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)
Related
I am trying to install Platypus and have gotten the following error message:
building 'htslibWrapper' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.linux-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC
htslibWrapper.c:243:25: fatal error: htslib/bgzf.h: No such file or directory
#include "htslib/bgzf.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
I am new to Bioinformatics and cannot seem to find a working solution online.
Sometimes the bioinformatics applications don't describe thier dependencies all that well. See this link for a possible solution
Install htslib from http://www.htslib.org/download/ and copy c headers to Platypus root folder:
cp -r htslib-x.x.x/htslib platypus_folder/
Build again
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
After this command sudo gem install cocoapods I got error below.
I think it is connected to the wrong path for Xcode 5. When I installed it I save it on Desktop but them moved it to the Application folder. I use Xcode 4.6.3 as well as Xcode 5. How can I change path to solve this issue. Command line tools are installed on both XCodes.
Building native extensions. This could take a while...
ERROR: Error installing cocoapods:
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 '/Users/alex/Desktop/Xcode 5.app/Contents/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
clang: error: no such file or directory: 'generator.o'
make: *** [generator.bundle] Error 1
Gem files will remain installed in /Library/Ruby/Gems/1.8/gems/json-1.8.0 for inspection.
Results logged to /Library/Ruby/Gems/1.8/gems/json-1.8.0/ext/json/ext/generator/gem_make.out
I have run this command in terminal
sudo xcode-select -switch /Applications/Xcode.app
it works for me
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.
I am having trouble installing pyipopt on ubuntu 12.04. During linking, I receive the error:
/usr/bin/ld: cannot find -lcoinhsl
Even though I know that this library is installed and the .so and .la files are available in /home/mostafa/MyBuilds/CoinIpopt/build/lib/
does anyone have a solution for this?
below is the complete return of running setup.py build:
root#ubuntu:~/MyBuilds/pyipopt# sudo python setup.py build
running build
running build_ext
building 'pyipopt' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/home/mostafa/MyBuilds/CoinIpopt/build/include/coin/ -I/usr/include/python2.7 -c src/callback.c -o build/temp.linux-x86_64-2.7/src/callback.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/home/mostafa/MyBuilds/CoinIpopt/build/include/coin/ -I/usr/include/python2.7 -c src/pyipopt.c -o build/temp.linux-x86_64-2.7/src/pyipopt.o
src/pyipopt.c: In function ‘set_intermediate_callback’:
src/pyipopt.c:452:15: warning: variable ‘myowndata’ set but not used [-Wunused-but-set-variable]
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relrobuild/temp.linux-x86_64-2.7/src/callback.o build/temp.linux-x86_64-2.7/src/pyipopt.o -L/home/mostafa/MyBuilds/CoinIpopt/build/lib/ -lipopt -lblas -lcoinhsl -lcoinmetis -llapack -ldl -lm -o build/lib.linux-x86_64-2.7/pyipopt.so -Wl,--rpath -Wl,/home/mostafa/MyBuilds/CoinIpopt/build/lib/
/usr/bin/ld: cannot find -lcoinhsl
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
-Ldir
Add directory dir to the list of directories to be searched for -l.
You may install your coinhsl library in one of your standard libraries directories and run 'ldconfig` before doing your ppyipopt install
I had a similar problem with another library and the reason why it didn't found it, was that I didn't run the make install (after running ./configure and make) for that library. The make install may require root privileges (in this case use: sudo make install). After running the make install you should have the so files in the correct folder, i.e. here /usr/local/lib and not in the folder mentioned by you.
you can add the Path to coinhsl lib to LD_LIBRARY_PATH variable. May be that will help.
export LD_LIBRARY_PATH=/xx/yy/zz:$LD_LIBRARY_PATH
where /xx/yy/zz represent the path to coinhsl lib.