Pandas Install Error on Mac - xcode

When I execute
sudo pip install pandas
I get the error:
creating build/temp.macosx-10.9-intel-2.7/pandas/src/datetime
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -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 x86_64 -arch i386 -pipe -Ipandas/src/klib -Ipandas/src -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pandas/index.c -o build/temp.macosx-10.9-intel-2.7/pandas/index.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'cc' failed with exit status 1
I have installed xcode and xcode command line tools.
In fact, I can confirm that cc is installed by executing:
cc -v
which returns:
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

These flags ended up letting me install it:
export CFLAGS=-Qunused-arguments
export CPPFLAGS=-Qunused-arguments
and then (of course):
sudo -E pip install pandas
Thanks #user3378649 for the flags suggestion - that got me thinking along the right track!

Can you please these commands for more information.
As long as you didn't mention what you used to overcome this problem, I'd suggest different approaches to help narrow down in order to find the problem:
First Solution :
Run these flags :
export ARCHFLAGS="-Wno-error=unused-command-line-argument-hard-error-in-future"
if it doesn't work
run these flags :
export CFLAGS=-Qunused-arguments
export CPPFLAGS=-Qunused-arguments
Second Solution :
Get Homebrew - it's a one-line shell script to install!
Edit your .profile, or whatever is appropriate, and put /usr/local/bin at the start of -your PATH so that Homebrew binaries are found before system binaries
brew install python - this installs a newer version of python in /usr/local
run "pip install pandas"
Third Solution :
use easy_install.
Execute the following command in Terminal
PATH="/Library/Frameworks/Python.framework/Versions/Current/bin:$(PATH)}"
export PATH
Then :
$ sudo easy_install pandas

Related

Installing geopandas on Python 2.6

This is in continuation with my earlier question Geospatial Analytics in Python
I started a new question to keep the 2 issues logically separate.
I have trying to install geopandas on python 2.6
surprisingly, geopandas is already installed by GeoSeries doesn't work and it needs a package "Fiona". I followed the instruction provided here
I installed the libraries required by searching and following the suggestions (including dev libraries thinking I'll get the .h files), I am however stuck with these two issues:
https://github.com/Toblerity/Fiona
after cloning from git and python setup.py install on Fiona, I get the error:
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.6 -c fiona/_geometry.c -o build/temp.linux-x86_64-2.6/fiona/_geometry.o
gcc: fiona/_geometry.c: No such file or directory
pip install geopandas gives
fiona/_transform.cpp:269:18: error: gdal.h: No such file or directory
fiona/_transform.cpp:270:26: error: gdal_version.h: No such file or directory
fiona/_transform.cpp:271:22: error: cpl_conv.h: No such file or directory
fiona/_transform.cpp:272:24: error: cpl_string.h: No such file or directory
fiona/_transform.cpp:273:21: error: cpl_vsi.h: No such file or directory
fiona/_transform.cpp:274:22: error: ogr_core.h: No such file or directory
Any help with sorting the issues and getting geopandas installed will be greatly appreciated
On Linux Mint, Python 2.7.10 (Anaconda):
sudo apt-get install libgeos-dev
sudo apt-get install libgdal-dev
pip install geopandas
Successfully installed descartes-1.0.1 fiona-1.6.2 geopandas-0.1.1 pyproj-1.9.4
I would recommend moving to 2.7.10. The two development libraries were all that I needed on my system. It seems that you are likely missing libgdal-dev.

ld: framework not found Python

I am trying to install a python module (SPArse Modeling Software) but the install script doesn't seem to be able to find the system's default Python.framework. This is an almost new (no migration assistant) Mac OS 10.9.5 system with both the default system python and Anaconda installed. I briefly installed Enthought Canopy but removed it when I decided to go with Anaconda. /System/Library/Frameworks/Python.framework exists and seems to have all the files you would expect.
In terminal, this is what happens:
bash-3.2$ which python
//anaconda/bin/python
bash-3.2$ cd spams-python
bash-3.2$ python setup.py build
running build
running build_py
running build_ext
building '_spams_wrap' extension
gcc -fno-strict-aliasing -I//anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dictLearn -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7/ -I//anaconda/include/python2.7 -c spams_wrap.cpp -o build/temp.macosx-10.5-x86_64-2.7/spams_wrap.o -DNDEBUG -DUSE_BLAS_LIB -fPIC -fopenmp -m32
clang: warning: argument unused during compilation: '-fopenmp'
#Omitting some irrelevant (I think) warnings#
4 warnings generated.
gcc -bundle -undefined dynamic_lookup -L//anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/spams_wrap.o -L//anaconda/lib -lstdc++ -lblas -llapack -o build/lib.macosx-10.5-x86_64-2.7/_spams_wrap.so -m32 -framework Python
ld: framework not found Python
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'gcc' failed with exit status 1
So, my question is, is my diagnosis of the problem correct? How can I tell GCC where Python.framework is? Is there some environment variable that isn't set correctly?
The Anaconda Python is not a Framework build of Python. If the module expects that it's not going to work. Commenting out commenting out "'-framework', 'Python'" in setup.py sounds like a good start, and if it works, then it probably is the right solution.
Compile it with gcc-5, and I successed.

Error when installing Cython for use with Buildozer

I've run into an error while installing Kivy, which told me to install Cython, so I did.
Except I run into an error, I've tried installing with pip,easy_install, manually but it results in the same. I also tried installing a older version of Cython but no luck.
Error message:
Command /usr/bin/python -c "import setuptools, tokenize;file='/private/tmp/pip_build_root/Cython/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-nXMqSR-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/Cython
Storing debug log for failure in /Users/jorn/Library/Logs/pip.log
When I install manually I get this error:
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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Cython/Plex/Scanners.c -o build/temp.macosx-10.8-intel-2.7/Cython/Plex/Scanners.o
unable to execute clang: No such file or directory
error: command 'clang' failed with exit status 1
I have read and tried all solutions I could find but none work..
I'm running on Mac osx 10.8.5
Ok, thanks to what #RaynP just said about it being a osx/clang issue I found the solution:
credits to this blog: http://kaspermunck.github.io/2014/03/fixing-clang-error/
The error is related to Xcode 5.1.
You will have to download the cython-master from GitHub. Installing with pip will not work and results in another error.
in terminal go to the cython-master file and enter: sudo ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future python setup.py install
This is a workaround the error.
Now I have installed Cython and can finally compile my app with Kivy/Buildozer:D

MySqlDB: llvm-gcc-4.2: error. Even after installing XCode 4.6.3 and storing MySQL include folder in XAMPP

I took the following steps after reading suggestions from http://andhikalegawa.wordpress.com/2012/01/05/installing-mysql-python-on-snow-leopard-using-xampp-mysql/
Downloaded MySQL-python-1.2.4b4 and unzipped
Changed the mysql_config = /Applications/XAMPP/xamppfiles/bin/mysql_config (as I am using XAMPP 1.7.3)
Downloaded mysql-5.1.70-osx10.6-x86 (I could not find 5.1.55 which is the version used in XAMPP) kept the include folder at /Applications/XAMPP/xamppfiles/
I am new to development so, downloaded XCode 4.6.3 with command line tools.
Logically it should have worked I am getting the following error
running build
running build_py
copying MySQLdb/release.py -> build/lib.macosx-10.7-intel-2.7/MySQLdb
running build_ext
building '_mysql' extension
creating build/temp.macosx-10.7-intel-2.7
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 -pipe -Dversion_info=(1,2,4,'beta',4) -D_version_=1.2.4b4 -I/Applications/XAMPP/xamppfiles/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.7-intel-2.7/_mysql.o -mmacosx-version-min=10.4 -arch i386 -arch ppc -D_P1003_1B_VISIBLE -DSIGNAL_WITH_VIO_CLOSE -DSIGNALS_DONT_BREAK_READ -DIGNORE_SIGHUP_SIGQUIT -DDONT_DECLARE_CXA_PURE_VIRTUAL
In file included from _mysql.c:44:
/Applications/XAMPP/xamppfiles/include/my_config.h:1088:1: warning: "HAVE_WCSCOLL" redefined
In file included from /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:8,
from _mysql.c:29:
/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/pyconfig.h:891:1: warning: this is the location of the previous definition
llvm-gcc-4.2: error trying to exec '/usr/bin/../llvm-gcc-4.2/bin/powerpc-apple-darwin11-llvm-gcc-4.2': execvp: No such file or directory
lipo: can't figure out the architecture type of: /var/folders/6p/8bxdl12d2nq05dmwbmdzttt40000gn/T//cc0v0ehE.out
error: command 'llvm-gcc-4.2' failed with exit status 255
Looks like it's trying to compile universal for PowerPC, which you probably don't have?
error trying to exec '/usr/bin/../llvm-gcc-4.2/bin/powerpc-apple-darwin11-llvm-gcc-4.2'
I would suggest setting the ARCHFLAGS:
shell> rm -Rf build/
shell> ARCHFLAGS="-arch i386" /usr/bin/python setup.py build
Or instead of i386, on 64-bit x86_64. But since you are downloading 32-bit MySQL, might be good to use i386.
Good luck! (Shameless advert: you can always try MySQL Connector/Python)

Error installing localtunnel

I run sudo gem install localtunnel and I get the following output. Now I am used homebrew to instal rbenv to install ruby and when i run brew doctor it says xcode is out of date but when i open up xcode and go to about it is the newest version, here is my error output for sudo gem install localtunnel
ERROR: Error installing localtunnel:
ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby extconf.rb
creating Makefile
make
xcrun cc -I. -I/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin12.0 -I/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin12.0 -I. -DJSON_GENERATOR -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -fno-common -arch i386 -arch x86_64 -g -O3 -pipe -fno-common -DENABLE_DTRACE -fno-common -pipe -fno-common -c generator.c
xcrun: Error: could not stat active Xcode path '/Developer'. (No such file or directory)
cc -arch i386 -arch x86_64 -pipe -bundle -undefined dynamic_lookup -o generator.bundle generator.o -L. -L/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib -L. -arch i386 -arch x86_64 -lruby -lpthread -ldl -lobjc
i686-apple-darwin11-llvm-gcc-4.2: generator.o: No such file or directory
i686-apple-darwin11-llvm-gcc-4.2: generator.o: No such file or directory
lipo: can't figure out the architecture type of: /var/tmp//ccfplODR.out
make: *** [generator.bundle] Error 1
Xcode 4 is not installed in /Developer anymore, but xcrun seems to expect it there.
I would install the "Command Line Tools" first (Xcode preferences -> Downloads -> Components).
If that does not help, call
sudo xcode-select -switch /Applications/Xcode.app
to explicitly set the path for xcrun.
My Ruby Version was out of date, I had to run rbenv install 1.9.3-p0 and than set it to the global.

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