[Users] x86_64 link-time errors on MacOS Mojave

[Bernard Kelly]

Hi Roland, everyone:

I just came back to this problem in the last day or two, and with some
experimentation, I fixed it by adding the following lines to my
config-info ---that is, to
simfactory/mdb/optionlists/osx-macports.cfg:

HDF5_INC_DIRS=/opt/local/include
HDF5_LIBS=hdf5 hdf5_cpp hdf5_hl
HDF5_LIB_DIRS=/opt/local/lib

That is, it wasn't enough to just say "HDF5_DIR=/opt/local"

Hope this helps if someone else runs into problems (and thanks for the
help getting here),

Bernard

On Fri, 21 Jun 2019 at 14:20, Haas, Roland <rhaas at illinois.edu> wrote:
>
> Hello Bernard,
>
> unfortunately (or fortunately) it linked fine for me. No errors were
> reported.
>
> Looking at the installed ports I also cannot see anything strange.
>
> I am not sure what else I could now do to help debug this. Possibly
> some other package that you have installed is interfering or there is
> some environment variable set?
>
> Yours,
> Roland
>
> > Hi Roland.
> >
> > Here's the result of uname -a:
> >
> > Darwin gs66-dodder 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25
> > 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64
> >
> > Attached is the full list of installed ports (a bit longer than yours)
> >
> > Bernard
> >
> > On Thu, 20 Jun 2019 at 12:44, Haas, Roland <rhaas at illinois.edu> wrote:
> > >
> > > Hello Bernard,
> > >
> > > > I did a clean, from-scratch compilation after copying that 18.2.0
> > > > Darwin architecture file to 18.6.0.
> > > >
> > > > Sadly, no change. Still fails at link time with all the "Undefined
> > > > _H5xxxx" errors.
> > > Ok. Since it starts with at "_" I almost suspected it may be some
> > > Fortran binding but then it is being called from C++ code.
> > >
> > > My own test is still compiling (slow VM).
> > >
> > > Could you include the output of:
> > >
> > > * sudo port installed
> > > * uname -a
> > >
> > > I have included my own output to give you an idea of what I am looking
> > > for (note that I cannot tell yet if compiling in my VM will encounter
> > > the same error you see).
> > >
> > > Yours,
> > > Roland
> > >
> > > --
> > > My email is as private as my paper mail. I therefore support encrypting
> > > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> >
> >
> >
>
>
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://pgp.mit.edu .



-- 
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Bernard Kelly -- CRESST Assistant Research Scientist, NASA/GSFC
Gravitational Astrophysics Laboratory --- Code 663

Phone: +1 (301) 286-7243 *** Fax: +1 (301) 286-2226
Web: http://science.gsfc.nasa.gov/sed/bio/bernard.j.kelly
ORCID: orcid.org/0000-0002-3326-4454
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