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 > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss