<div dir="ltr">Hi Joao and Peter.<div><br></div><div>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?</div>
<div><br></div><div>Peter,</div><div>I ran the commands you listed and here is the output:</div><div>**************************************</div>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ xcode-select --print-path</p>
<p class="">/Applications/Xcode.app/Contents/Developer</p>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ xcode-select --version</p>
<p class="">xcode-select version 2333.</p>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ which gcc</p>
<p class="">/usr/bin/gcc</p>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ gcc -v</p>
<p class="">Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1</p>
<p class="">Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)</p>
<p class="">Target: x86_64-apple-darwin13.2.0</p>
<p class="">Thread model: posix</p>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ which clang</p>
<p class="">/usr/bin/clang</p>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ clang -v</p>
<p class="">Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)</p>
<p class="">Target: x86_64-apple-darwin13.2.0</p>
<p class="">Thread model: posix</p>
<p class="">Marks-MacBook-Pro-3:~ markbudde$ cd /Users/markbudde/Downloads/biopython-1.64 </p>
<p class="">Marks-MacBook-Pro-3:biopython-1.64 markbudde$ python setup.py build</p>
<p class="">running build</p>
<p class="">running build_py</p>
<p class="">running build_ext</p>
<p class="">building 'Bio.cpairwise2' extension</p>
<p class="">Compiling with an SDK that doesn't seem to exist: /Developer/SDKs/MacOSX10.5.sdk</p>
<p class="">Please check your Xcode installation</p>
<p class="">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</p>
<p class="">clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.5.sdk'</p>
<p class=""><span class=""><b>error: </b></span><b>unable to open output file</b></p>
<p class=""><b> 'build/temp.macosx-10.5-i386-2.7/Bio/cpairwise2module.o': 'Error opening</b></p>
<p class=""><b> output file 'build/temp.macosx-10.5-i386-2.7/Bio/cpairwise2module.o':</b></p>
<p class=""><b> Permission denied'</b></p>
<p class="">1 error generated.</p>
<div>error: command 'gcc' failed with exit status 1 </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jul 18, 2014 at 3:32 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">On Fri, Jul 18, 2014 at 7:03 AM, Mark Budde <<a href="mailto:markbudde@gmail.com">markbudde@gmail.com</a>> wrote:<br>
> Hi Peter,<br>
> Xcode 5.1.1 is installed on my machine, and I have successfully installed<br>
> older versions of Biopython. I have followed the instructions about<br>
> installing xcode command line tools, but that also doesn't solve the<br>
> problem.<br>
<br>
</div>Does xcode-select give any output? There are a few more options<br>
like --reset which might be useful...<br>
<br>
On my Mac OS X 10.9.3 machine with Xcode 5.1.1,<br>
<br>
$ xcode-select --print-path<br>
/Applications/Xcode.app/Contents/Developer<br>
$ xcode-select --version<br>
xcode-select version 2333.<br>
<br>
$ which gcc<br>
/usr/bin/gcc<br>
$ gcc -v<br>
Configured with:<br>
--prefix=/Applications/Xcode.app/Contents/Developer/usr<br>
--with-gxx-include-dir=/usr/include/c++/4.2.1<br>
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)<br>
Target: x86_64-apple-darwin13.3.0<br>
Thread model: posix<br>
<br>
$ which clang<br>
/usr/bin/clang<br>
$ clang -v<br>
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)<br>
Target: x86_64-apple-darwin13.3.0<br>
Thread model: posix<br>
<div class=""><br>
> I installed EPD over a year ago, so I might have to try a fresh<br>
> install, but was hoping to avoid that if this is a known problem. Since<br>
> nobody else seems to have run into this problem, I guess it must be specific<br>
> to something about my machine.<br>
> Thanks again,<br>
> Mark<br>
<br>
</div>Maybe Joao's reply is relevant, but updating EPD sound worth<br>
trying too. However, not having gcc available at the command<br>
line is the immediate problem.<br>
<span class="HOEnZb"><font color="#888888"><br>
Peter<br>
</font></span></blockquote></div><br></div>