[lsst-dm-stack-users] clang confused by Mac OS X Mavericks upgrade, won't build healpy

Tue Aug 5 12:50:37 PDT 2014

OK, as Peter guessed, it was something in my shell. I don't know what
though: the stack and the sims package both installed first time for my new
user, and so now I am just using her installation. Thanks for the
suggestions! I'll remember this next time I migrate laptops and upgrade OSs
at the same time...

Cheers

Phil

On Mon, Aug 4, 2014 at 6:53 PM, Phil Marshall <dr.phil.marshall at gmail.com>
wrote:

>
> OK, it's not the PYTHONPATH (thanks Chris!)
>
> I'll try the new user test next (thanks Peter!)
>
>
> On Mon, Aug 4, 2014 at 6:25 PM, Peter Yoachim <yoachim at uw.edu> wrote:
>
>> Hi Phil,
>>
>> Similarly, you can try making a new user and install the stack and MAF
>> with that.  If it works, the problem is probably somewhere in your shell
>> environment.
>>
>> Peter
>>
>> Sent from the future via my iPhone 8Z
>>
>> > On Aug 4, 2014, at 5:28 PM, Chris Walter <chris.walter at duke.edu> wrote:
>> >
>> > Hi Phil,
>> >
>> > This is just a thought; but just in case, make sure you don't have any
>> other versions of python pieces other than the anaconda one putting
>> themselves in the various load paths.  I had a problem like that once and
>> there was some old ipython I had tried to install once and forgotten about
>> that was screwing things up.
>> >
>> > You can check PYTHONPATH
>> >
>> > and also
>> >
>> > $ python
>> >>>> import sys
>> >>>> sys.path
>> >
>> > and see if there is anything before the anaconda and LSST stuff.
>> >
>> > -Chris
>> >
>> >
>> >> On Aug 4, 2014, at 8:16 PM, Phil Marshall <dr.phil.marshall at gmail.com>
>> wrote:
>> >>
>> >>
>> >> Here's something odd: the setup.py output says that no Cython >= 0.16
>> was found, but that's not true:
>> >>
>> >> python
>> >> Python 2.7.5 |Anaconda 1.8.0 (x86_64)| (default, Oct 24 2013, 07:02:20)
>> >> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
>> >> Type "help", "copyright", "credits" or "license" for more information.
>> >>>>> import Cython
>> >>>>> print Cython.__version__
>> >> 0.19.2
>> >>
>> >> So when healpy is being built, it must not be with knowledge of this
>> python distribution somehow...
>> >>
>> >>
>> >> Phil
>> >>
>> >>
>> >>
>> >> On Mon, Aug 4, 2014 at 4:28 PM, Lynne Jones <ljones.uw at gmail.com>
>> wrote:
>> >> Simon generated the eups build stuff for MAF, so I’m not that familiar
>> with what’s going on unfortunately.
>> >> Anyone else see anything?
>> >>
>> >>
>> >>> On Aug 4, 2014, at 4:12 PM, Phil Marshall <dr.phil.marshall at gmail.com>
>> wrote:
>> >>>
>> >>>
>> >>> Thanks Lynne!
>> >>>
>> >>> I already removed /Developer, so that's not it either!
>> >>>
>> >>> I found some more clues (possibly) in the
>> EupsBuildDir/DarwinX86/healpy-1.7.4/build.log file:
>> >>>
>> >>> pkg-config is not installed, falling back to pykg-config
>> >>> No Cython >= 0.16 found, defaulting to pregenerated c version.
>> >>> running build
>> >>> running build_py
>> >>> creating build
>> >>> creating build/lib.macosx-10.5-x86_64-2.7
>> >>> creating build/lib.macosx-10.5-x86_64-2.7/healpy
>> >>>
>> >>> Why would eups think that I am running macosx-10.5? It should be
>> 10.9...
>> >>> Attaching the whole log file for you, in case it helps.
>> >>>
>> >>> Thanks!
>> >>>
>> >>> Phil
>> >>>
>> >>>
>> >>>
>> >>> On Mon, Aug 4, 2014 at 4:05 PM, Lynne Jones <ljones.uw at gmail.com>
>> wrote:
>> >>> Hi Phil,
>> >>>
>> >>> Thanks for getting going with your sims_maf install :)
>> >>>
>> >>> The answer is indeed in your migration from old Mac 10.6 to new
>> Mavericks.
>> >>> The new Xcode does NOT use a /Developer directory, but it also does
>> not delete the old /Developer directory (Mavericks instead puts its Xcode
>> stuff elsewhere).
>> >>> The existence of the old /Developer directory, although it does not
>> confuse the mac itself (even though it’s not used), DOES confuse python’s
>> distutils.
>> >>>
>> >>> The workaround I have seen so far (pending Simon figuring out
>> something very clever to do with the install) is to either temporarily or
>> permanently rename or remove your /Developer directory.
>> >>> I don’t believe you have any need for it with Mavericks, however, I
>> am suspicious that perhaps something does (otherwise, why wouldn’t Xcode
>> remove it?).
>> >>>
>> >>> Anyway, if you rename it, you will sooner or later find out if you
>> need it or not … and if something complains, you can move it back later.
>> >>> Renaming it should let the installation of healpy proceed.
>> >>>
>> >>> (this is documented on our install page, but I thought it was only
>> pyephem that had the problem).
>> >>>
>> >>> Lynne
>> >>>
>> >>>
>> >>>> On Aug 4, 2014, at 3:48 PM, Jim Bosch <talljimbo at gmail.com> wrote:
>> >>>>
>> >>>> More sophisticated suggestions will have to come from devs with more
>> experience with Macs and/or HealPy than I have, but the first thing to try
>> would be to make sure your old attempt isn't still causing problems for
>> more recent ones:
>> >>>>
>> >>>> eups distrib clean healpy 1.7.4
>> >>>>
>> >>>>
>> >>>> On Mon, Aug 4, 2014 at 4:40 PM, Phil Marshall <
>> dr.phil.marshall at gmail.com> wrote:
>> >>>>
>> >>>> Hi,
>> >>>>
>> >>>> Perhaps someone else who has migrated to a new Mac machine has seen
>> this problem too. I am trying to install sims_maf with
>> >>>>
>> >>>> eups distrib install sims_maf -t sims
>> >>>>
>> >>>> and it's failing on the healpy package, with error:
>> >>>>
>> >>>> clang: warning: no such sysroot directory:
>> '/Developer/SDKs/MacOSX10.5.sdk'
>> >>>> In file included from
>> /Users/pjm/lsst/EupsBuildDir/DarwinX86/healpy-1.7.4/healpy-1.7.4/healpixsubmodule/src/cxx/autotools/cxxsupport/announce.cc:40:
>> >>>> In file included from
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iostream:38:
>> >>>> In file included from
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ios:215:
>> >>>>
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:90:10:
>> fatal error: 'wchar.h' file not found
>> >>>> #include <wchar.h>  // for mbstate_t
>> >>>>          ^
>> >>>> 1 error generated.
>> >>>> make: *** [cxxsupport/announce.lo] Error 1
>> >>>>
>> >>>>
>> >>>> I think clang is confused by my migrating from a laptop running OS X
>> 10.6 to one running Mavericks: it can't find the wchar.h header file, even
>> though I did what the internet suggested, which was to install the Xcode
>> command line tools with
>> >>>>
>> >>>> xcode-select --install
>> >>>>
>> >>>> This did indeed place a wchar.h into my /usr/include directory, but
>> for some reason it is still not being detected by eups' build script. Any
>> ideas for what I should try next?
>> >>>>
>> >>>> Thanks!
>> >>>>
>> >>>> Phil
>> >>>>
>> >>>>
>> >>>>
>> >>>> _______________________________________________
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>> >>>> lsst-dm-stack-users at listserv.lsstcorp.org
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>> >>>>
>> >>>>
>> >>>> _______________________________________________
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>> >>>
>> >>>
>> >>> <build.log>
>> >>
>> >>
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>> >
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