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

Jim Meador jmeador45 at mac.com
Mon Jan 31 04:49:38 UTC 2011

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/plplot'
Making install in lib
make[2]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib'
make[3]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/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/plplot/lib'
make[2]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot/lib'
make[2]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot'
make[3]: Entering directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot'
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/plplot'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/Users/jmeador/newApps/MolBioChemSoftware/MolBioGeneral/EMBOSS/EMBOSS-6.3.1/plplot'
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 graphs 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.

More information about the EMBOSS mailing list