[MINC-users] Building bicpl-1.6.4 on Ubuntu 12.04

[Andrew Wood]

Hi Andrew,

I'm actually building all of the BIC/MNI stuff from scratch (tarball
releases).

So my configure command was really this:
./configure --with-minc2 --prefix=/my/build/ --with-build-path=/my/build/
--with-image-ppm

It may be worth noting that the script I use to build this stuff used to
work on Ubuntu 10.04.

I'm looking at an old build log, and the gcc command which is currently
failing actually worked on 10.04 (i.e. it didn't have -lpbm either). So
something must have changed in the ppm/pbm libraries? Or perhaps I had
statically linked a library before which is currently trying to link
dynamically?

I'm stumped..

Thanks,
Andrew





On Wed, Jun 4, 2014 at 9:59 AM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Andrew,
>
> Sorry, I should have been more clear, you'll need to build the
> dependencies using the new packaging system. Libtool then picks up the
> libraries from the .la files in these for subsequent packages.
>
> In this case my memory tells me it's EBTKS that you need to build from
> scratch so that the .la files for it include the correct things. In
> this case -lpbm
>
>
>
> a
>
> On 4 June 2014 23:50, Andrew Wood <andrew at biospective.com> wrote:
> > Hi Andrew,
> >
> > I'd grabbed bicpl-1.6.4 from http://packages.bic.mni.mcgill.ca/tgz/.
> I've
> > switched over to the CMake system where possible, but the bicpl releases
> > all predate Vlad's CMake build system, so are we not stuck with libtool
> for
> > this?
> >
> > I could grab a release from Github, but I'd just be rerunning the
> > autotools, no?
> >
> > Thanks,
> > Andrew
> >
> >
> > On Tue, Jun 3, 2014 at 9:12 PM, Andrew Janke <a.janke at gmail.com> wrote:
> >
> >> Hi Andrew,
> >>
> >> No you haven't made a mistake with the configure args. It's a
> >> shortcoming of how libtool is handled in the old MINC build system for
> >> binary packages packages.
> >>
> >> If you build MINC from source (any release) or use any of the later
> >> packages (mni-toolkit) you shouldn't see this problem.
> >>
> >> In any case I'd recommend shifting to Vlad's new CMake build system
> >> for MINC as very little of the old autoconf/make code will now be kept
> >> up to date.
> >>
> >> ta
> >>
> >>
> >> a
> >>
> >>
> >> On 4 June 2014 06:53, Andrew Wood <andrew at biospective.com> wrote:
> >> > Hi all,
> >> >
> >> > I'm trying to build bicpl-1.6.4 on Ubuntu 12.04 and am having some
> >> trouble.
> >> >
> >> > Here's my configure command:
> >> > ./configure --with-minc2 --with-build-path=/usr/local/bic/
> >> --with-image-ppm
> >> >
> >> > Everything goes well until the Testing/ subdirectory, where I get
> this:
> >> >
> >> > gcc -g -O2 -o test_rgb_io test_rgb_io.o  -L/usr/local/bic//lib
> >> > ../.libs/libbicpl.a -lppm -lvolume_io2 -lminc2 /usr/lib/libhdf5.so
> >> > -lpthread -lz -lnetcdf -lm
> >> > /usr/bin/ld: ../.libs/libbicpl.a(rgb_io.o): undefined reference to
> symbol
> >> > 'pm_freerow'
> >> > /usr/bin/ld: note: 'pm_freerow' is defined in DSO
> /usr/lib64/libpbm.so.9
> >> so
> >> > try adding it to the linker command line
> >> > /usr/lib64/libpbm.so.9: could not read symbols: Invalid operation
> >> >
> >> >
> >> > Manually running the gcc command with "-lpbm" at the end, as
> suggested by
> >> > the prompt, works fine. Is there a good reason that the build system
> >> isn't
> >> > passing along the linker flags? Have I made a mistake with the
> configure
> >> > args?
> >> >
> >> > Thanks,
> >> > Andrew
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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