Trouble with make command

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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maxwellphenderson
Posts: 22
Joined: Mon Mar 07, 2011 12:17 am

Trouble with make command

Post by maxwellphenderson » Wed Mar 09, 2011 2:17 am

Currently, I am trying to install NEURON using python as an interpreter. I have successfully installed OS X Developer Tools for my Mac and have been going through the steps for installing from source using both:

http://www.davison.webfactional.com/not ... on-python/

and

http://www.neuron.yale.edu/neuron/downl ... ilestd_osx

I am currently running into issues when I run the make command in these steps:

Code: Select all

tar xzf iv-mm.tar.gz
  cd iv-mm
  ./configure --prefix=$IDIR/iv --enable-carbon # if this fails, you probably don't have the developer tools installed
  make
  make install
Here is the errors I am receiving:

Code: Select all

c-76-124-119-109:iv-17 maxwellhenderson$ make
Making all in src
Making all in lib
 g++ -DHAVE_CONFIG_H -I. -I. -I../include -g -O2 -DMAC=1 -Dcarbon=1 -DSYSV=1 -c IV-Mac/canvas.cpp  -fno-common -DPIC -o IV-Mac/.libs/canvas.o
In file included from IV-Mac/canvas.cpp:59:
../include/IV-Mac/window.h: In member function 'void MACwindow::setport()':
../include/IV-Mac/window.h:112: error: 'GetWindowPort' was not declared in this scope
../include/IV-Mac/window.h:112: error: 'SetPort' was not declared in this scope
../include/IV-Mac/window.h: In static member function 'static ivWindowRep* ivWindowRep::rc(OpaqueWindowPtr*)':
../include/IV-Mac/window.h:192: error: 'GetWRefCon' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::beginPaint()':
IV-Mac/canvas.cpp:331: error: 'ClipRect' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual ivCoord MACcanvas::width() const':
IV-Mac/canvas.cpp:405: error: 'GetWindowPort' was not declared in this scope
IV-Mac/canvas.cpp:405: error: 'GetPortBounds' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual ivCoord MACcanvas::height() const':
IV-Mac/canvas.cpp:419: error: 'GetWindowPort' was not declared in this scope
IV-Mac/canvas.cpp:419: error: 'GetPortBounds' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual ivPixelCoord MACcanvas::pwidth() const':
IV-Mac/canvas.cpp:433: error: 'GetWindowPort' was not declared in this scope
IV-Mac/canvas.cpp:433: error: 'GetPortBounds' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual ivPixelCoord MACcanvas::pheight() const':
IV-Mac/canvas.cpp:447: error: 'GetWindowPort' was not declared in this scope
IV-Mac/canvas.cpp:447: error: 'GetPortBounds' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::initClip()':
IV-Mac/canvas.cpp:518: error: 'ClipRect' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::push_clipping(osboolean)':
IV-Mac/canvas.cpp:534: error: 'ClipRect' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::pop_clipping()':
IV-Mac/canvas.cpp:557: error: 'ClipRect' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::clip()':
IV-Mac/canvas.cpp:605: error: 'ClipRect' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::stroke(const ivColor*, const ivBrush*)':
IV-Mac/canvas.cpp:922: error: 'MoveTo' was not declared in this scope
IV-Mac/canvas.cpp:924: error: 'LineTo' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::fill(const ivColor*)':
IV-Mac/canvas.cpp:953: error: 'OpenPoly' was not declared in this scope
IV-Mac/canvas.cpp:955: error: 'MoveTo' was not declared in this scope
IV-Mac/canvas.cpp:957: error: 'LineTo' was not declared in this scope
IV-Mac/canvas.cpp:962: error: 'ClosePoly' was not declared in this scope
IV-Mac/canvas.cpp:963: error: 'PaintPoly' was not declared in this scope
IV-Mac/canvas.cpp:964: error: 'KillPoly' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'void MACcanvas::color(const ivColor*)':
IV-Mac/canvas.cpp:999: error: 'RGBForeColor' was not declared in this scope
IV-Mac/canvas.cpp:1021: error: 'PenMode' was not declared in this scope
IV-Mac/canvas.cpp:1025: error: 'PenMode' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'void MACcanvas::brush(const ivBrush*)':
IV-Mac/canvas.cpp:1052: error: 'PenSize' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::flush()':
IV-Mac/canvas.cpp:1173: error: 'TextFont' was not declared in this scope
IV-Mac/canvas.cpp:1174: error: 'TextFace' was not declared in this scope
IV-Mac/canvas.cpp:1175: error: 'TextSize' was not declared in this scope
IV-Mac/canvas.cpp:1176: error: 'TextMode' was not declared in this scope
IV-Mac/canvas.cpp:1178: error: 'MoveTo' was not declared in this scope
IV-Mac/canvas.cpp:1179: error: 'DrawText' was not declared in this scope
IV-Mac/canvas.cpp: In member function 'virtual void MACcanvas::image(const ivRaster*, ivCoord, ivCoord)':
IV-Mac/canvas.cpp:1285: error: 'GetGWorld' was not declared in this scope
IV-Mac/canvas.cpp:1288: error: 'GetPortBitMapForCopyBits' was not declared in this scope
IV-Mac/canvas.cpp:1293: error: 'CopyBits' was not declared in this scope
make[2]: *** [IV-Mac/canvas.lo] Error 1
Making all in include
make[2]: Nothing to be done for `all'.
Making all in bin
Making all in idemo
/bin/sh ../../../libtool --mode=link g++ -g -O2 -DMAC=1 -Dcarbon=1 -DSYSV=1 -framework Carbon  -o idemo main.o ../../lib/libIVhines.la  
libtool: link: cannot find the library `../../lib/libIVhines.la' or unhandled argument `../../lib/libIVhines.la'
make[3]: *** [idemo] Error 1
Any help would be greatly appreciated! Thanks!

hines
Site Admin
Posts: 1571
Joined: Wed May 18, 2005 3:32 pm

Re: Trouble with make command

Post by hines » Wed Mar 09, 2011 11:58 am

../include/IV-Mac/window.h:112: error: 'GetWindowPort' was not declared in this scope
Carbon is not available for a 64 bit build of NEURON. You must build using x11 or build
a 32-bit verson of NEURON.

maxwellphenderson
Posts: 22
Joined: Mon Mar 07, 2011 12:17 am

Re: Trouble with make command

Post by maxwellphenderson » Wed Mar 09, 2011 1:55 pm

Oh ok, thank you! If I could pester you with an additional question.... I have MATLAB on my computer, and whenever I run MATLAB, X11 automatically boots up and runs. I copied the same X11 folder into my iv-17 folder in my neuron directory. But, when I run:

Code: Select all

./configure --prefix=$DIR/iv --enable-X11
it seems that it is unable to find X11. This is what i keep getting as ouput (OK until last line):

Code: Select all

checking build system type... i686-apple-darwin10.6.0
checking host system type... i686-apple-darwin10.6.0
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... yes
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 ANSI C... none needed
checking for a sed that does not truncate output... /usr/bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking for /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -E
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm output from gcc object... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking if gcc supports -fno-rtti -fno-exceptions... rm: conftest.dSYM: is a directory
no
checking for gcc option to produce PIC... -fno-common
checking if gcc PIC flag -fno-common works... rm: conftest.dSYM: is a directory
yes
checking if gcc static flag -static works... rm: conftest.dSYM: is a directory
no
checking if gcc supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the gcc linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.6.0 dyld
checking how to hardcode library paths into programs... immediate
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
configure: creating libtool
appending configuration tag "CXX" to libtool
rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
checking for ld used by g++... /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common
checking if g++ PIC flag -fno-common works... rm: conftest.dSYM: is a directory
yes
checking if g++ static flag -static works... rm: conftest.dSYM: is a directory
no
checking if g++ supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.6.0 dyld
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking whether the compiler implements namespaces... yes
checking whether the compiler has stringstream... yes
We are able to run a c++ program that uses streams
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 malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
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 for unistd.h... (cached) yes
checking osfcn.h usability... no
checking osfcn.h presence... no
checking for osfcn.h... no
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking stropts.h usability... no
checking stropts.h presence... no
checking for stropts.h... no
checking sys/conf.h usability... yes
checking sys/conf.h presence... yes
checking for sys/conf.h... yes
checking for X... no
configure: error: cannot find X11
Thanks again!

ted
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Posts: 5509
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Trouble with make command

Post by ted » Fri Mar 11, 2011 8:45 pm

A little clarification would be useful.
whenever I run MATLAB, X11 automatically boots up and runs.
So your Mac has the executable code for X11.
when I run:
./configure --prefix=$DIR/iv --enable-X11
it seems that it is unable to find X11
So your Mac does NOT have the X11 development library.

Executable code and development libraries are two different things. End users who only run applications and never do any software development can get along perfectly fine without development libraries--they only need the executable code for any program they want to run, plus any "helper" programs that may also be required (as is the case for Matlab and X11, for example). But if you want to compile program ABC, and ABC needs the PQR development library, then the PQR development library better be installed on your computer, or you're stuck.

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