gistfile1.txt

#Note: this was done 5 days ago (ie prior to the previous gist)

192-168-1-2:~ agrimm$ sudo port install emboss
Password:
--->  Computing dependencies for EMBOSS
--->  Fetching EMBOSS
--->  Attempting to fetch EMBOSS-6.0.1.tar.gz from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/EMBOSS
--->  Verifying checksum(s) for EMBOSS
--->  Extracting EMBOSS
--->  Configuring EMBOSS
--->  Building EMBOSS
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
Command output: mv -f .deps/water.Tpo .deps/water.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT whichdb.o -MD -MP -MF .deps/whichdb.Tpo -c -o whichdb.o whichdb.c
mv -f .deps/vectorstrip.Tpo .deps/vectorstrip.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT wobble.o -MD -MP -MF .deps/wobble.Tpo -c -o wobble.o wobble.c
mv -f .deps/whichdb.Tpo .deps/whichdb.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT wordcount.o -MD -MP -MF .deps/wordcount.Tpo -c -o wordcount.o wordcount.c
mv -f .deps/wordcount.Tpo .deps/wordcount.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT wordfinder.o -MD -MP -MF .deps/wordfinder.Tpo -c -o wordfinder.o wordfinder.c
mv -f .deps/wobble.Tpo .deps/wobble.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT wordmatch.o -MD -MP -MF .deps/wordmatch.Tpo -c -o wordmatch.o wordmatch.c
mv -f .deps/wordmatch.Tpo .deps/wordmatch.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT wossname.o -MD -MP -MF .deps/wossname.Tpo -c -o wossname.o wossname.c
mv -f .deps/wordfinder.Tpo .deps/wordfinder.Po
/usr/bin/gcc-4.2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DX_DISPLAY_MISSING=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I../nucleus -I../ajax -I../plplot  -DAJ_MACOSXLF -I/opt/local/include -DLENDIAN -DNO_AUTH  -O2 -arch x86_64  -MT yank.o -MD -MP -MF .deps/yank.Tpo -c -o yank.o yank.c
mv -f .deps/wossname.Tpo .deps/wossname.Po
/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 
mv -f .deps/yank.Tpo .deps/yank.Po
/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 
mkdir .libs
/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 
/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
ld: library not found for -lX11
collect2: ld returned 1 exit status
make[2]: *** [abiview] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [aaindexextract] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
 
Error: Status 1 encountered during processing.
192-168-1-2:~ agrimm$ 
 
192-168-1-2:~ agrimm$ sudo port selfupdate
Password:
--->  Updating the ports tree
--->  Updating MacPorts base sources using rsync
MacPorts base version 1.8.1 installed,
MacPorts base version 1.8.2 downloaded.
--->  MacPorts base is outdated, installing new version 1.8.2
Installing new MacPorts release in /opt/local as root:admin; permissions 0755; Tcl-Package in /Library/Tcl
 
 
The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated
192-168-1-2:~ agrimm$ sudo port upgrade outdated
--->  Computing dependencies for p5-uri
--->  Fetching p5-uri
--->  Attempting to fetch URI-1.52.tar.gz from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/perl5
--->  Verifying checksum(s) for p5-uri
--->  Extracting p5-uri
--->  Configuring p5-uri
--->  Building p5-uri
--->  Staging p5-uri into destroot
--->  Deactivating p5-uri @1.51_0
--->  Computing dependencies for p5-uri
--->  Installing p5-uri @1.52_0
--->  Activating p5-uri @1.52_0
--->  Cleaning p5-uri
--->  Computing dependencies for readline
--->  Fetching readline
--->  Attempting to fetch readline-6.1.tar.gz from http://mirror.pacific.net.au/pub1/gnu/gnu/readline
--->  Attempting to fetch readline-6.1.tar.gz from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/readline
--->  Verifying checksum(s) for readline
--->  Extracting readline
--->  Applying patches to readline
--->  Configuring readline
--->  Building readline
--->  Staging readline into destroot
--->  Deactivating readline @6.0.000_2+darwin
--->  Computing dependencies for readline
--->  Installing readline @6.1.000_1+darwin
--->  Activating readline @6.1.000_1+darwin
--->  Cleaning readline
--->  Computing dependencies for rsync
--->  Fetching rsync
--->  Attempting to fetch rsync-3.0.7.tar.gz from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/rsync
--->  Verifying checksum(s) for rsync
--->  Extracting rsync
--->  Applying patches to rsync
--->  Configuring rsync
--->  Building rsync
--->  Staging rsync into destroot
--->  Deactivating rsync @3.0.6_0
--->  Computing dependencies for rsync
--->  Installing rsync @3.0.7_0
--->  Activating rsync @3.0.7_0
--->  Cleaning rsync
192-168-1-2:~ agrimm$ port --version
Error: global does not accept --version
Usage: port
        [-bcdfknopqRstuvy] [-D portdir] [-F cmdfile] action [privopts] [actionflags]
        [[portname|pseudo-portname|port-url] [@version] [+-variant]... [option=value]...]...
    
"port help" or "man 1 port" for more information.
192-168-1-2:~ agrimm$ port @version
Unrecognized action "@version"
192-168-1-2:~ agrimm$ port -v
MacPorts 1.8.2
Entering interactive mode... ("help" for help, "quit" to quit)
[Users/agrimm] > quit
Goodbye
192-168-1-2:~ agrimm$ sudo port selfupdate
--->  Updating the ports tree
--->  Updating MacPorts base sources using rsync
MacPorts base version 1.8.2 installed,
MacPorts base version 1.8.2 downloaded.
--->  MacPorts base is already the latest version
 
The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated
192-168-1-2:~ agrimm$ sudo port upgrade outdated
Error: No ports matched the given expression
192-168-1-2:~ agrimm$ sudo port install emboss
--->  Computing dependencies for EMBOSS
--->  Building EMBOSS
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
Command output: Making all in PRINTS
make[3]: Nothing to be done for `all'.
Making all in PROSITE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_CORE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_FAM
make[3]: Nothing to be done for `all'.
Making all in JASPAR_PHYLOFACTS
make[3]: Nothing to be done for `all'.
Making all in JASPAR_CNE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_POLII
make[3]: Nothing to be done for `all'.
Making all in JASPAR_SPLICE
make[3]: Nothing to be done for `all'.
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/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 
/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
make[2]: *** [abiview] Error 1
make[2]: *** Waiting for unfinished jobs....
ld: library not found for -lX11
collect2: ld returned 1 exit status
make[2]: *** [aaindexextract] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
 
Error: Status 1 encountered during processing.
Before reporting a bug, first run the command again with the -d flag to get complete output.
192-168-1-2:~ agrimm$ sudo port install -d emboss
--->  Computing dependencies for EMBOSS
--->  Building EMBOSS
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
Command output: Making all in PRINTS
make[3]: Nothing to be done for `all'.
Making all in PROSITE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_CORE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_FAM
make[3]: Nothing to be done for `all'.
Making all in JASPAR_PHYLOFACTS
make[3]: Nothing to be done for `all'.
Making all in JASPAR_CNE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_POLII
make[3]: Nothing to be done for `all'.
Making all in JASPAR_SPLICE
make[3]: Nothing to be done for `all'.
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
make[2]: *** [aaindexextract] Error 1
make[2]: *** Waiting for unfinished jobs....
/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 
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: Status 1 encountered during processing.
Before reporting a bug, first run the command again with the -d flag to get complete output.
192-168-1-2:~ agrimm$ sudo port -d install emboss
DEBUG: Found port in file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/science/EMBOSS
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/EMBOSS
DEBUG: OS Platform: darwin
DEBUG: OS Version: 10.2.0
DEBUG: Mac OS X Version: 10.6
DEBUG: System Arch: i386
DEBUG: setting option os.universal_supported to yes
DEBUG: org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
DEBUG: org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
DEBUG: org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
DEBUG: adding the default universal variant
DEBUG: Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
DEBUG: Requested variant darwin is not provided by port EMBOSS.
DEBUG: Requested variant i386 is not provided by port EMBOSS.
DEBUG: Requested variant macosx is not provided by port EMBOSS.
--->  Computing dependencies for EMBOSS
DEBUG: Executing org.macports.main (EMBOSS)
DEBUG: Skipping completed org.macports.fetch (EMBOSS)
DEBUG: Skipping completed org.macports.checksum (EMBOSS)
DEBUG: Skipping completed org.macports.extract (EMBOSS)
DEBUG: Skipping completed org.macports.patch (EMBOSS)
DEBUG: Skipping completed org.macports.configure (EMBOSS)
--->  Building EMBOSS
DEBUG: Executing org.macports.build (EMBOSS)
DEBUG: Environment: MACOSX_DEPLOYMENT_TARGET='10.6'
DEBUG: Assembled 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'
Making all in plplot
Making all in lib
make[2]: Nothing to be done for `all'.
make[2]: Nothing to be done for `all-am'.
Making all in ajax
make[1]: Nothing to be done for `all'.
Making all in nucleus
make[1]: Nothing to be done for `all'.
Making all in emboss
Making all in acd
make[2]: Nothing to be done for `all'.
Making all in data
Making all in AAINDEX
make[3]: Nothing to be done for `all'.
Making all in CODONS
make[3]: Nothing to be done for `all'.
Making all in REBASE
make[3]: Nothing to be done for `all'.
Making all in PRINTS
make[3]: Nothing to be done for `all'.
Making all in PROSITE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_CORE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_FAM
make[3]: Nothing to be done for `all'.
Making all in JASPAR_PHYLOFACTS
make[3]: Nothing to be done for `all'.
Making all in JASPAR_CNE
make[3]: Nothing to be done for `all'.
Making all in JASPAR_POLII
make[3]: Nothing to be done for `all'.
Making all in JASPAR_SPLICE
make[3]: Nothing to be done for `all'.
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
make[2]: *** [aaindexextract] Error 1
make[2]: *** Waiting for unfinished jobs....
/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 
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>