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 jmeado...@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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