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

[Jim Meador]

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" <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
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at 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.
>