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graehl / pygr

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Can't build in Lion, because gcc-4.0 is gone after xcode 4 killed xcode 3 #135

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
So, on my Lion 10.7.2, and apparently on all Lions, gcc-4.0 is forever gone. 
:-( And thus, pygr can't compile.

python setup.py installrunning install
running bdist_egg
running egg_info
writing pygr.egg-info/PKG-INFO
writing top-level names to pygr.egg-info/top_level.txt
writing dependency_links to pygr.egg-info/dependency_links.txt
reading manifest file 'pygr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '.gitignore' found anywhere in 
distribution
warning: no previously-included files matching '*.py[co]' found anywhere in 
distribution
writing manifest file 'pygr.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.3-fat/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-10.3-fat-2.7
creating build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/__init__.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/annotation.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/blast.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/classutil.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/coordinator.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/Data.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/dbfile.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/downloader.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/graphquery.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/logger.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/mapping.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/metabase.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/nlmsa_utils.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/parse_blast.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/schema.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/seqdb.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/sequence.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/sequtil.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/sqlgraph.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/translationDB.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/xnestedlist.py -> build/lib.macosx-10.3-fat-2.7/pygr
creating build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/__init__.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/catalog_downloads.py -> 
build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/leelabdb.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/maf2nclist.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/maf2VSgraph.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/seqref.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/splicegraph.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/ucsc_ensembl_annot.py -> 
build/lib.macosx-10.3-fat-2.7/pygr/apps
running build_ext
building 'pygr.seqfmt' extension
creating build/temp.macosx-10.3-fat-2.7
creating build/temp.macosx-10.3-fat-2.7/pygr
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g -O2 
-DNDEBUG -g -O3 
-I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
pygr/seqfmt.c -o build/temp.macosx-10.3-fat-2.7/pygr/seqfmt.o
unable to execute gcc-4.0: No such file or directory
error: command 'gcc-4.0' failed with exit status 1

So I've spent some time looking it up. And with "some time", I mean several 
hours. 
http://hints.macworld.com/article.php?story=20110318050811544
http://useyourloaf.com/blog/2011/7/20/hello-lion-goodbye-xcode-3.html

Etc. Hundreds of Mac users, complaining that gcc 4.0 apparently doesn't work in 
Lion anymore. Lion doesn't allow xcode 3.0.

Am I really the first Lion user to try to build pygr, and notice this? Or is 
there a way around this death crippling.

Original issue reported on code.google.com by m...@swarm.nu on 9 Nov 2011 at 1:20

GoogleCodeExporter commented 9 years ago 
Hi, thanks for the report. Could you please make sure that your build directory 
is empty and try again? The fact Python quite clearly states in your output it 
thinks it's building Pygr on MacOS 10.3 is... suspicious.

Original comment by mare...@gmail.com on 10 Nov 2011 at 3:47

GoogleCodeExporter commented 9 years ago 
I can't disagree with that. 
I emptied the build folder, and ran it again:

sudo easy_install pygr
Password:
Searching for pygr
Reading http://pypi.python.org/simple/pygr/
Reading http://code.google.com/p/pygr/
Best match: pygr 0.8.2
Downloading http://pygr.googlecode.com/files/pygr-0.8.2.tar.gz
Processing pygr-0.8.2.tar.gz
Running pygr-0.8.2/setup.py -q bdist_egg --dist-dir 
/tmp/easy_install-VCfR1c/pygr-0.8.2/egg-dist-tmp-RVO0NV
warning: no previously-included files matching '.gitignore' found anywhere in 
distribution
warning: no previously-included files matching '*.py[co]' found anywhere in 
distribution
unable to execute gcc-4.0: No such file or directory
error: Setup script exited with error: command 'gcc-4.0' failed with exit 
status 1

No 10.3 this time,  and now build folder is empty.

Original comment by m...@swarm.nu on 10 Nov 2011 at 7:48

GoogleCodeExporter commented 9 years ago 
Also, when I just try to execute the setup.py, I get the same error, again with 
the 10.3's:

python setup.py install 
running install
running bdist_egg
running egg_info
writing pygr.egg-info/PKG-INFO
writing top-level names to pygr.egg-info/top_level.txt
writing dependency_links to pygr.egg-info/dependency_links.txt
reading manifest file 'pygr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '.gitignore' found anywhere in 
distribution
warning: no previously-included files matching '*.py[co]' found anywhere in 
distribution
writing manifest file 'pygr.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.3-fat/egg
running install_lib
running build_py
creating build/lib.macosx-10.3-fat-2.7
creating build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/__init__.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/annotation.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/blast.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/classutil.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/coordinator.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/Data.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/dbfile.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/downloader.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/graphquery.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/logger.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/mapping.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/metabase.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/nlmsa_utils.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/parse_blast.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/schema.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/seqdb.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/sequence.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/sequtil.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/sqlgraph.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/translationDB.py -> build/lib.macosx-10.3-fat-2.7/pygr
copying pygr/xnestedlist.py -> build/lib.macosx-10.3-fat-2.7/pygr
creating build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/__init__.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/catalog_downloads.py -> 
build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/leelabdb.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/maf2nclist.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/maf2VSgraph.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/seqref.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/splicegraph.py -> build/lib.macosx-10.3-fat-2.7/pygr/apps
copying pygr/apps/ucsc_ensembl_annot.py -> 
build/lib.macosx-10.3-fat-2.7/pygr/apps
running build_ext
building 'pygr.seqfmt' extension
creating build/temp.macosx-10.3-fat-2.7
creating build/temp.macosx-10.3-fat-2.7/pygr
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g -O2 
-DNDEBUG -g -O3 
-I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
pygr/seqfmt.c -o build/temp.macosx-10.3-fat-2.7/pygr/seqfmt.o
unable to execute gcc-4.0: No such file or directory
error: command 'gcc-4.0' failed with exit status 1

Original comment by m...@swarm.nu on 10 Nov 2011 at 7:51