Develop Reference

OSX: pyosmium setup error

I'm running a setup Python script for Pyosmium on OSX 10.11, Python version is 2.7:
python setup.py install
running install
running build
running build_py
running build_ext
building 'osmium._osmium' extension
gcc -fno-strict-aliasing -I/Users/stephen/anaconda/include -arch x86_64
-DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include
-I../libosmium/include -I/Users/stephen/anaconda/include/python2.7 -c
lib/osmium.cc -o build/temp.macosx-10.5-x86_64-2.7/lib/osmium.o -std=c++0x
-stdlib=libstdc++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
In file included from lib/osmium.cc:1:
../libosmium/include/osmium/visitor.hpp:36:10: fatal error: 'type_traits' file not found
As far as possible I've most available dependencies using Brew. And added required directories for supporting developments.
Though it's clear I am dealing with a level here that I am not at all familiar with.
My guess at the moment is the compiler that's been called - gcc, should this be Any ideas would be much appreciated!
Thank you,
Stephen.

Pip/easy_install ignoring ARCHFLAGS in SciPy installation?

I'm trying to compile SciPy for both 32-bit and 64-bit architectures, since some of the applications that use the library are only one arch or the other, following advice from a few SO questions. This command has worked for me in a similar build about two months ago, but now it seems that some of the compiled shared libraries are only targeting x86_64:
sudo ARCHFLAGS="-arch i386 -arch x86_64" pip install scipy
I've tried several versions of this command, including setting the environment variables before sudo, including -m32 -m64 in FFlags, using the OSX Command Line Tools, a full Xcode install, using clang instead of the LLVM that comes with OSX following the official SciPy install instructions, easy_install instead of pip and even ./configure'ing separately, etc., but I can't seem to get it to work. Oddly, some of the .so's are building with both architectures, but some are not:
dhcp-10-249-71-202:~ kastman$ file /Library/Python/2.7/site-packages/scipy/optimize/*.so
/Library/Python/2.7/site-packages/scipy/optimize/_cobyla.so: Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/_lbfgsb.so: Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/_minpack.so: Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/_nnls.so: Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/_slsqp.so: Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/_zeros.so: Mach-O universal binary with 2 architectures
/Library/Python/2.7/site-packages/scipy/optimize/_zeros.so (for architecture i386): Mach-O bundle i386
/Library/Python/2.7/site-packages/scipy/optimize/_zeros.so (for architecture x86_64): Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/minpack2.so: Mach-O 64-bit bundle x86_64
/Library/Python/2.7/site-packages/scipy/optimize/moduleTNC.so: Mach-O universal binary with 2 architectures
/Library/Python/2.7/site-packages/scipy/optimize/moduleTNC.so (for architecture i386): Mach-O bundle i386
/Library/Python/2.7/site-packages/scipy/optimize/moduleTNC.so (for architecture x86_64): Mach-O 64-bit bundle x86_64
Looking at the make log, it looks like the args are being passed successfully for both the libraries that seem to work and those that don't:
# Minpack doesn't build fat binaries
/usr/local/bin/gfortran -Wall -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.7-intel-2.7/build/src.macosx-10.7-intel-2.7/scipy/optimize/minpack2/minpack2module.o build/temp.macosx-10.7-intel-2.7/build/src.macosx-10.7-intel-2.7/fortranobject.o build/temp.macosx-10.7-intel-2.7/scipy/optimize/minpack2/dcsrch.o build/temp.macosx-10.7-intel-2.7/scipy/optimize/minpack2/dcstep.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2 -Lbuild/temp.macosx-10.7-intel-2.7 -lgfortran -o build/lib.macosx-10.7-intel-2.7/scipy/optimize/minpack2.so
building 'scipy.optimize._slsqp' extension
compiling C sources
C compiler: clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe
#... but moduleTNC does.
llvm-gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.7-intel-2.7/scipy/optimize/tnc/moduleTNC.o build/temp.macosx-10.7-intel-2.7/scipy/optimize/tnc/tnc.o -Lbuild/temp.macosx-10.7-intel-2.7 -o build/lib.macosx-10.7-intel-2.7/scipy/optimize/moduleTNC.so
building 'scipy.optimize._cobyla' extension
compiling C sources
C compiler: clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe
Is it possible that the difference is the gfortran compiler I'm using? I used brew install gfortran which is supposed to be good according to the SciPy documentation. I would think the important line would be the C compiler: clang line, which appears to be nearly identical, including both -arch's.
The last most detailed build I've tried was:
sudo env ARCHFLAGS="-arch i386 -arch x86_64" ARCH="i386 x86_64" CC="clang" CXX="clang" FFLAGS="-ff2c -m32 -m64" pip install scipy
Does anyone have suggestions about how to further diagnose this?
(OSX 10.7, recent MacBookPro, compiling with gcc from the CLI tools and from Xcode)

Pulling from source and building appears to correctly create fat binaries. I'm not sure if this is a bug that's already been fixed (I didn't see anything on the scipy dev list) or if it has to do with pip/easy_install, but here's what I did to get it to work:
git clone https://github.com/scipy/scipy.git; cd scipy
export ARCHFLAGS='-arch i386 -arch x86_64'
python setup.py config
python setup.py build
sudo python setup.py install
No special CC environment variables, gfortran was from brew install gfortran, and surprisingly it looks like gcc was llvm-gcc.

Installing PIL on OS X Lion: initialization from incompatible pointer type

I want to run python's ndimage to do some image analysis. I have a 64-bit Mac running OSX Lion and Python 2.7. When I tried to run commands from ndimage commands I found out that I need to install PIL.
I downloaded that and unzipped it (for now into the downloads folder, is there a better place to do it?). I run setup.py and get these messages:
running install
running build
running build_py
running build_ext
--- using frameworks at /System/Library/Frameworks
building '_imaging' extension
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -DHAVE_LIBZ -I/System/Library/Frameworks/Tcl.framework/Headers -I/System/Library/Frameworks/Tk.framework/Headers -IlibImaging -I/Library/Frameworks/Python.framework/Versions/2.7/include -I/usr/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _imaging.c -o build/temp.macosx-10.6-intel-2.7/_imaging.o
unable to execute gcc-4.2: No such file or directory
error: command 'gcc-4.2' failed with exit status 1
I read Failed to build PIL on Mac OS X 10.7 Lion and made sure that I have the 32/64 bit version of python 2.7 installed (Mac OS X 64-bit/32-bit x86-64/i386 Installer (2.7.2) for Mac OS X 10.6 and 10.7 ). I also have Xcode installed. Am I doing something stupid here?
Edit 1:
looking further, I have found this gcc-4.2 failed with exit status 1. I've tried entering this when I get the error:
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -DHAVE_LIBZ -I/System/Library/Frameworks/Tcl.framework/Headers -I/System/Library/Frameworks/Tk.framework/Headers -IlibImaging -I/Library/Frameworks/Python.framework/Versions/2.7/include -I/usr/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _imaging.c -o build/temp.macosx-10.6-intel-2.7/_imaging.o
and I get these messages:
_imaging.c:3017: warning: initialization from incompatible pointer type
_imaging.c:3077: warning: initialization from incompatible pointer type
_imaging.c:3017: warning: initialization from incompatible pointer type
_imaging.c:3077: warning: initialization from incompatible pointer type
Edit 2:
I'm not sure if this is the right way to go, but I found a post on installing pil on OSX Leopard and, following its advice, got rid of the -arch i386 part of the command and entered:
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch x86_64 -g -O2 -DNDEBUG -g -O3 -DHAVE_LIBZ -I/System/Library/Frameworks/Tcl.framework/Headers -I/System/Library/Frameworks/Tk.framework/Headers -IlibImaging -I/Library/Frameworks/Python.framework/Versions/2.7/include -I/usr/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _imaging.c -o build/temp.macosx-10.6-intel-2.7/_imaging.o
Now I only get two errors:
_imaging.c:3017: warning: initialization from incompatible pointer type
_imaging.c:3077: warning: initialization from incompatible pointer type
From what I can tell at this point the program poops out and doesn't finish compiling. Can anyone help me take it from here?

https://github.com/kennethreitz/osx-gcc-installer/downloads
Download GCC for lion. It solved all the error: command 'gcc-4.2' failed with exit status 1
problems.

I have had very good success with the MacPorts Python Imaging Library (PIL), Pandas, Numpy and other numerical analysis packages on both Lion and Mountain Lion.
Recently there were some significant upgrades with gcc for integration with the latest numerical Python modules on MacPorts. Looked like a very significant effort. I recommend MacPorts unless you are determined to hash through a native install of PIL on Lion.

I had compiling problems with PIL with Mountain Lion and python 2.7. I used Pillow instead, it's a friendly PIL fork with wider platform support.
regardins your setup questions:
I use macports for python 2.7 and other open source stuff on my mac (libpng, libjpeg, etc for PILLOW)
virtualenv for creating a virtual python environment (venv will be built-in into python 3.3)
I put source code under ~/src (instead Downloads folder)

Installing PIL on MAC OS X LION 10.7.2 with PIP INSTALLER

I am trying to install PIL using PIP installer, and I'm getting this:
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -IlibImaging -I/System/Library/Frameworks/Python.framework/Versions/2.7/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _imaging.c -o build/temp.macosx-10.7-intel-2.7/_imaging.o
unable to execute llvm-gcc-4.2: No such file or directory
error: command 'llvm-gcc-4.2' failed with exit status 1
Any clues what the problem might be ?
I have Mac OS X Lion and LLVM is installed in the XCODE Developer tools... What can be wrong ?

i got the same error.
but additionally need to install the "commandline tools" under settings
edit:
just a few keywords for google, if someone is looking for this!
easy_install pip gcc not found mac osx xcode
may be a moderator add this keywords to the question

Are you sure you have actually run the Xcode installer (usually found in /Applications)? Downloading it from the Mac App Store doesn't automatically run the installer.

Check that you have installed XCode. Try installing a PIL from homebrew package manager

Installing PIL on OS X Snow Leopard w/Xcode4 (no PPC support)

Xcode4 dropped PPC support, so when I try building PIL, it throws hate:
Bens-MacBook-Air:Imaging-1.1.7 bkeating$ python setup.py build
running buildrunning build_pyrunning build_ext
--- using frameworks at /System/Library/Frameworks
building '_imaging' extension
/usr/bin/gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -DHAVE_LIBJPEG -DHAVE_LIBZ -I/System/Library/Frameworks/Tcl.framework/Headers -I/System/Library/Frameworks/Tk.framework/Headers -I/usr/local/include/freetype2 -IlibImaging -I/System/Library/Frameworks/Python.framework/Versions/2.6/include -I/usr/local/include -I/usr/include -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c decode.c -o build/temp.macosx-10.6-universal-2.6/decode.o
/usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler (/usr/bin/../libexec/gcc/darwin/ppc/as or /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not installed
Installed assemblers are:
/usr/bin/../libexec/gcc/darwin/x86_64/as for architecture x86_64
/usr/bin/../libexec/gcc/darwin/i386/as for architecture i386
decode.c:688: fatal error: error writing to -: Broken pipe
compilation terminated.
lipo: can't open input file: /var/folders/jW/jW0VkC8uEb4lAjcJou+OaU+++TI/-Tmp-//ccEmCpUp.out (No such file or directory)
error: command '/usr/bin/gcc-4.0' failed with exit status 1
I ran that first line, manually, and removed the -arch ppc option and it didn't report back with any errors, but rerunning the build process ignores this manual attempt. `gcc-4.0 also does not exist, I symlinked it to gcc-4.2.
I could go ahead and install Xcode3 and then 4, but I want to muck up my fresh install.
Is there anyway to tell PIL to not compile for PPC? I did a grep across the distribution but i did not find a single mention of PPC. Any ideas?

The solution has nothing to do with PIL but rather setting gcc's ARCHFLAGS:
ARCHFLAGS="-arch i386 -arch x86_64" sudo pip install PIL

ARCHFLAGS doesn't seem to get passed into sudo. I had to do
sudo -s
then ARCHFLAGS="-arch i386 -arch x86_64" pip install PIL
to make it work.

A better way to solve this issue, in my opinion, would be to edit your ~/.profile or /etc/bashrc and add the line:
export ARCHFLAGS="-arch i386 -arch x86_64"
Will save messing around with any future installations (I've just had to do this for installing lots of Perl modules in CPAN)!

Just to help others...
I had to use ARCHFLAGS="-arch x86_64" before building imaging with my Snow Leopard/XCode 4 system i.e. having "-arch i386" in their stopped it working for me.