[lsst-dm-stack-users] clang confused by Mac OS X Mavericks upgrade, won't build healpy
Peter Yoachim
yoachim at uw.edu
Tue Aug 5 15:49:54 PDT 2014
It should be relatively painless to compare the output of the "env"
shell command between the two user accounts to figure out where the
problem is.
P
On 08/05/14 12:50, Phil Marshall wrote:
>
> 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 <mailto: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
> <mailto: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 <mailto: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
> <mailto: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 <mailto: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
> <mailto: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 <mailto: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 <mailto: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
> <mailto: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
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> lsst-dm-stack-users mailing list
> >>>> lsst-dm-stack-users at listserv.lsstcorp.org
> <mailto:lsst-dm-stack-users at listserv.lsstcorp.org>
> >>>>
> https://listserv.lsstcorp.org/mailman/listinfo/lsst-dm-stack-users
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> lsst-dm-stack-users mailing list
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> <mailto:lsst-dm-stack-users at listserv.lsstcorp.org>
> >>>>
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> >>>
> >>>
> >>> <build.log>
> >>
> >>
> >> _______________________________________________
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> >
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