[EMBOSS] can't install emboss 6.3.1 in mac os x 10.6

[Iain Drummond]

I seem to remember that i could bypass this issue by configuring EMBOSS to
install without x11. I realize that's not what you want to do. I think the
problem stems from the directory structure Apple uses for x11; i.e. Its not
where EMBOSS thinks it is. Maybe Apple put xll in a new place with 10.6?

Iain Drummond


On 1/30/11 11:49 PM, "Jim Meador" <jmeador45 at mac.com> wrote:

> Hi Everyone,
> 
> I am wanting to pgrade EMBOSS 6.3.1 on Mac OS X 10.6.6 (MacBook Pro 2.2 GHz,
> 4GB) from EMBOSS 6.2.0 that was installed in Leopoard (10.5) before I upgraded
> to Snow Leopard (10.6) and it seems to not do the make process correctly,
> where in the plplot directory, the .libs directory does not get created, so
> when I do sudo make install, it fails with these error messages:
> 
> Making install in plplot
> make[1]: Entering directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot'
> Making install in lib
> make[2]: Entering directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot/lib'
> make[3]: Entering directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot/lib'
> make[3]: Nothing to be done for `install-exec-am'.
> test -z "/usr/local/share/EMBOSS" || ../.././install-sh -c -d
> "/usr/local/share/EMBOSS"
>  /usr/bin/install -c -m 644 plstnd5.fnt plxtnd5.fnt '/usr/local/share/EMBOSS'
> make[3]: Leaving directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot/lib'
> make[2]: Leaving directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot/lib'
> make[2]: Entering directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot'
> make[3]: Entering directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot'
> test -z "/usr/local/lib" || .././install-sh -c -d "/usr/local/lib"
>  /bin/sh ../libtool   --mode=install /usr/bin/install -c   libeplplot.la
> '/usr/local/lib'
> libtool: install: /usr/bin/install -c .libs/libeplplot.3.dylib
> /usr/local/lib/libeplplot.3.dylib
> install: .libs/libeplplot.3.dylib: No such file or directory
> make[3]: *** [install-libLTLIBRARIES] Error 71
> make[3]: Leaving directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory
> `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/p
> lplot'
> make: *** [install-recursive] Error 1
> 
> When I look in the source directory, /EMBOSS-6.3.1/plplot/ there is no .libs
> directory as there is in another installation on a newer MacBook Pro that I
> was able to successfully install this same software (10.6.6, 2.6 GHz, 8GB).
> 
> My setup is a little more complicated than I would like, since I have
> installed the eBiotools-3.0.1-leopard software which sets up an older version
> of emboss 5.0.0 within a /usr/ebiotools/ directory and uses a very nice gui
> program to access these older emboss programs, called "eBioX" (and I don't
> want to lose this). So I have been installing the newer 6.x version of emboss
> to use at the commandline and with kemboss, both of which work, sort of. I
> have to play with the environment variables to get the text output programs to
> work, but I cannot get the graphics to work from various emboss programs that
> try to make graphs, such as "charge". The text-based programs work but I want
> to get the graphics working as well as it does from the ebiotools versions and
> will probably need to re-make emboss 6.3.1 after (re)installing gd and libpng.
> However, on this mac, neither ps nor x11 work. On the newer mac, with 6.3.1
> installed, I don't have png or gif support, but I can at least get g!
>  raphs in ps and x11 to work.
> 
> Does anyone have any ideas of what I may be doing wrong? Is it possible that
> some environment variable could be causing this?
> 
> Any ideas will be greatly appreciated.
> Thanks,
> Jim
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> 




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