mac homebrew install #295
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ghost
assigned 
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Which version of Xcode do you have installed? It might be this bug: In which case, you should pull from the CPhomebrew repository (I just If that doesn't work, I also created a branch to test another possible I don't have a Lion system, but will try to offer as much assistance as I can. |
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Hi Ray, Thanks for your help. I spent some time on this today and yesterday, but haven't had any luck. I have a working development environment in Ubuntu which I'm using in a different context so I understand if you don't want to get sidetracked into this problem. On Feb 21, 2012, at 11:59:19, Thouis (Ray) Jones wrote:
The install attempt which yielded the error message in my previous email was with Xcode 3.2.5. I reinstalled Xcode to a previous version (3.2.4) that I had working awhile ago on a
If I do 'brew install qrupdate' I get a different error than the one described in the above link: ==> /usr/local/bin/gfortran -Os -w -pipe -march=core2 -msse4 -fno-underscoring -c dotwrp.f90
when I do that it seems 'brew' is looking in the wrong place: jmclaughlin:~ jmclaughlin$ brew uninstall gfortran && brew install gfortran looks like the gfortran is here: /Users/jmclaughlin/CPhomebrew/Cellar/gfortran I'm not familiar enough with homebrew to know what to do.
did these commands: but it failed during the make. not sure how much or if any of this error message is helpful: ==> Exit Status: 2 Error: Failed executing: make -- this error looks the same as the previous one (attached below)
Maybe this just isn't going to work at the moment. If I have time I'll try reinstalling the Xcode 3.2.5 and try again with your suggestions. That install attempt made it farther than when using the older Xcode versions.
Here's my last error during cphomebrew build: [ 75%] [ 75%] /tmp/homebrew-mysql-connector-c-universal-6.0.2-bIPa/mysql-connector-c-6.0.2/include/my_atomic.h: In function ‘my_atomic_cas32’: Error: Failed executing: make Your gcc 4.0.x version is older than the recommended version. It may be advisable |
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I suggest upgrading to the latest Xcode, as I think it's more likely The problem you're seeing with "brew uninstall gfortran" is that you need to run the The Mysql error is strange, as it appears to be an LLVM error, which |
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BTW, I merged the possible fortran fix into master, and updated from upstream. I also fixed the download of libhdf5-universal, which I had broken earlier. You should switch to master and git pull. |
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Haven't heard anything more. Closing. |
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Hi Ray, Sorry, I'm up to my eyeballs in other projects. Linux version of CP runs without issue, so I haven't gone back to get the mac homebrew working. The problem was installing the homebrew on osx Lion system. I suspect the next time I cycle around and try again the install will probably work. Keep up the good work, CP is awesome! -John On May 2, 2012, at 03:50:34, Thouis (Ray) Jones wrote:
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As an aside, openmicroscopy users & devs were running into similar issues with our forked homebrew repo. We just finished moving to using an homebrew-alt / tap-based approach which looks promising. With the hope that it might help,
Might be worth our collectively trying to get this into https://github.com/Homebrew/homebrew-science Cheers, |
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Hi, /usr/local/bin/gfortran -Wall -arch i686 -arch x86_64 -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/src/dct.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/src/dst.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/fortranobject.o -Lbuild/temp.macosx-10.6-intel-2.7 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-intel-2.7/scipy/fftpack/_fftpack.so ld: library not found for -lgcc ld: library not found for -lgcc lipo: can't figure out the architecture type of: /var/folders/hy/s1139xz94mn3vw0zrrz881fh0000gp/T//ccI0QKHd.out ld: library not found for -lgcc ld: library not found for -lgcc lipo: can't figure out the architecture type of: /var/folders/hy/s1139xz94mn3vw0zrrz881fh0000gp/T//ccI0QKHd.out error: Command "/usr/local/bin/gfortran -Wall -arch i686 -arch x86_64 -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/src/dct.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/src/dst.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/fortranobject.o -Lbuild/temp.macosx-10.6-intel-2.7 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-intel-2.7/scipy/fftpack/_fftpack.so" failed with exit status 1 |
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Hi Marc, Ray recommends: Hope that helps, --Lee |
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Hi Lee, yes this has worked and scipy installed and matplotlib too. My gfortran version was 4.2.1. After the uninstall and reinstall it is still 4.2.1??? In any case it completed the installation successfully. I failed to start CP, because h5py was not found. After pip installing that I received this error when firing up CP Should I start a new thread for this? |
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Try this (with CP virtualenv activated): On Wed, Nov 7, 2012 at 11:59 AM, Marckobudo notifications@github.comwrote:
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doesn't seem to have helped File "/Users/bickle/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/h5py/init.py", line 1, in |
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Just to check, you're starting CP with the pythonw32 (not just python) |
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yep it's w32. I did that mistake in the past and it fails much earlier. Marc Bickle, PhD phone +49 351 210 2595 On Nov 7, 2012, at 8:59 PM, Thouis (Ray) Jones wrote:
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Could you please run and run "file" on the libhdf5.dylib found by the second command, and post |
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hmm, I guess you wanted more than this… any suggestions? (cpdev)screening-mac-11:~ bickle$ file /Users/bickle/CPhomebrew/Cellar/cellprofiler-dev-python/1/ Marc Bickle, PhD phone +49 351 210 2595 On 7 Nov 2012, at 22:07, Thouis (Ray) Jones wrote:
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Oh, it looks like things got mangled by email. Here's what I meant: |
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(updated yet again to get formatting correct) |
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is this any better? (cpdev)screening-mac-11:~ bickle$ file /Users/bickle/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/h5py/_errors.so Marc Bickle, PhD phone +49 351 210 2595 On 8 Nov 2012, at 14:45, Thouis (Ray) Jones wrote:
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Oh, I see that an earlier command got mangled, as well. With the virtualenv activated, can you run: and let me know if that works? |
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Okay, we're having progress here, but still it failed in the end. Here is the log screening-mac-11:~ bickle$ . CPhomebrew/bin/activate-cpdev Marc Bickle, PhD phone +49 351 210 2595 On 8 Nov 2012, at 15:03, Thouis (Ray) Jones wrote:
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It's like the cellprofiler-dev script was never run. Weird. Given that, the next things to do are: |
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This did still not resolve the issue. I am sorry. I imagine I might have done something wrong at the beginning. Maybe I should restart from the beginning. If you could just tell me what you think should be different for Lion, I could give it a shot. (cpdev)screening-mac-11:~ bickle$ pythonw32 CellProfiler/CellProfiler.py phone +49 351 210 2595 On 8 Nov 2012, at 15:45, Thouis (Ray) Jones wrote:
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I would make one more attempt before giving up. |
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I had an error on uninstall? cpdev)screening-mac-11:~ bickle$ CPhomebrew/bin/brew uninstall cellprofiler-dev Marc Bickle, PhD phone +49 351 210 2595 On 8 Nov 2012, at 17:14, Thouis (Ray) Jones wrote:
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Very odd. Could you run the install afterward? |
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Hi Ray, sorry, what do you mean by that? Marc Bickle, PhD phone +49 351 210 2595 On 8 Nov 2012, at 17:34, Thouis (Ray) Jones wrote:
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After you got the error from the uninstall, were you able to run "brew |
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I just pushed a new version to the mountain-lion branch. If you're |
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Yes, I'm game. Due to the time difference, I'm not at my computer so I'll try in the morning. How do I get the mountain lion branch? I have btw lion installed. I tried installing over the weekend on my MacAir and failed but with a different problem, but I think it is best to solve one problem at the time. Marc Bickle, PhD phone +49 351 210 2595 On Nov 12, 2012, at 8:51 PM, Thouis (Ray) Jones wrote:
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To get to the mountain-lion branch, you can do this after the git clone cd CPhomebrew |
Hi, I apologize if this is not the place, but I tried to install the Homebrew cellprofiler development version for mac and it failed pretty far into the process. My mac is brand new and running 10.7.3 Thanks for taking a look! -John
Here's the message from the pip.log:
/Users/jmclaughlin/CPhomebrew/bin/gfortran -Wall -arch i686 -arch x86_64 -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/src/dct.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/fortranobject.o -Lbuild/temp.macosx-10.6-intel-2.7 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-intel-2.7/scipy/fftpack/_fftpack.so
ld: library not found for -lgcc
ld: library not found for -lgcc
lipo: can't figure out the architecture type of: /var/folders/h9/mzp4k_r93pq1fzf6b9_4ljh816lyrk/T//ccPQ6k9T.out
ld: library not found for -lgcc
ld: library not found for -lgcc
lipo: can't figure out the architecture type of: /var/folders/h9/mzp4k_r93pq1fzf6b9_4ljh816lyrk/T//ccPQ6k9T.out
error: Command "/Users/jmclaughlin/CPhomebrew/bin/gfortran -Wall -arch i686 -arch x86_64 -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/drfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zrfft.o build/temp.macosx-10.6-intel-2.7/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/scipy/fftpack/src/dct.o build/temp.macosx-10.6-intel-2.7/build/src.macosx-10.6-intel-2.7/fortranobject.o -Lbuild/temp.macosx-10.6-intel-2.7 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.6-intel-2.7/scipy/fftpack/_fftpack.so" failed with exit status 1
Command /Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/bin/python -c "import setuptools;file='/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/build/scipy/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" install --single-version-externally-managed --record /var/folders/h9/mzp4k_r93pq1fzf6b9_4ljh816lyrk/T/pip-rNINyf-record/install-record.txt --install-headers /Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/bin/../include/site/python2.7 failed with error code 1 in /Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/build/scipy
Exception information:
Traceback (most recent call last):
File "/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/basecommand.py", line 104, in main
status = self.run(options, args)
File "/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/commands/install.py", line 250, in run
requirement_set.install(install_options, global_options)
File "/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/req.py", line 1133, in install
requirement.install(install_options, global_options)
File "/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/req.py", line 577, in install
cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)
File "/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/init.py", line 256, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command /Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/bin/python -c "import setuptools;file='/Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/build/scipy/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" install --single-version-externally-managed --record /var/folders/h9/mzp4k_r93pq1fzf6b9_4ljh816lyrk/T/pip-rNINyf-record/install-record.txt --install-headers /Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/bin/../include/site/python2.7 failed with error code 1 in /Users/jmclaughlin/CPhomebrew/Cellar/cellprofiler-dev-python/1/cpdev/build/scipy
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