Notice: VERBATIM blocks are not thread safe
- Notice: LINEAR is not thread safe.
- sed "s/_reg()/_reg_()/" ./vclmp.c > vclmp.tmp
- mv vclmp.tmp ./vclmp.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./apcount )
- Translating ./apcount.mod into ./apcount.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./apcount.c > apcount.tmp
- mv apcount.tmp ./apcount.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./svclmp )
- Translating ./svclmp.mod into ./svclmp.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./svclmp.c > svclmp.tmp
- mv svclmp.tmp ./svclmp.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./oclmp )
- Translating ./oclmp.mod into ./oclmp.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./oclmp.c > oclmp.tmp
- mv oclmp.tmp ./oclmp.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./xmech )
- Translating ./xmech.mod into ./xmech.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./xmech.c > xmech.tmp
- mv xmech.tmp ./xmech.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./netstim )
- Translating ./netstim.mod into ./netstim.c
- Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
- only affects and is affected by discrete events. As such it is not
- located in a section and is not associated with an integrator
- Thread Safe
- sed "s/_reg()/_reg_()/" ./netstim.c > netstim.tmp
- mv netstim.tmp ./netstim.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./intfire1 )
- Translating ./intfire1.mod into ./intfire1.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./intfire1.c > intfire1.tmp
- mv intfire1.tmp ./intfire1.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./intfire2 )
- Translating ./intfire2.mod into ./intfire2.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./intfire2.c > intfire2.tmp
- mv intfire2.tmp ./intfire2.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./intfire4 )
- Translating ./intfire4.mod into ./intfire4.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./intfire4.c > intfire4.tmp
- mv intfire4.tmp ./intfire4.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./expsyn )
- Translating ./expsyn.mod into ./expsyn.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./expsyn.c > expsyn.tmp
- mv expsyn.tmp ./expsyn.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./exp2syn )
- Translating ./exp2syn.mod into ./exp2syn.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./exp2syn.c > exp2syn.tmp
- mv exp2syn.tmp ./exp2syn.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./ppmark )
- Translating ./ppmark.mod into ./ppmark.c
- Thread Safe
- sed "s/_reg()/_reg_()/" ./ppmark.c > ppmark.tmp
- mv ppmark.tmp ./ppmark.c
- (MODLUNIT=../../share/lib/nrnunits.lib ; \
- export MODLUNIT ; ../nmodl/nocmodl ./pattern )
- Translating ./pattern.mod into ./pattern.c
- Notice: Use of POINTER is not thread safe.
- Notice: VERBATIM blocks are not thread safe
- Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
- only affects and is affected by discrete events. As such it is not
- located in a section and is not associated with an integrator
- sed "s/_reg()/_reg_()/" ./pattern.c > pattern.tmp
- mv pattern.tmp ./pattern.c
- if test -d ../../.hg ; then \
- sh ../../hg2nrnversion_h.sh ../.. > ./nrnversion.h.tmp ; \
- if cmp ./nrnversion.h.tmp ./nrnversion.h ; then \
- echo "nrnversion.h not changed" ; \
- rm ./nrnversion.h.tmp ; \
- else \
- mv ./nrnversion.h.tmp ./nrnversion.h ; \
- echo "updated nrnversion.h" ; \
- fi \
- else \
- if test -d ../../.svn && svnversion ../.. ; then \
- if test "`svnversion ../..`" != "`sed -n 's/.*SVN_CHANGESET.*(\([^)]*\).*/\1/p' ./nrnversion.h`" ; then \
- sh ../../svn2nrn_h.sh ../.. > ./nrnversion.h.tmp; \
- if test -s ./nrnversion.h.tmp ; then \
- mv ./nrnversion.h.tmp ./nrnversion.h ; \
- fi ; \
- echo "updated nrnversion.h" ; \
- else \
- echo "nrnversion.h not changed" ; \
- fi \
- fi \
- fi
- make all-am
- make[4]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnoc'
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT hh.lo -MD -MP -MF .deps/hh.Tpo -c -o hh.lo hh.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT hh.lo -MD -MP -MF .deps/hh.Tpo -c hh.c -fPIC -DPIC -o .libs/hh.o
- mv -f .deps/hh.Tpo .deps/hh.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT feature.lo -MD -MP -MF .deps/feature.Tpo -c -o feature.lo feature.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT feature.lo -MD -MP -MF .deps/feature.Tpo -c feature.c -fPIC -DPIC -o .libs/feature.o
- mv -f .deps/feature.Tpo .deps/feature.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT passive.lo -MD -MP -MF .deps/passive.Tpo -c -o passive.lo passive.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT passive.lo -MD -MP -MF .deps/passive.Tpo -c passive.c -fPIC -DPIC -o .libs/passive.o
- mv -f .deps/passive.Tpo .deps/passive.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT stim.lo -MD -MP -MF .deps/stim.Tpo -c -o stim.lo stim.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT stim.lo -MD -MP -MF .deps/stim.Tpo -c stim.c -fPIC -DPIC -o .libs/stim.o
- mv -f .deps/stim.Tpo .deps/stim.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT syn.lo -MD -MP -MF .deps/syn.Tpo -c -o syn.lo syn.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT syn.lo -MD -MP -MF .deps/syn.Tpo -c syn.c -fPIC -DPIC -o .libs/syn.o
- mv -f .deps/syn.Tpo .deps/syn.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT vclmp.lo -MD -MP -MF .deps/vclmp.Tpo -c -o vclmp.lo vclmp.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT vclmp.lo -MD -MP -MF .deps/vclmp.Tpo -c vclmp.c -fPIC -DPIC -o .libs/vclmp.o
- mv -f .deps/vclmp.Tpo .deps/vclmp.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT apcount.lo -MD -MP -MF .deps/apcount.Tpo -c -o apcount.lo apcount.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT apcount.lo -MD -MP -MF .deps/apcount.Tpo -c apcount.c -fPIC -DPIC -o .libs/apcount.o
- mv -f .deps/apcount.Tpo .deps/apcount.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT svclmp.lo -MD -MP -MF .deps/svclmp.Tpo -c -o svclmp.lo svclmp.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT svclmp.lo -MD -MP -MF .deps/svclmp.Tpo -c svclmp.c -fPIC -DPIC -o .libs/svclmp.o
- mv -f .deps/svclmp.Tpo .deps/svclmp.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT oclmp.lo -MD -MP -MF .deps/oclmp.Tpo -c -o oclmp.lo oclmp.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT oclmp.lo -MD -MP -MF .deps/oclmp.Tpo -c oclmp.c -fPIC -DPIC -o .libs/oclmp.o
- mv -f .deps/oclmp.Tpo .deps/oclmp.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT xmech.lo -MD -MP -MF .deps/xmech.Tpo -c -o xmech.lo xmech.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT xmech.lo -MD -MP -MF .deps/xmech.Tpo -c xmech.c -fPIC -DPIC -o .libs/xmech.o
- mv -f .deps/xmech.Tpo .deps/xmech.Plo
- if test -d ../../.hg ; then \
- sh ../../hg2nrnversion_h.sh ../.. > ./nrnversion.h.tmp ; \
- if cmp ./nrnversion.h.tmp ./nrnversion.h ; then \
- echo "nrnversion.h not changed" ; \
- rm ./nrnversion.h.tmp ; \
- else \
- mv ./nrnversion.h.tmp ./nrnversion.h ; \
- echo "updated nrnversion.h" ; \
- fi \
- else \
- if test -d ../../.svn && svnversion ../.. ; then \
- if test "`svnversion ../..`" != "`sed -n 's/.*SVN_CHANGESET.*(\([^)]*\).*/\1/p' ./nrnversion.h`" ; then \
- sh ../../svn2nrn_h.sh ../.. > ./nrnversion.h.tmp; \
- if test -s ./nrnversion.h.tmp ; then \
- mv ./nrnversion.h.tmp ./nrnversion.h ; \
- fi ; \
- echo "updated nrnversion.h" ; \
- else \
- echo "nrnversion.h not changed" ; \
- fi \
- fi \
- fi
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT netstim.lo -MD -MP -MF .deps/netstim.Tpo -c -o netstim.lo netstim.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT netstim.lo -MD -MP -MF .deps/netstim.Tpo -c netstim.c -fPIC -DPIC -o .libs/netstim.o
- mv -f .deps/netstim.Tpo .deps/netstim.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT intfire1.lo -MD -MP -MF .deps/intfire1.Tpo -c -o intfire1.lo intfire1.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT intfire1.lo -MD -MP -MF .deps/intfire1.Tpo -c intfire1.c -fPIC -DPIC -o .libs/intfire1.o
- mv -f .deps/intfire1.Tpo .deps/intfire1.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT intfire2.lo -MD -MP -MF .deps/intfire2.Tpo -c -o intfire2.lo intfire2.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT intfire2.lo -MD -MP -MF .deps/intfire2.Tpo -c intfire2.c -fPIC -DPIC -o .libs/intfire2.o
- mv -f .deps/intfire2.Tpo .deps/intfire2.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT intfire4.lo -MD -MP -MF .deps/intfire4.Tpo -c -o intfire4.lo intfire4.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT intfire4.lo -MD -MP -MF .deps/intfire4.Tpo -c intfire4.c -fPIC -DPIC -o .libs/intfire4.o
- mv -f .deps/intfire4.Tpo .deps/intfire4.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT expsyn.lo -MD -MP -MF .deps/expsyn.Tpo -c -o expsyn.lo expsyn.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT expsyn.lo -MD -MP -MF .deps/expsyn.Tpo -c expsyn.c -fPIC -DPIC -o .libs/expsyn.o
- mv -f .deps/expsyn.Tpo .deps/expsyn.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT exp2syn.lo -MD -MP -MF .deps/exp2syn.Tpo -c -o exp2syn.lo exp2syn.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT exp2syn.lo -MD -MP -MF .deps/exp2syn.Tpo -c exp2syn.c -fPIC -DPIC -o .libs/exp2syn.o
- mv -f .deps/exp2syn.Tpo .deps/exp2syn.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT ppmark.lo -MD -MP -MF .deps/ppmark.Tpo -c -o ppmark.lo ppmark.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT ppmark.lo -MD -MP -MF .deps/ppmark.Tpo -c ppmark.c -fPIC -DPIC -o .libs/ppmark.o
- mv -f .deps/ppmark.Tpo .deps/ppmark.Plo
- /bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT pattern.lo -MD -MP -MF .deps/pattern.Tpo -c -o pattern.lo pattern.c
- libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT pattern.lo -MD -MP -MF .deps/pattern.Tpo -c pattern.c -fPIC -DPIC -o .libs/pattern.o
- mv -f .deps/pattern.Tpo .deps/pattern.Plo
- /bin/sh ../../libtool --tag=CC --mode=link mpicc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -Wl,-O1,--sort-common,--as-needed,-z,relro -o libnrnoc.la -rpath /usr/lib cabcode.lo capac.lo clamp.lo eion.lo extcelln.lo fadvance.lo fstim.lo hh.lo feature.lo init.lo nrnnemo.lo passive.lo passive0.lo point.lo psection.lo solve.lo synapse.lo treeset.lo hoc_init.lo code.lo hoc_oop.lo stim.lo syn.lo vclmp.lo seclist.lo method3.lo apcount.lo hocprax.lo svclmp.lo oclmp.lo xmech.lo secref.lo ldifus.lo hocusr.lo nrnversion.lo netstim.lo intfire1.lo intfire2.lo intfire4.lo expsyn.lo exp2syn.lo ppmark.lo pattern.lo nrntimeout.lo -lm -ldl
- libtool: link: rm -fr .libs/libnrnoc.la .libs/libnrnoc.lai .libs/libnrnoc.so .libs/libnrnoc.so.0 .libs/libnrnoc.so.0.0.0
- libtool: link: mpicc -shared -fPIC -DPIC .libs/cabcode.o .libs/capac.o .libs/clamp.o .libs/eion.o .libs/extcelln.o .libs/fadvance.o .libs/fstim.o .libs/hh.o .libs/feature.o .libs/init.o .libs/nrnnemo.o .libs/passive.o .libs/passive0.o .libs/point.o .libs/psection.o .libs/solve.o .libs/synapse.o .libs/treeset.o .libs/hoc_init.o .libs/code.o .libs/hoc_oop.o .libs/stim.o .libs/syn.o .libs/vclmp.o .libs/seclist.o .libs/method3.o .libs/apcount.o .libs/hocprax.o .libs/svclmp.o .libs/oclmp.o .libs/xmech.o .libs/secref.o .libs/ldifus.o .libs/hocusr.o .libs/nrnversion.o .libs/netstim.o .libs/intfire1.o .libs/intfire2.o .libs/intfire4.o .libs/expsyn.o .libs/exp2syn.o .libs/ppmark.o .libs/pattern.o .libs/nrntimeout.o -lm -ldl -march=x86-64 -mtune=generic -O2 -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-soname -Wl,libnrnoc.so.0 -o .libs/libnrnoc.so.0.0.0
- libtool: link: (cd ".libs" && rm -f "libnrnoc.so.0" && ln -s "libnrnoc.so.0.0.0" "libnrnoc.so.0")
- libtool: link: (cd ".libs" && rm -f "libnrnoc.so" && ln -s "libnrnoc.so.0.0.0" "libnrnoc.so")
- libtool: link: ( cd ".libs" && rm -f "libnrnoc.la" && ln -s "../libnrnoc.la" "libnrnoc.la" )
- /bin/sh ../../libtool --tag=CC --mode=link mpicc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -Wl,-O1,--sort-common,--as-needed,-z,relro -o nrnoc ocmain.o nrnnoiv.o ocnoiv.o cprop.o ../oc/modlreg.o libnrnoc.la ../oc/liboc.la ../memacs/libmemacs.la ../scopmath/libscopmath.la ../sparse13/libsparse13.la ../nrnmpi/libnrnmpi.la -lreadline -lncurses -lm -ldl
- libtool: link: mpicc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -o .libs/nrnoc ocmain.o nrnnoiv.o ocnoiv.o cprop.o ../oc/modlreg.o ./.libs/libnrnoc.so ../oc/.libs/liboc.so ../memacs/.libs/libmemacs.so ../scopmath/.libs/libscopmath.so ../sparse13/.libs/libsparse13.so ../nrnmpi/.libs/libnrnmpi.so -lreadline -lncurses -lm -ldl
- make[4]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnoc'
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnoc'
- Making all in ivos
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos'
- make all-recursive
- make[4]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos'
- Making all in InterViews
- make[5]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos/InterViews'
- make[5]: Nothing to be done for 'all'.
- make[5]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos/InterViews'
- Making all in OS
- make[5]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos/OS'
- make[5]: Nothing to be done for 'all'.
- make[5]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos/OS'
- make[5]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos'
- make[5]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos'
- make[4]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos'
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/ivos'
- Making all in nrnpython
- make[3]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnpython'
- if test inithoc.cpp -ot ../../src/nrnpython/inithoc.cpp ; then \
- cp ../../src/nrnpython/inithoc.cpp inithoc.cpp ; \
- fi
- make all-am
- make[4]: Entering directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnpython'
- /bin/sh ../../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -I. -I../../src/nrniv -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/nrnmpi -I../../src/gnu -I/usr/include/python3.5m -I../../src/ivos -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT nrnpy_hoc.lo -MD -MP -MF .deps/nrnpy_hoc.Tpo -c -o nrnpy_hoc.lo nrnpy_hoc.cpp
- libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -I. -I../../src/nrniv -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/nrnmpi -I../../src/gnu -I/usr/include/python3.5m -I../../src/ivos -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT nrnpy_hoc.lo -MD -MP -MF .deps/nrnpy_hoc.Tpo -c nrnpy_hoc.cpp -fPIC -DPIC -o .libs/nrnpy_hoc.o
- In file included from ../../src/gnu/d_vec.h:26:0,
- from ../../src/gnu/d_avec.h:31,
- from ../../src/ivoc/ivocvect.h:5,
- from nrnpy_hoc.cpp:6:
- ../../src/gnu/neuron_gnu_builtin.h:77:22: error: 'double abs(double)' conflicts with a previous declaration
- double abs(double arg);
- ^
- In file included from /usr/include/c++/6.1.1/math.h:36:0,
- from /usr/include/python3.5m/pyport.h:328,
- from /usr/include/python3.5m/Python.h:50,
- from ./nrnpython.h:15,
- from nrnpy_hoc.cpp:1:
- /usr/include/c++/6.1.1/cmath:85:3: note: previous declaration 'constexpr double std::abs(double)'
- abs(double __x)
- ^~~
- In file included from ../../src/gnu/d_vec.h:26:0,
- from ../../src/gnu/d_avec.h:31,
- from ../../src/ivoc/ivocvect.h:5,
- from nrnpy_hoc.cpp:6:
- ../../src/gnu/neuron_gnu_builtin.h:78:20: error: 'float abs(float)' conflicts with a previous declaration
- float abs(float arg);
- ^
- In file included from /usr/include/c++/6.1.1/math.h:36:0,
- from /usr/include/python3.5m/pyport.h:328,
- from /usr/include/python3.5m/Python.h:50,
- from ./nrnpython.h:15,
- from nrnpy_hoc.cpp:1:
- /usr/include/c++/6.1.1/cmath:91:3: note: previous declaration 'constexpr float std::abs(float)'
- abs(float __x)
- ^~~
- In file included from ../../src/gnu/d_vec.h:26:0,
- from ../../src/gnu/d_avec.h:31,
- from ../../src/ivoc/ivocvect.h:5,
- from nrnpy_hoc.cpp:6:
- ../../src/gnu/neuron_gnu_builtin.h:80:18: error: 'long int abs(long int)' conflicts with a previous declaration
- long abs(long arg);
- ^
- In file included from /usr/include/c++/6.1.1/ext/string_conversions.h:41:0,
- from /usr/include/c++/6.1.1/bits/basic_string.h:5402,
- from /usr/include/c++/6.1.1/string:52,
- from /usr/include/c++/6.1.1/bits/locale_classes.h:40,
- from /usr/include/c++/6.1.1/bits/ios_base.h:41,
- from /usr/include/c++/6.1.1/ios:42,
- from /usr/include/c++/6.1.1/ostream:38,
- from /usr/include/c++/6.1.1/iostream:39,
- from ../../src/ivos/ivstrm.h:23,
- from ../../src/ivos/ivstream.h:11,
- from ./../../nrnconf.h:362,
- from ./nrnpython.h:10,
- from nrnpy_hoc.cpp:1:
- /usr/include/c++/6.1.1/cstdlib:172:3: note: previous declaration 'long int std::abs(long int)'
- abs(long __i) { return __builtin_labs(__i); }
- ^~~
- Makefile:567: recipe for target 'nrnpy_hoc.lo' failed
- make[4]: *** [nrnpy_hoc.lo] Error 1
- make[4]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnpython'
- Makefile:454: recipe for target 'all' failed
- make[3]: *** [all] Error 2
- make[3]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src/nrnpython'
- Makefile:492: recipe for target 'all-recursive' failed
- make[2]: *** [all-recursive] Error 1
- make[2]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4/src'
- Makefile:628: recipe for target 'all-recursive' failed
- make[1]: *** [all-recursive] Error 1
- make[1]: Leaving directory '/home/dan/pkgbuilds/neuron/src/nrn-7.4'
- Makefile:485: recipe for target 'all' failed
- make: *** [all] Error 2
- ==> ERROR: A failure occurred in build().
- Aborting...
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