Hi Iain, I think you have the right idea. I had installed XQuartz which actually fixed some other issues I was having (but created new ones ;-) and I think I need to re-configure with x11=/opt/x11 or something like that. So I think you have the answer and thank you for the help. Sincerely, Jim (just around the corner in Cambridge)
On Jan 31, 2011, at 11:05 AM, Iain Drummond wrote: > 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