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pip3 installation failed with error code 1, is this an xcode update issue or other? #135
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@lisagayledavis I am not certain that we have the 5.5.0
Once you do this you can install using |
@mandli Thanks for your post, and I've made a lot progress, but I'm still getting hung up a bit on the python setup. Following your instructions, I was able to download the tarball directly and get v5.5.0 unpacked. I was able to pip3 install, and I set my $CLAW variable in my .bash_profile file and "source"-d it. That seems to have taken care of most of the issues. I'm not sure if the newest error is related to pyclaw or to my anaconda3 installation. Below is the command info that I run and the error message.
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@lisagayledavis It looks like your C compiler isn't working. I think you have stripped out an important part of the traceback; could you post the whole thing? |
Hi @ketch, actually, from the command that I show below, that was all the error message I got from the terminal. Thanks!
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I am a little confused, did you already run |
Yes, I did run the pip3install command. I think it might be my python path that's the problem. I was trying to follow online testing instructions. My CLAW variable and the FC are set correctly in my .bash_profile file. But my python path in there was set by the anaconda installer. That part of the file looks like: # added by Anaconda3 5.2.0 installer So, when I try to test, I cd into the directory and run the LisaDavisMacBookPro:~ lisadavis$ ======================================================================
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Please try the following:
I'm assuming that $CLAW points to your clawpackv5.5.0 directory. |
@ketch Yes, my .bash_profile file contains the lines export CLAW=~/clawpack_src/clawpack-v5.5.0 Following your directions, I did the uninstall command and got Then Then Obtaining file:///Users/lisadavis/clawpack_src/clawpack-v5.5.0
Command "/Users/lisadavis/anaconda3/bin/python -c "import setuptools, tokenize;file='/Users/lisadavis/clawpack_src/clawpack-v5.5.0/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" develop --no-deps" failed with error code 1 in /Users/lisadavis/clawpack_src/clawpack-v5.5.0/ |
Okay, can you post your install.log? |
Sorry, you mentioned that earlier. Here it is. |
Okay, the actual error (from the log file) is this:
Looks like there is an issue with your C compiler. I'm guessing that you have installed two of them (with XCode and homebrew) and things are getting mixed up between them. Others here (@mandli?) may be able to say more. Anyway, I googled that error and came to this page, where some possible fixes are suggested: https://stackoverflow.com/questions/14694912/ld-library-not-found-for-lgcc-ext-10-5 |
I think @ketch is right, there's probably something weird going on with a compiler version. I also would suspect that Anaconda's compiler may be at fault. Do you know which compilers you have installed? |
@mandli and @ketch I poked around online to see what I should be checking. Not sure how to find multiple compilers. See below for the results of checking for gcc, g++ and cc. What does that output mean...the I also did a $ $ $ $ $ $ From my .bash_profile: |
So it's "complicated". Hmm. Are you still using MacPorts or is this leftover from a previous installation? |
Hmm, "complicated" is not reassuring --- from doctors or from computer people. :-) I'm following up on the MacPorts question as soon as I can. In the meantime, maybe I should be asking the following: What C compiler should I be using in order for Clawpack to work properly? And where should that C compiler be located in my files? Thanks! |
I don't think there's necessarily a preferred compiler other than you need a Fortran compiler. My own macOS setup consists of:
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To be clear, any compiler is fine. The issue is that your system is trying to use parts of two different compilers together, and that doesn't work. |
Thanks @mandli and @ketch, this makes sense, and actually @ketch had suggested to me that this might be the issue when I initially asked him about my original error messages. I'll try uninstalling all of it --- anaconda and clawpack --- then reinstalling clawpack to see if that fixes the issue. I'll post in a fresh thread if I have other errors that I can't resolve. Thanks for all your patience and assistance Guys! -- Lisa |
I'm attempting to install clawpack for python v3 on Mac OS X.
(Background--I currently have clawpack for python2 installed and running smoothly on my machine, and I installed anaconda3 recently for a separate project.) I updated my xcode installation through the app store prior to this installation attempt, but I'm not convinced that it worked. Is the error at the bottom of this posting indicating that there is an xcode problem, or something else? Thanks! --- Lisa
Using pip with the following command:
pip3 install --src=$HOME/clawpack_src --user -e \ git+https://github.com/clawpack/clawpack.git@v5.5.0#egg=clawpack-v5.5.0
Here is the output:
"Obtaining clawpack-v5.5.0 from git+https://github.com/clawpack/clawpack.git@v5.5.0#egg=clawpack-v5.5.0
Updating ./clawpack_src/clawpack-v5.5.0 clone (to revision v5.5.0)
Running setup.py (path:/Users/lisadavis/clawpack_src/clawpack-v5.5.0/setup.py) egg_info for package clawpack-v5.5.0 produced metadata for project name clawpack. Fix your #egg=clawpack-v5.5.0 fragments."
This was followed by several messages of the flavor:
"Requirement already satisfied: numpy>=1.6 in ./anaconda3/lib/python3.6/site-packages (from clawpack) (1.14.3)
Requirement already satisfied: matplotlib>=1.0.1 in ./anaconda3/lib/python3.6/site-packages (from clawpack) (2.2.2)
Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=1.0.1->clawpack) (0.10.0)"
and finally:
"Command "/Users/lisadavis/anaconda3/bin/python -c "import setuptools, tokenize;file='/Users/lisadavis/clawpack_src/clawpack-v5.5.0/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" develop --no-deps --user --prefix=" failed with error code 1 in /Users/lisadavis/clawpack_src/clawpack-v5.5.0/"
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