[EMBOSS] Installing emboss ends with an error (OSX 10.6 macport 1.8.2 )

[ajb at ebi.ac.uk]

Hello Tõnu,

That specific error shows that EMBOSS is unable to find the X11
(X windows) libraries.

Usually X11 is an optional, rather than default, installation option on
your Apple MacOSX installation DVD. See, for example,

http://www.macworld.com/article/142454/2009/08/install_snow_leopard.html

After installing x11 then, on the EMBOSS side, either do a fresh
extraction of the code or type "make clean" and do the
./configure command again.

If you have installed X11 and are getting that error then let us
know.

HTH

Alan



> Hi!
>
> I tried to install emboss into my mac (OSX 10.6 snow leopard ) by using
> macport (1.8.2) but finished with an error. It seems to me that I tangled
> into missing library (probably libjpeg), but I am still not sure about it.
>  I used command "locate" to see which libjpeg libraries are installed and
> it seems that they are there.
>
>  locate libjpeg
> /Applications/VLC.app/Contents/MacOS/lib/libjpeg.7.dylib
> /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries/libjpeg.jnilib
> /System/Library/Tcl/8.4/Img1.4/libjpegtcl1.0.dylib
> /System/Library/Tcl/8.5/Img1.4/libjpegtcl1.0.dylib
>
> What I am missing, and how to overcome this probelme?
> The part of macport debug output is below.
>
>
> % sudo port -d install emboss
> Password:
>
> ................ deleted ..............
>
> make[3]: Nothing to be done for `all-am'.
> /bin/sh ../libtool --tag=CC   --mode=link /usr/bin/gcc-4.2  -O2 -arch
> x86_64   -L/opt/local/lib -o aaindexextract aaindexextract.o
> ../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la
> ../plplot/libeplplot.la -lX11  -lm
> /bin/sh ../libtool --tag=CC   --mode=link /usr/bin/gcc-4.2  -O2 -arch
> x86_64   -L/opt/local/lib -o abiview abiview.o ../nucleus/libnucleus.la
> ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libeplplot.la -lX11  -lm
> /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/aaindexextract aaindexextract.o
>  -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib
> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
> ../plplot/.libs/libeplplot.dylib -lX11 -lm
> ld: library not found for -lX11
> collect2: ld returned 1 exit status
> /usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/abiview abiview.o
> -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib
> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
> ../plplot/.libs/libeplplot.dylib -lX11 -lm
> make[2]: *** [aaindexextract] Error 1
> make[2]: *** Waiting for unfinished jobs....
> ld: library not found for -lX11
> collect2: ld returned 1 exit status
> make[2]: *** [abiview] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
> Error: Target org.macports.build returned: shell command " cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1"
> && /usr/bin/make -j2 all " returned error 2
> DEBUG: Backtrace: shell command " cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_EMBOSS/work/EMBOSS-6.0.1"
> && /usr/bin/make -j2 all " returned error 2
>     while executing
> "command_exec build"
>     (procedure "portbuild::build_main" line 9)
>     invoked from within
> "$procedure $targetname"
> Warning: the following items did not execute (for EMBOSS):
> org.macports.activate org.macports.build org.macports.destroot
> org.macports.install
> Error: Status 1 encountered during processing.
> To report a bug, see <http://guide.macports.org/#project.tickets>
>
>
> Best Regards,
> Tõnu Margus
>
>
> Department of bioinformatics
> Tartu University
> Riia 23, 51010
> Estonia
>
> tel: +372 737637
> www: http://bioinfo.ut.ee/
>
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>