[yt-users] install failure

[Nathan Goldbaum]

Hi Mordecai,

We've had some reports about incompatibilities with the install script on
OS X Mavericks recently, but I don't think this error has been reported
before. Unfortunately getting the install script to work portably in all
cases is a labor of love and sometimes errors like these crop up.

Googling for your error returns this discussion on the readline mailing
list: https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html.
Apparently the version you're compiling needs to be patched to compile
cleanly on mavericks.  I haven't checked whether the patch has made its way
into a readline release.

I'm not sure what exactly is compiling readline (IPython maybe?), but
earlier in the install script we should have installed a pure-python
version of the readline library from pypi if we were unable to import it.
It would help to figure out what went wrong if you could upload the full
install log somewhere.

Do you have a python environment setup on your laptop already?  It's very
straightforward to install yt using anaconda, canopy, or a manually
configured python environment, bypassing all the bootstrapping that the
install script must do.  Take a look at the following page in the
documentation:

http://yt-project.org/doc/installing.html#installing-yt-using-anaconda
http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-source

Hope that's helpful.

-Nathan


On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <mordecai at amnh.org>
wrote:

> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS
> X v10.9.4.  I am using the install script, with the options set as follows:
>
>
> # Here's where you put the HDF5 path if you like; otherwise it'll download
> it
> # and install it on its own
> #HDF5_DIR=/opt/local/lib
>
> # If you need to supply arguments to the NumPy or SciPy build, supply them
> here
> # This one turns on gfortran manually:
> #NUMPY_ARGS="--fcompiler=gnu95"
> # If you absolutely can't get the fortran to work, try this:
> #NUMPY_ARGS="--fcompiler=fake"
>
> INST_HG=0       # Install Mercurial or not?  If hg is not already
>                 # installed, yt cannot be installed.
> INST_ZLIB=1     # On some systems (Kraken) matplotlib has issues with
>                 # the system zlib, which is compiled statically.
>                 # If need be, you can turn this off.
> INST_BZLIB=1    # On some systems, libbzip2 is missing.  This can
>                 # lead to broken mercurial installations.
> INST_PNG=1      # Install a local libpng?  Same things apply as with zlib.
> INST_FTYPE=1    # Install FreeType2 locally?
> INST_ENZO=0     # Clone a copy of Enzo?
> INST_SQLITE3=1  # Install a local version of SQLite3?
> INST_PYX=1      # Install PyX?  Sometimes PyX can be problematic without a
>                 # working TeX installation.
> INST_0MQ=1      # Install 0mq (for IPython) and affiliated bindings?
> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
> INST_SCIPY=0    # Install scipy?
>
>
> After downloading and activating Xcode command line tools, I got the
> script to complete successfully. I activated it using the activate.csh
> script.
>
> However, when I then try to start yt, it pauses for 30 seconds or so, and
> then issues the response “Abort”, with no further errors.  I get the same
> response if I try to import yt into the python (running in the yt
> environment). Abort, and return to the command line.
>
> I have tried erasing the yt-x86_64 directory and reinstalling from
> scratch, with no change in behavior.  I also examined the yt_install.log.
> I found a number of, presumably irrelevant, errors in the configuration
> tests, but also an error at the end of the long section on building Ipython
> (almost at the end of the script, just before readline assembly that looks
> possibly relevant:
>
>     gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`
> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2
> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so
> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so
> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so
> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so
> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so
> tilde.so compat.so -lncurses
>     Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>     Target: x86_64-apple-darwin13.3.0
>     Thread model: posix
>     clang: error: invalid argument '-compatibility_version 6' only allowed
> with '-dynamiclib'
>     clang: error: invalid argument '-compatibility_version 6' only allowed
> with '-dynamiclib'
>     make[1]: *** [libreadline.6.2.dylib] Error 1
>     make: [shared] Error 2 (ignored)
>
> Any insight on how to proceed?
>
> Best,
>
> Mordecai
>
>
> --
> Mordecai-Mark Mac Low  Curator & Professor
> +1-212-496-3443          Department of Astrophysics
> +1-212-769-5007 (fax)    American Museum of Natural History
> mmaclow (Skype, Hangout)     79th St at CPW, NY, NY, 10024-5192, USA
>
>
>
>
>
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