[Biopython] upgrade problems on Mac

[Mark Budde]

Hi Joao and Peter.

Joao, I did upgrade to Mavericks. I'm not sure what my profile and bashrc
files are, so I'm not sure how I would check them. I have tried
reinstalling xcode, just by running the installer. Do I need to uninstall
it first if I want the old locations/definitions to update?

Peter,
I ran the commands you listed and here is the output:
**************************************

Marks-MacBook-Pro-3:~ markbudde$ xcode-select --print-path

/Applications/Xcode.app/Contents/Developer

Marks-MacBook-Pro-3:~ markbudde$ xcode-select --version

xcode-select version 2333.

Marks-MacBook-Pro-3:~ markbudde$ which gcc

/usr/bin/gcc

Marks-MacBook-Pro-3:~ markbudde$ gcc -v

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1

Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)

Target: x86_64-apple-darwin13.2.0

Thread model: posix

Marks-MacBook-Pro-3:~ markbudde$ which clang

/usr/bin/clang

Marks-MacBook-Pro-3:~ markbudde$ clang -v

Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)

Target: x86_64-apple-darwin13.2.0

Thread model: posix

Marks-MacBook-Pro-3:~ markbudde$ cd
/Users/markbudde/Downloads/biopython-1.64

Marks-MacBook-Pro-3:biopython-1.64 markbudde$ python setup.py build

running build

running build_py

running build_ext

building 'Bio.cpairwise2' extension

Compiling with an SDK that doesn't seem to exist:
/Developer/SDKs/MacOSX10.5.sdk

Please check your Xcode installation

gcc -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk
-Qunused-arguments -Qunused-arguments
-I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7 -c
Bio/cpairwise2module.c -o
build/temp.macosx-10.5-i386-2.7/Bio/cpairwise2module.o

clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.5.sdk'

*error: **unable to open output file*

*      'build/temp.macosx-10.5-i386-2.7/Bio/cpairwise2module.o': 'Error
opening*

*      output file
'build/temp.macosx-10.5-i386-2.7/Bio/cpairwise2module.o':*

*      Permission denied'*

1 error generated.
error: command 'gcc' failed with exit status 1


On Fri, Jul 18, 2014 at 3:32 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> On Fri, Jul 18, 2014 at 7:03 AM, Mark Budde <markbudde at gmail.com> wrote:
> > Hi Peter,
> > Xcode 5.1.1 is installed on my machine, and I have successfully installed
> > older versions of Biopython. I have followed the instructions about
> > installing xcode command line tools, but that also doesn't solve the
> > problem.
>
> Does xcode-select give any output? There are a few more options
> like --reset which might be useful...
>
> On my Mac OS X 10.9.3 machine with Xcode 5.1.1,
>
> $ xcode-select --print-path
> /Applications/Xcode.app/Contents/Developer
> $ xcode-select --version
> xcode-select version 2333.
>
> $ which gcc
> /usr/bin/gcc
> $ gcc -v
> Configured with:
> --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
> Target: x86_64-apple-darwin13.3.0
> Thread model: posix
>
> $ which clang
> /usr/bin/clang
> $ clang -v
> Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
> Target: x86_64-apple-darwin13.3.0
> Thread model: posix
>
> > I installed EPD over a year ago, so I might have to try a fresh
> > install, but was hoping to avoid that if this is a known problem. Since
> > nobody else seems to have run into this problem, I guess it must be
> specific
> > to something about my machine.
> > Thanks again,
> > Mark
>
> Maybe Joao's reply is relevant, but updating EPD sound worth
> trying too. However, not having gcc available at the command
> line is the immediate problem.
>
> Peter
>
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