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agrimm/Emboss installation attempt fixed by xeyes.txt

Created January 9, 2010 11:01
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A failed attempt at installing emboss fixed by installing xeyes
Raw
Emboss installation attempt fixed by xeyes.txt
Disclaimer: as far as I can tell, the only difference between the two emboss installation attempts is installing xeyes, but I'm not 100% certain.
#==============================================================
#Two attempts at installing emboss before I tried installing xeyes, one without -d, one with -d
#Note: another couple of attempts prior to this can be seen in http://gist.github.com/272838
#==============================================================
Last login: Sat Jan 9 19:51:26 on console
192-168-1-5:~ agrimm$ port list emboss
EMBOSS @6.0.1 science/EMBOSS
192-168-1-5:~ agrimm$ sudo port install emboss
Password:
---> 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
/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
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.
Before reporting a bug, first run the command again with the -d flag to get complete output.
192-168-1-5:~ 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/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[2]: *** Waiting for unfinished jobs....
/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[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 $targetname"
Warning: the following items did not execute (for EMBOSS): org.macports.activate org.macports.build org.macports.destroot org.macports.install
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>
192-168-1-5:~ agrimm$ date #Done a bit later
Sat 9 Jan 2010 20:59:49 EST
192-168-1-5:~ agrimm$
#=================
# Installing xeyes
#=================
Last login: Sat Jan 9 20:01:44 on ttys001
192-168-1-5:~ agrimm$ sudo port install xeyes
Password:
---> Computing dependencies for xeyes
---> Fetching groff
---> Attempting to fetch groff-1.20.1.tar.gz from http://mirror.pacific.net.au/pub1/gnu/gnu/groff
---> Verifying checksum(s) for groff
---> Extracting groff
---> Configuring groff
---> Building groff
---> Staging groff into destroot
---> Installing groff @1.20.1_1
---> Activating groff @1.20.1_1
---> Cleaning groff
---> Fetching xorg-bigreqsproto
---> Attempting to fetch bigreqsproto-1.1.0.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-bigreqsproto
---> Verifying checksum(s) for xorg-bigreqsproto
---> Extracting xorg-bigreqsproto
---> Configuring xorg-bigreqsproto
---> Building xorg-bigreqsproto
---> Staging xorg-bigreqsproto into destroot
---> Installing xorg-bigreqsproto @1.1.0_0
---> Activating xorg-bigreqsproto @1.1.0_0
---> Cleaning xorg-bigreqsproto
---> Fetching xorg-inputproto
---> Attempting to fetch inputproto-2.0.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-inputproto
---> Verifying checksum(s) for xorg-inputproto
---> Extracting xorg-inputproto
---> Configuring xorg-inputproto
---> Building xorg-inputproto
---> Staging xorg-inputproto into destroot
---> Installing xorg-inputproto @2.0_0
---> Activating xorg-inputproto @2.0_0
---> Cleaning xorg-inputproto
---> Fetching xorg-kbproto
---> Attempting to fetch kbproto-1.0.4.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-kbproto
---> Verifying checksum(s) for xorg-kbproto
---> Extracting xorg-kbproto
---> Configuring xorg-kbproto
---> Building xorg-kbproto
---> Staging xorg-kbproto into destroot
---> Installing xorg-kbproto @1.0.4_0
---> Activating xorg-kbproto @1.0.4_0
---> Cleaning xorg-kbproto
---> Fetching xorg-xproto
---> Attempting to fetch xproto-7.0.16.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-xproto
---> Verifying checksum(s) for xorg-xproto
---> Extracting xorg-xproto
---> Configuring xorg-xproto
---> Building xorg-xproto
---> Staging xorg-xproto into destroot
---> Installing xorg-xproto @7.0.16_0
---> Activating xorg-xproto @7.0.16_0
---> Cleaning xorg-xproto
---> Fetching xorg-libXau
---> Attempting to fetch libXau-1.0.5.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libXau
---> Verifying checksum(s) for xorg-libXau
---> Extracting xorg-libXau
---> Configuring xorg-libXau
---> Building xorg-libXau
---> Staging xorg-libXau into destroot
---> Installing xorg-libXau @1.0.5_0
---> Activating xorg-libXau @1.0.5_0
---> Cleaning xorg-libXau
---> Fetching xorg-libXdmcp
---> Attempting to fetch libXdmcp-1.0.3.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libXdmcp
---> Verifying checksum(s) for xorg-libXdmcp
---> Extracting xorg-libXdmcp
---> Configuring xorg-libXdmcp
---> Building xorg-libXdmcp
---> Staging xorg-libXdmcp into destroot
---> Installing xorg-libXdmcp @1.0.3_0
---> Activating xorg-libXdmcp @1.0.3_0
---> Cleaning xorg-libXdmcp
---> Fetching xorg-util-macros
---> Attempting to fetch util-macros-1.4.1.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-util-macros
---> Verifying checksum(s) for xorg-util-macros
---> Extracting xorg-util-macros
---> Configuring xorg-util-macros
---> Building xorg-util-macros
---> Staging xorg-util-macros into destroot
---> Installing xorg-util-macros @1.4.1_0
---> Activating xorg-util-macros @1.4.1_0
---> Cleaning xorg-util-macros
---> Fetching xorg-xcmiscproto
---> Attempting to fetch xcmiscproto-1.2.0.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-xcmiscproto
---> Verifying checksum(s) for xorg-xcmiscproto
---> Extracting xorg-xcmiscproto
---> Configuring xorg-xcmiscproto
---> Building xorg-xcmiscproto
---> Staging xorg-xcmiscproto into destroot
---> Installing xorg-xcmiscproto @1.2.0_0
---> Activating xorg-xcmiscproto @1.2.0_0
---> Cleaning xorg-xcmiscproto
---> Fetching xorg-xextproto
---> Attempting to fetch xextproto-7.1.1.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-xextproto
---> Verifying checksum(s) for xorg-xextproto
---> Extracting xorg-xextproto
---> Configuring xorg-xextproto
---> Building xorg-xextproto
---> Staging xorg-xextproto into destroot
---> Installing xorg-xextproto @7.1.1_0
---> Activating xorg-xextproto @7.1.1_0
---> Cleaning xorg-xextproto
---> Fetching xorg-xf86bigfontproto
---> Attempting to fetch xf86bigfontproto-1.2.0.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-xf86bigfontproto
---> Verifying checksum(s) for xorg-xf86bigfontproto
---> Extracting xorg-xf86bigfontproto
---> Configuring xorg-xf86bigfontproto
---> Building xorg-xf86bigfontproto
---> Staging xorg-xf86bigfontproto into destroot
---> Installing xorg-xf86bigfontproto @1.2.0_0
---> Activating xorg-xf86bigfontproto @1.2.0_0
---> Cleaning xorg-xf86bigfontproto
---> Fetching xorg-xtrans
---> Attempting to fetch xtrans-1.2.5.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-xtrans
---> Verifying checksum(s) for xorg-xtrans
---> Extracting xorg-xtrans
---> Configuring xorg-xtrans
---> Building xorg-xtrans
---> Staging xorg-xtrans into destroot
---> Installing xorg-xtrans @1.2.5_0
---> Activating xorg-xtrans @1.2.5_0
---> Cleaning xorg-xtrans
---> Fetching xorg-libX11
---> Attempting to fetch libX11-1.3.2.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libX11
---> Verifying checksum(s) for xorg-libX11
---> Extracting xorg-libX11
---> Configuring xorg-libX11
---> Building xorg-libX11
---> Staging xorg-libX11 into destroot
---> Installing xorg-libX11 @1.3.2_0
---> Activating xorg-libX11 @1.3.2_0
---> Cleaning xorg-libX11
---> Fetching xorg-libXext
---> Attempting to fetch libXext-1.1.1.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libXext
---> Verifying checksum(s) for xorg-libXext
---> Extracting xorg-libXext
---> Configuring xorg-libXext
---> Building xorg-libXext
---> Staging xorg-libXext into destroot
---> Installing xorg-libXext @1.1.1_0
---> Activating xorg-libXext @1.1.1_0
---> Cleaning xorg-libXext
---> Fetching p5-locale-gettext
---> Attempting to fetch gettext-1.05.tar.gz from http://mirror.aarnet.edu.au/pub/CPAN/modules/by-module/Locale
---> Verifying checksum(s) for p5-locale-gettext
---> Extracting p5-locale-gettext
---> Applying patches to p5-locale-gettext
---> Configuring p5-locale-gettext
---> Building p5-locale-gettext
---> Staging p5-locale-gettext into destroot
---> Installing p5-locale-gettext @1.05_0
---> Activating p5-locale-gettext @1.05_0
---> Cleaning p5-locale-gettext
---> Fetching help2man
---> Attempting to fetch help2man-1.37.1.tar.gz from http://mirror.pacific.net.au/pub1/gnu/gnu/help2man
---> Verifying checksum(s) for help2man
---> Extracting help2man
---> Configuring help2man
---> Building help2man
---> Staging help2man into destroot
---> Installing help2man @1.37.1_1
---> Activating help2man @1.37.1_1
---> Cleaning help2man
---> Fetching m4
---> Attempting to fetch m4-1.4.13.tar.bz2 from http://mirror.pacific.net.au/pub1/gnu/gnu/m4
---> Verifying checksum(s) for m4
---> Extracting m4
---> Applying patches to m4
---> Configuring m4
---> Building m4
---> Staging m4 into destroot
---> Installing m4 @1.4.13_0
---> Activating m4 @1.4.13_0
---> Cleaning m4
---> Fetching autoconf
---> Attempting to fetch autoconf-2.65.tar.bz2 from http://mirror.pacific.net.au/pub1/gnu/gnu/autoconf
---> Verifying checksum(s) for autoconf
---> Extracting autoconf
---> Configuring autoconf
---> Building autoconf
---> Staging autoconf into destroot
---> Installing autoconf @2.65_0
---> Activating autoconf @2.65_0
---> Cleaning autoconf
---> Fetching automake
---> Attempting to fetch automake-1.11.1.tar.bz2 from http://mirror.pacific.net.au/pub1/gnu/gnu/automake
---> Verifying checksum(s) for automake
---> Extracting automake
---> Configuring automake
---> Building automake
---> Staging automake into destroot
---> Installing automake @1.11.1_0
---> Activating automake @1.11.1_0
---> Cleaning automake
---> Fetching libtool
---> Attempting to fetch libtool-2.2.6b.tar.gz from http://mirror.pacific.net.au/pub1/gnu/gnu/libtool
---> Verifying checksum(s) for libtool
---> Extracting libtool
---> Configuring libtool
---> Building libtool
---> Staging libtool into destroot
---> Installing libtool @2.2.6b_0
---> Activating libtool @2.2.6b_0
---> Cleaning libtool
---> Fetching xorg-libice
---> Attempting to fetch libICE-1.0.6.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libice
---> Verifying checksum(s) for xorg-libice
---> Extracting xorg-libice
---> Configuring xorg-libice
---> Building xorg-libice
---> Staging xorg-libice into destroot
---> Installing xorg-libice @1.0.6_0
---> Activating xorg-libice @1.0.6_0
---> Cleaning xorg-libice
---> Fetching xorg-libsm
---> Attempting to fetch libSM-1.1.1.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libsm
---> Verifying checksum(s) for xorg-libsm
---> Extracting xorg-libsm
---> Configuring xorg-libsm
---> Building xorg-libsm
---> Staging xorg-libsm into destroot
---> Installing xorg-libsm @1.1.1_0
---> Activating xorg-libsm @1.1.1_0
---> Cleaning xorg-libsm
---> Fetching xorg-libXt
---> Attempting to fetch libXt-1.0.7.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libXt
---> Verifying checksum(s) for xorg-libXt
---> Extracting xorg-libXt
---> Applying patches to xorg-libXt
---> Configuring xorg-libXt
---> Building xorg-libXt
---> Staging xorg-libXt into destroot
---> Installing xorg-libXt @1.0.7_1
---> Activating xorg-libXt @1.0.7_1
---> Cleaning xorg-libXt
---> Fetching xorg-libXmu
---> Attempting to fetch libXmu-1.0.5.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xorg-libXmu
---> Verifying checksum(s) for xorg-libXmu
---> Extracting xorg-libXmu
---> Configuring xorg-libXmu
---> Building xorg-libXmu
---> Staging xorg-libXmu into destroot
---> Installing xorg-libXmu @1.0.5_0
---> Activating xorg-libXmu @1.0.5_0
---> Cleaning xorg-libXmu
---> Fetching xeyes
---> Attempting to fetch xeyes-1.0.1.tar.bz2 from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/xeyes
---> Verifying checksum(s) for xeyes
---> Extracting xeyes
---> Configuring xeyes
---> Building xeyes
---> Staging xeyes into destroot
---> Installing xeyes @1.0.1_1
---> Activating xeyes @1.0.1_1
---> Cleaning xeyes
192-168-1-5:~ agrimm$ date
Sat 9 Jan 2010 20:52:40 EST
192-168-1-5:~ agrimm$ exit
logout
[Process completed]
#=============================
Successfully installing emboss
#=============================
Last login: Sat Jan 9 20:44:45 on ttys003
192-168-1-5:~ agrimm$ sudo port -d install emboss
Password:
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/abiview abiview.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib /opt/local/lib/libX11.dylib /opt/local/lib/libXau.dylib /opt/local/lib/libXdmcp.dylib -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 /opt/local/lib/libX11.dylib /opt/local/lib/libXau.dylib /opt/local/lib/libXdmcp.dylib -lm
creating abiview
creating aaindexextract
/bin/sh ../libtool --tag=CC --mode=link /usr/bin/gcc-4.2 -O2 -arch x86_64 -L/opt/local/lib -o acdc acdc.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 acdpretty acdpretty.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/acdc acdc.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib /opt/local/lib/libX11.dylib /opt/local/lib/libXau.dylib /opt/local/lib/libXdmcp.dylib -lm
/usr/bin/gcc-4.2 -O2 -arch x86_64 -o .libs/acdpretty acdpretty.o -L/opt/local/lib ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib ../plplot/.libs/libeplplot.dylib /opt/local/lib/libX11.dylib /opt/local/lib/libXau.dylib /opt/local/lib/libXdmcp.dylib -lm
creating acdc
creating acdpretty
#===================================================
And so on and so on - far too much output for a gist
#===================================================
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