# -*- org -*-
#+TODO: TODO BROKEN DEFERRED | CANTTEST IGNORE DONE

# This file lists general tasks as well as the current status of all
# GNU packages (including sub-projects GNOME and GNUstep). Note that
# some packages are listed as IGNORED, generally due to being retired
# packages or non-software packages; these are counted as completed
# tasks. BROKEN packages do not build correctly; these are not
# counted as completed tasks. DEFERRED packages typically do not yet
# have a release available and will be implemented upon their
# availability; these are not counted as completed. CANTTEST packages
# have hardware or software dependencies that make testing their build
# process difficult or impossible.
#
# Note: this file is best viewed in Emacs Org-Mode
#

to do : learn org-mode

this file is out of date

* General tasks [0%]
** TODO Old tasks, pre-Brandon...to be reconsidered [88%]
*** DONE libc breaks everything when it is installed (bad ABI)
    CLOSED: [2013-01-14 Mon 00:13]
*** DONE Karl: I think the most important thing to support is configure
  CLOSED: [2011-03-01 Tue 13:54]
  :LOGBOOK:
  - State "DONE"       from ""           [2011-03-01 Tue 13:54]
  :END:
--prefix=/somewhere.  Probably that, and just about everything, can
simply be passed to the subdirs.  So the job of top level
configure/makefile would be to loop over all supported subdirs and call
configure/make for each.
*** DONE Karl: Based on my experience with TeX Live, I expect it would also be
greatly appreciated if it was possible to say
  configure --disable-foobar
to explicitly disable building of any package foobar for whatever
  reason. (done: see IGNORE_DEPS in gar.conf.mk)
*** DONE util/buildit.sh needs to delete old logs/*.FAIL entries
    CLOSED: [2011-04-13 Wed 11:56]
    - State "DONE"       [2011-04-13 Wed 11:56]
*** IGNORE nettle needs --libdir => lib instead of lib64
    CLOSED: [2013-11-06 Wed 23:49]
*** IGNORE texinfo needs make install-tex TEXMF=/gnu
    CLOSED: [2013-11-06 Wed 23:49]
*** DONE build bazaar tries to build the zlib dependency. But here I get the
    error Message:
      cd work/zlib-1.2.5 &&  ./configure '--prefix=/usr/local/gltools/gnu' '--exec-prefix=/usr/local/gltools/gnu/arch_a'
      unknown option: --exec-prefix=/usr/local/gltools/gnu/arch_a
      (Brandon: seems to work...done)
*** DONE for i.e. make the installation puts its files
     /usr/local/gltools/gnu/packages/make-3.81/arch_a/ and
     /usr/local/gltools/gnu/packages/make-3.81/share/, but installing from
     a second architecture deletes the whole
     /usr/local/gltools/gnu/packages/make-3.81 tree. (done: GARPROFILE)
*** TODO deletion of the whole packages tree for a project would also delete
    any customization in the share tree while installing for arch_b (like
    in share/emacs/23.3/site-lisp/ or share/emacs/site-lisp/).
** TODO re-implement tests and verify packages
*** mainly need to check projects not using gar.lib/auto.mk for test targets
*** re-enable USE_TESTS in gar.lib/auto.mk
** TODO GAR/GARStow decrufting
*** TODO (maybe) rename GAR* variables to GSRC* (ie GARNAME -> GSRCNAME)
**** not really necessary but GSRC is pretty removed from GAR by now so
     it wouldn't hurt anything and it might help the variables to make
     more immediate sense.
**** TODO GARNAME
**** TODO GARDIR
**** TODO GARVERSION
**** TODO GARCHIVEDIR
**** TODO GARPROFILE
**** TODO GARARCH
**** TODO GARBALLDIR
*** TODO (maybe) rename gar.* files to gsrc.* (ie gar.lib.mk -> gsrc.lib.mk)
**** TODO gar.mk
**** TODO gar.lib.mk
**** TODO gar.env.mk
**** TODO gar.lib/
**** TODO gar.master.mk
*** TODO clean out unnecessary sites from gar.master.mk
*** TODO (maybe) clean out unnecessary rules from gar.lib.mk
** TODO Add missing gpg-keyrings
aris
c-graph
remotecontrol
* GNU packages [424/473] [89%]
** IGNORE 3dkit
*** decommissioned
** DONE 3dldf
   CLOSED: [2012-12-16 Sun 20:11]
** DONE a2ps
   CLOSED: [2012-12-16 Sun 20:11]
** IGNORE abcsh
   CLOSED: [2012-12-16 Sun 20:11]
*** decommissioned
** DONE acct
   CLOSED: [2012-12-16 Sun 20:11]
** DONE acm
   CLOSED: [2012-12-16 Sun 20:11]
** DONE adns
   CLOSED: [2012-12-16 Sun 20:12]
** DONE aeneas
   CLOSED: [2012-12-16 Sun 20:12]
*** decommissioned
** IGNORE aetherspace
   CLOSED: [2013-03-24 Sun 16:23]
*** retired
** DONE alive
   CLOSED: [2012-12-16 Sun 20:12]
** DONE anubis
   CLOSED: [2012-12-16 Sun 20:12]
** DONE apl
   CLOSED: [2013-10-04 Fri 16:49]
** DONE archimedes
   CLOSED: [2012-12-16 Sun 20:12]
** DONE aris
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE aroundme
   CLOSED: [2012-12-16 Sun 20:12]
*** decommissioned
** DONE aspell
   CLOSED: [2012-12-16 Sun 20:12]
** DONE auctex
   CLOSED: [2012-12-16 Sun 20:12]
** DONE autoconf
   CLOSED: [2012-12-16 Sun 20:12]
** DONE autoconf-archive
   CLOSED: [2012-12-16 Sun 20:12]
** DONE autogen
   CLOSED: [2012-12-16 Sun 20:12]
** DONE automake
   CLOSED: [2012-12-16 Sun 20:12]
** DONE avl
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE awacs
   CLOSED: [2012-12-22 Sat 19:07]
*** (decommissioned)
** DONE ballandpaddle
   CLOSED: [2012-12-16 Sun 20:12]
** DONE barcode
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bash
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bayonne
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bazaar
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bc
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE bfd
   CLOSED: [2012-12-16 Sun 21:23]
*** packaged with binutil
** DONE binutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bison
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bool
   CLOSED: [2012-12-16 Sun 20:12]
** DONE bpel2owfn
   CLOSED: [2013-10-04 Fri 12:56]
** DONE c-graph
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ccaudio
   CLOSED: [2013-10-04 Fri 13:51]
** DONE ccd2cue
   CLOSED: [2013-11-07 Thu 10:37]
** DONE ccide
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ccrtp
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ccscript
   CLOSED: [2013-10-09 Wed 15:28]
*** ucommon-related errors
** DONE cfengine
   CLOSED: [2012-12-16 Sun 20:12]
** DONE cflow
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE cfs-el
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE cgicc
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE checker
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE chess
   CLOSED: [2012-12-16 Sun 20:12]
** CANTTEST cim
*** not x86_64 compatible; can't test without building a VM
** DONE classpath
   CLOSED: [2012-12-16 Sun 20:12]
** DONE classpathx-activation
   CLOSED: [2013-11-28 Thu 19:47]
** BROKEN classpathx-comm
** IGNORE classpathx-jaxp
   CLOSED: [2013-11-06 Wed 23:24]
merged into classpath
** DONE classpathx-mail
   CLOSED: [2013-11-28 Thu 20:00]
** DONE classpathx-servletapi
   CLOSED: [2013-11-06 Wed 23:25]

** DONE clisp
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED cobol
*** still in early (stalled?) development
** DONE combine
   CLOSED: [2012-12-16 Sun 20:12]
** DONE commoncpp
   CLOSED: [2012-12-16 Sun 20:12]
** DONE complexity
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE config:
   CLOSED: [2012-12-16 Sun 20:16]
*** dev package (no install) only; low priority
** IGNORE cons
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE coreutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE cpio
   CLOSED: [2012-12-16 Sun 20:12]
** DONE cppi
   CLOSED: [2012-12-16 Sun 20:12]
** DONE cssc
   CLOSED: [2012-12-16 Sun 20:12]
** DONE cursynth
   CLOSED: [2014-03-18 Tue 22:17]
** DONE dap
   CLOSED: [2012-12-16 Sun 20:12]
** DONE datamash
   CLOSED: [2014-08-03 Sun 10:52]
** IGNORE dc:
   CLOSED: [2012-12-16 Sun 20:16]
*** installed as part of bc
** DONE ddd
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ddrescue
   CLOSED: [2012-12-16 Sun 20:12]
** DONE dejagnu
   CLOSED: [2012-12-16 Sun 20:12]
** DONE denemo
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE dgs
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE dico
   CLOSED: [2012-12-16 Sun 20:12]
** DONE diction
   CLOSED: [2012-12-16 Sun 20:12]
** DONE direvent
   CLOSED: [2014-10-06 Mon 20:14]
** DONE diffutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE dionysus
   CLOSED: [2012-12-16 Sun 20:12]
** DONE dismal
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE dld
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE dmd
   CLOSED: [2012-12-16 Sun 20:12]
** DONE dominion
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE dotgnu
   CLOSED: [2013-01-15 Tue 22:41]
*** decommissioned
** IGNORE dotgnu-forum
   CLOSED: [2013-01-15 Tue 22:42]
*** decommissioned
** IGNORE dotgnu-pnet
   CLOSED: [2013-01-15 Tue 22:42]
*** decommissioned
** IGNORE dr.genius
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED dr-geo
*** GNU version is long unmaintained
** DONE easejs
   CLOSED: [2014-07-08 Tue 19:47]
** DONE ed
   CLOSED: [2012-12-16 Sun 20:12]
** DONE edma
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE elib
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE electric
   CLOSED: [2012-12-16 Sun 20:12]
** DONE emacs
   CLOSED: [2012-12-16 Sun 20:12]
** DONE emacs-muse
   CLOSED: [2012-12-16 Sun 20:12]
** DONE emms
   CLOSED: [2012-12-16 Sun 20:12]
** DONE enscript
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED eprints
*** not sure about the status of this
** DEFERRED epsilon
*** no release available
** DONE fdisk
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ferret
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE ffp
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE fhp
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE findutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE fisicalab
   CLOSED: [2013-12-29 Sun 14:44]
** DONE fontutils
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE free (gnu.free)
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE freedink
   CLOSED: [2012-12-16 Sun 20:12]
** DONE freefont
   CLOSED: [2012-12-16 Sun 20:12]
** DONE freeipmi
   CLOSED: [2012-12-16 Sun 20:12]
** DONE freetalk
   CLOSED: [2012-12-16 Sun 20:12]
** DONE fribidi
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gama
   CLOSED: [2012-12-16 Sun 20:12]
** DONE garpd
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gawk
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gcal
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gcc
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gceb
   CLOSED: [2013-03-30 Sat 12:46]
** DONE gcide
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gcl
   CLOSED: [2013-10-04 Fri 12:27]
** DONE gcompris
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gcron
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gdb
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gdbm
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gengen
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gengetopt
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gettext
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gfe
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gforth
   CLOSED: [2012-12-16 Sun 20:12]
** CANTTEST ggradebook
*** requires GTK+ 1
** IGNORE ggv
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE ghostscript
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gicqd
   CLOSED: [2012-12-16 Sun 20:
*** decommissioned
** DONE gidfwizard
   CLOSED: [2013-03-30 Sat 12:46]
** DONE gift
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gimp
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE giptables
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gjdoc
   CLOSED: [2013-11-28 Thu 20:03]
** BROKEN gleem
*** extremely inflexible Makefile
** DONE global
   CLOSED: [2012-12-16 Sun 20:12]
** DONE glpk
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED glue
*** no release available
** DONE gmediaserver
   CLOSED: [2013-02-03 Sun 23:41]
*** libupnp errors
** IGNORE gmorph
   CLOSED: [2013-10-09 Wed 15:14]
*** decommissioned
** DONE gmp
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnash
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnat
   CLOSED: [2012-12-16 Sun 21:30]
*** packaged with gcc
** DONE gnats
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnatsweb
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnochive
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE gnotary
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE gnotepad+
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED gnowsys
***  no release available
** IGNORE gnu-crypto
   CLOSED: [2012-12-16 Sun 20:16]
***  generally merged with classpath; low priority
** DONE gnu-c-manual
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnu-pw-mgr
   CLOSED: [2013-11-07 Thu 23:19]
no release yet
** IGNORE gnu-queue
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED gnuae
***  no release available
** DONE gnubatch
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnubios
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gnubg
** IGNORE gnucad
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gnubiff
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnubik
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnucap
   CLOSED: [2013-03-19 Tue 11:19]
** DONE gnucash
   CLOSED: [2012-12-16 Sun 22:28]
** IGNORE gnucomm
   CLOSED: [2012-12-16 Sun 20:16]
*** see individual packages (sipwitch etc)
** DONE gnudos
   CLOSED: [2014-07-08 Tue 19:46]
** DONE gnue-appserver
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnue-common
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnue-forms
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnue-navigator
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnue-reports
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnufi
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED gnufm
no release available
** DONE gnugo
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnuit
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnujdoc
   CLOSED: [2012-12-16 Sun 20:16]
*** just documentation
** DONE gnujump
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED gnukart
***  only one ancient release
** IGNORE gnulib
   CLOSED: [2012-12-16 Sun 20:16]
***  dev-only (no install) package; low priority
** CANTTEST gnumach
** DEFERRED gnumed
***  strange (non-existent?) install procedure; needs research
** DONE gnump3d
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnun
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnunet
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnunet-fuse
   CLOSED: [2013-12-28 Sat 22:24]
** DONE gnunet-gtk
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnupedia
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gnupg
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnupod
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnuprologjava
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnuradio
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnurobots
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnuschool
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnushogi
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnuskies
   CLOSED: [2013-10-09 Wed 15:17]
*** decommissioned
** BROKEN gnusound
*** gnome hell
** DEFERRED gnuspeech
*** no release available
** DONE gnuspool
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnusql
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE gnustandards
   CLOSED: [2012-12-16 Sun 20:16]
*** not a package?
** DONE gnutls
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnutrition
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnuts
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE gnuzilla
   CLOSED: [2012-12-16 Sun 20:16]
*** see icecat
** IGNORE goldwater
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE goodbye
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE goose
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE goptical
   CLOSED: [2012-12-16 Sun 20:12]
** BROKEN gpaint
*** Requires outdated GTK2, or some other Gnome hell
** DONE gperf
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gphoto
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gprolog
   CLOSED: [2012-12-16 Sun 20:12]
** DONE grabcomics
   CLOSED: [2013-01-16 Wed 23:12]
** IGNORE graphics
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** BROKEN greg
*** requires ancient libtool
** DONE grep
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gretl
   CLOSED: [2012-12-16 Sun 20:12]
** DONE groff
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE grover
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE grub
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gsasl
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gsegrafix
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gsl
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gsrc
   CLOSED: [2012-12-16 Sun 20:16]
*** infinite recursion
** DONE gss
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gtick
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gtkeditor
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE gtkeyboard
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gtypist
   CLOSED: [2012-12-16 Sun 20:12]
** DONE guile
   CLOSED: [2012-12-16 Sun 20:12]
** DONE guile-clutter
   CLOSED: [2013-01-15 Tue 22:14]
** DONE guile-dbi
   CLOSED: [2012-12-16 Sun 20:12]
** DONE guile-gnome-platform
   CLOSED: [2012-12-16 Sun 20:12]
** TODO guile-gstreamer
*** Build fails due to not finding guile-gnome-glib
maybe due to being significantly older than the guile-gnome-platform package
** DONE guile-gtk
   CLOSED: [2012-12-16 Sun 20:12]
** BROKEN guile-gtksourceview
*** Build fails due to not finding guile-gnome-glib
maybe due to being significantly older than the guile-gnome-platform package
** DONE guile-ncurses
   CLOSED: [2012-12-16 Sun 20:12]
** DONE guile-opengl
   CLOSED: [2014-07-08 Tue 19:47]
** DONE guile-rpc
   CLOSED: [2014-05-23 Fri 16:36]
*** only alpha releases available
** DONE guile-sdl
   CLOSED: [2013-04-20 Sat 10:34]
** TODO guix
** DONE gurgle
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE guss
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE gv
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gvpe
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gxmessage
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gzip
   CLOSED: [2012-12-16 Sun 20:12]
** CANTTEST halifax-viewer
*** requires GTK 1
** CANTTEST halifax-sender
*** requires GTK 1
** TODO health
** IGNORE hegemonie
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE hello
   CLOSED: [2012-12-16 Sun 20:12]
** DONE help2man
   CLOSED: [2012-12-16 Sun 20:12]
** DONE hp2xx
   CLOSED: [2012-12-16 Sun 20:12]
** DONE httptunnel
   CLOSED: [2012-12-16 Sun 20:12]
** TODO hurd
** BROKEN hyperbole
** DONE icecat
   CLOSED: [2012-12-16 Sun 20:12]
** DONE idutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ignuit
   CLOSED: [2013-01-20 Sun 16:43]
** DONE indent
   CLOSED: [2012-12-16 Sun 20:12]
** DONE inetlib
   CLOSED: [2013-11-23 Sat 13:26]
** DONE inetutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE intlfonts
   CLOSED: [2012-12-22 Sat 18:48]
** DONE jacal
   CLOSED: [2012-12-16 Sun 20:12]
** DONE java-getopt
   CLOSED: [2012-12-22 Sat 19:03]
** IGNORE jdresolve
   CLOSED: [2013-10-09 Wed 15:18]
*** decommissioned
** DONE jel
   CLOSED: [2012-12-16 Sun 20:12]
** DONE jwhois
   CLOSED: [2012-12-16 Sun 20:12]
** DONE kawa
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED kopi
*** no release available
** BROKEN leg
*** requires use of autoreconf, but that process fails
** IGNORE lengualibre
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE leonardo
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE less
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libassuan
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libc
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libcdio
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libextractor
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED libffcall
*** no release available
** DONE libgcrypt
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE libiberty
   CLOSED: [2012-12-22 Sat 19:42]
*** packaged with binutils and gcc
** DONE libiconv
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libidn
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libksba
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libmatheval
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libmicrohttpd
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE libopts
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED libredwg
*** no release available
** DEFERRED librefm (gnufm)
*** no release available
** DONE librejs
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libsigsegv
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libsrcinst
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libtasn1
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libtool
   CLOSED: [2012-12-16 Sun 20:12]
** DONE libunistring
   CLOSED: [2012-12-16 Sun 20:12]
** BROKEN libxmi
*** old libtool problems
** DONE lightning
   CLOSED: [2012-12-16 Sun 20:12]
** DONE lilypond
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED lims
no release yet
** DONE linux-libre
   CLOSED: [2012-12-16 Sun 20:12]
** DONE liquidwar6
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE lispintro
   CLOSED: [2012-12-22 Sat 19:47]
*** just documentation
** DONE lrzsz
   CLOSED: [2012-12-22 Sat 20:02]
** DONE lsh
   CLOSED: [2012-12-16 Sun 20:12]
** DONE m4
   CLOSED: [2012-12-16 Sun 20:12]
** DONE macchanger
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mailman
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mailutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE make
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE mana
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE marst
   CLOSED: [2012-12-16 Sun 20:12]
** DONE maverik
   CLOSED: [2013-03-18 Mon 23:37]
** DONE mc
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mcron
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mcsim
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mdk
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mediagoblin
   CLOSED: [2012-12-16 Sun 20:12]
** DONE melting
   CLOSED: [2012-12-22 Sat 20:38]
** IGNORE messenger
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED metaexchange
*** no release available
** DONE metahtml
   CLOSED: [2013-04-03 Wed 00:47]
*** build mysteriously fails
** IGNORE mgcp
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE mifluz
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mig
   CLOSED: [2012-12-16 Sun 20:12]
** DONE miscfiles
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mit-scheme
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE mll2html
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE moe
   CLOSED: [2012-12-16 Sun 20:12]
** DONE motti
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mpc
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mpfr
   CLOSED: [2012-12-16 Sun 20:12]
** DONE mtools
   CLOSED: [2012-12-16 Sun 20:12]
** DONE myserver
   CLOSED: [2012-12-16 Sun 20:12]
** DONE nana
   CLOSED: [2013-01-04 Fri 23:42]
** DONE nano
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ncurses
   CLOSED: [2012-12-16 Sun 20:12]
** DONE nettle
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE network
   CLOSED: [2012-12-16 Sun 20:16]
*** metaproject (see gnunet, social, gnufm)
** IGNORE obst
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE octal
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE ocrad
   CLOSED: [2012-12-16 Sun 20:12]
** DONE octave
   CLOSED: [2012-12-16 Sun 20:12]
** DONE oleo
   CLOSED: [2013-01-20 Sun 15:33]
** BROKEN orgadoc
*** Eiffel hell
** DONE osip
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE p2c
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** IGNORE packaging
   CLOSED: [2012-12-16 Sun 20:16]
*** retired metaproject
** BROKEN panorama
*** `configure' fails, apparently due to libtool; probably requires an old
version
** IGNORE paperclips
   CLOSED: [2013-10-09 Wed 15:34]
*** decommissioned
** DONE parallel
   CLOSED: [2012-12-16 Sun 20:12]
** DONE parted
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED pascal
*** only alpha releases available
** DONE patch
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE patchwork
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE paxutils
   CLOSED: [2013-01-16 Wed 23:55]
** DONE pcb
   CLOSED: [2013-01-17 Thu 00:04]
** DEFERRED pdf
*** no release available?
** DONE pem
   CLOSED: [2012-12-16 Sun 20:12]
** DONE pexec
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE pgccfd
   CLOSED: [2013-01-05 Sat 00:04]
*** package is documentation only
** DEFERRED phantom_home
*** extremely out-dated c++ code; defer until a new release
** DONE pies
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED pipo
*** can't find any release!
** IGNORE pips
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE plotutils
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE poc
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED polyxmass
*** no release available? currently unmaintained
** DEFERRED powerguru
*** no release available
** IGNORE proto
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE proxyknife
   CLOSED: [2012-12-16 Sun 20:12]
** DONE pspp
   CLOSED: [2012-12-16 Sun 20:12]
** DONE psychosynth
   CLOSED: [2013-01-05 Sat 18:17]
** DONE pth
   CLOSED: [2012-12-16 Sun 20:12]
** DONE pyconfigure
   CLOSED: [2012-12-16 Sun 20:16]
*** dev only (no install); low priority
** DEFERRED pythonwebkit
*** no release available
** IGNORE qexo
   CLOSED: [2013-01-12 Sat 11:24]
*** included in kawa
** DEFERRED quickthreads
*** no release available yet
** DONE R
   CLOSED: [2013-01-13 Sun 23:42]
** DONE radius
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE rat (decommissioned)
   CLOSED: [2012-12-16 Sun 20:16]
** DONE rcs
   CLOSED: [2012-12-16 Sun 20:12]
** DONE readline
   CLOSED: [2012-12-16 Sun 20:12]
** DONE recutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE reftex
   CLOSED: [2013-01-13 Sun 22:59]
** DONE remotecontrol
   CLOSED: [2013-01-11 Fri 20:30]
** BROKEN rottlog
*** permissions hell
** DONE rpge
   CLOSED: [2013-10-09 Wed 15:20]
** DONE rush
   CLOSED: [2012-12-16 Sun 20:12]
** DONE sauce
   CLOSED: [2013-01-17 Thu 22:10]
** BROKEN sather
*** super-unfriendly Make system
** DONE sauce
   CLOSED: [2012-12-16 Sun 20:12]
** DONE scm
   CLOSED: [2012-12-16 Sun 20:12]
** DONE screen
   CLOSED: [2012-12-16 Sun 20:12]
** DONE sed
   CLOSED: [2012-12-16 Sun 20:12]
** DONE serveez
   CLOSED: [2013-02-03 Sun 11:46]
** DONE sharutils
   CLOSED: [2012-12-16 Sun 20:12]
** DONE shishi
   CLOSED: [2012-12-16 Sun 20:12]
** DONE shmm
   CLOSED: [2012-12-16 Sun 20:12]
** DONE shtool
   CLOSED: [2012-12-16 Sun 20:12]
** DONE sipwitch
   CLOSED: [2012-12-16 Sun 20:12]
** DONE slib
   CLOSED: [2012-12-16 Sun 20:12]
** DONE smalltalk
   CLOSED: [2012-12-16 Sun 20:12]
** DONE smarteiffel
   CLOSED: [2012-12-16 Sun 20:12]
** DONE snakecharmer
   CLOSED: [2013-01-17 Thu 22:24]
** TODO social
** DONE solfege
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE songanizer
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE sourceinstall
   CLOSED: [2012-12-16 Sun 20:12]
** DONE sourceinstall-gtk
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE sovix
   CLOSED: [2013-04-03 Wed 00:52]
*** decommissioned
** CANTTEST spacechart
*** requires gtk1
** DONE speex
   CLOSED: [2013-01-17 Thu 22:28]
** DONE spell
   CLOSED: [2012-12-16 Sun 20:12]
** DONE sqltutor
   CLOSED: [2012-12-16 Sun 20:12]
** DONE src-highlite
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED stalkerfs
*** no release available
** DONE stow
   CLOSED: [2012-12-16 Sun 20:12]
** DONE stump
   CLOSED: [2013-01-17 Thu 22:44]
** DONE superopt
   CLOSED: [2012-12-16 Sun 20:12]
** DONE swbis
   CLOSED: [2013-04-03 Wed 22:51]
** IGNORE sweater
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED sysutils
*** no official release (but an SVN tag exists)
** IGNORE sxml
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE talkfilters
   CLOSED: [2013-01-14 Mon 00:12]
** DONE tar
   CLOSED: [2012-12-16 Sun 20:12]
** DONE termcap
   CLOSED: [2012-12-16 Sun 20:12]
** DONE termutils
   CLOSED: [2013-03-18 Mon 00:12]
** DONE teseq
   CLOSED: [2012-12-16 Sun 20:12]
** DONE teximpatient
   CLOSED: [2013-01-14 Mon 00:14]
*** just documentation
** DONE texinfo
   CLOSED: [2012-12-16 Sun 20:12]
** DONE texmacs
   CLOSED: [2013-03-18 Mon 22:32]
** DONE thales
   CLOSED: [2012-12-16 Sun 20:12]
** DONE time
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE toutdoux
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE tramp
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE trans-coord
   CLOSED: [2013-01-14 Mon 00:16]
*** GNU translation meta-project; see gnun
** DONE trueprint
   CLOSED: [2012-12-16 Sun 20:12]
** DONE ucommon
   CLOSED: [2012-12-16 Sun 20:12]
** TODO unifont
** DONE units
   CLOSED: [2012-12-16 Sun 20:12]
** DONE unrtf
   CLOSED: [2012-12-16 Sun 20:12]
** DONE userv
   CLOSED: [2012-12-16 Sun 20:12]
** DONE uucp
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE vc-changelog
   CLOSED: [2012-12-16 Sun 20:16]
*** see vc-dwim
** DONE vc-dwim
   CLOSED: [2012-12-16 Sun 20:12]
** DONE vcdimager
   CLOSED: [2012-12-16 Sun 20:12]
** DONE vera
   CLOSED: [2012-12-16 Sun 20:12]
** DEFERRED vmgen
*** no release available
** DONE vmslib
   CLOSED: [2013-01-15 Tue 22:33]
*** source release only, not built or installed
** IGNORE w3
   CLOSED: [2013-10-09 Wed 15:37]
*** now distributed with emacs via elpa
** DONE wb
   CLOSED: [2012-12-16 Sun 20:12]
** DONE wdiff
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE webpublish
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE websocket4j
   CLOSED: [2013-01-15 Tue 21:52]
** DONE webstump
   CLOSED: [2013-01-17 Thu 23:46]
** DONE wget
   CLOSED: [2012-12-16 Sun 20:12]
** DONE which
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE womb
   CLOSED: [2013-01-16 Wed 00:23]
*** just source code, but not an actual package per se
** DONE xaos
   CLOSED: [2013-01-16 Wed 00:22]
*** program segfaults
** IGNORE xbase
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE xboard
   CLOSED: [2012-12-16 Sun 20:12]
** TODO xhippo
*** requires gtk 1
** IGNORE xinfo
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** CANTTEST xlogmaster
*** requires GTK 1
** IGNORE xmhtml
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DEFERRED xmlat
*** no release available
** DONE xnee
   CLOSED: [2012-12-16 Sun 20:12]
** DONE xorriso
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE zebra
   CLOSED: [2012-12-16 Sun 20:16]
*** decommissioned
** DONE zile
   CLOSED: [2012-12-16 Sun 20:12]
** DONE zrtp
   CLOSED: [2012-12-16 Sun 20:12]
* GNOME packages
** Core [15/116] [12%]
*** TODO ModemManager
*** TODO NetworkManager
*** TODO at-spi2-atk
*** TODO at-spi2-core
*** DONE atk
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO atkmm
*** TODO baobab
*** TODO cantarell-fonts
*** TODO caribou
*** DONE clutter
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO clutter-gst
*** TODO clutter-gtk
*** DONE cogl
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE dconf
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO empathy
*** TODO eog
*** TODO epiphany
*** TODO evince
*** TODO evolution-data-server
*** TODO folks
*** DONE gcr
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE gdk-pixbuf
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO gdm
*** TODO geocode-glib
*** TODO gjs
*** DONE glib
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO glib-networking
*** TODO glibmm
*** TODO gmime
*** TODO gnome-backgrounds
*** TODO gnome-bluetooth
*** TODO gnome-calculator
*** TODO gnome-contacts
*** TODO gnome-control-center
*** DONE gnome-desktop
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO gnome-dictionary
*** TODO gnome-disk-utility
*** TODO gnome-font-viewer
*** TODO gnome-icon-theme
*** TODO gnome-icon-theme-extras
*** TODO gnome-js-common
*** DONE gnome-keyring
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO gnome-menus
*** TODO gnome-online-accounts
*** TODO gnome-online-miners
*** TODO gnome-packagekit
*** TODO gnome-screenshot
*** TODO gnome-session
*** TODO gnome-settings-daemon
*** TODO gnome-shell
*** TODO gnome-shell-extensions
*** TODO gnome-system-log
*** TODO gnome-system-monitor
*** TODO gnome-terminal
*** TODO gnome-themes-standard
*** TODO gnome-user-docs
*** TODO gnome-user-share
*** TODO gnome-video-effects
*** TODO gobject-introspection
*** TODO grillo
*** TODO grillo-plugins
*** TODO gsettings-desktop-schemas
*** TODO gssdp
*** TODO gst-plugins-base
*** TODO gst-plugins-good
*** TODO gstreamer
*** DONE gtk+ 2
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE gtk+ 3
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO gtk-doc
*** TODO gtkmm
*** DONE gtksourceview
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO gucharmap
*** TODO gupnp
*** TODO gupnp-igd
*** TODO gvfs
*** DONE json-glib
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO libchamplain
*** TODO libcroco
*** TODO libgdata
*** TODO libgee
*** TODO libgnome-keyring
*** TODO libgnomekbd
*** TODO libgsf
*** TODO libgtop
*** TODO libgweather
*** TODO libgxps
*** TODO libnotify
*** TODO libpeas
*** TODO libqmi
*** TODO librsvg
*** TODO libsecret
*** TODO libsigc++
*** TODO libsoup
*** TODO libwnck
*** TODO libzapojit
*** TODO mm-common
*** TODO mousetweaks
*** TODO mutter
*** DONE nautilus
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO network-manager-applet
*** DONE pango
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO pangomm
*** TODO pygobject
*** TODO rest
*** TODO seed
*** TODO sushi
*** TODO totem
*** TODO totem-pl-parser
*** TODO tracker
*** TODO vala
*** TODO vino
*** TODO vte
*** TODO yelp
*** TODO yelp-tools
*** TODO yelp-xsl
*** TODO zenity
** Apps [1/44] [2%]
*** TODO accerciser
*** TODO aisleriot
*** TODO anjuta
*** TODO bijiben
*** TODO brasero
*** TODO cheese
*** TODO devhelp
*** TODO evolution
*** TODO file-roller
*** TODO five-or-more
*** TODO four-in-a-row
*** TODO gedit
*** DONE glade
    CLOSED: [2012-12-16 Sun 20:12]
*** TODO gnome-boxes
*** TODO gnome-chess
*** TODO gnome-clocks
*** TODO gnome-color-manager
*** TODO gnome-devel-docs
*** TODO gnome-documents
*** TODO gnome-getting-started-docs
*** TODO gnome-initial-setup
*** TODO gnome-klotski
*** TODO gnome-mahjongg
*** TODO gnome-maps
*** TODO gnome-mines
*** TODO gnome-music
*** TODO gnome-nettool
*** TODO gnome-nibbles
*** TODO gnome-photos
*** TODO gnome-robots
*** TODO gnome-sudoku
*** TODO gnome-tetravex
*** TODO gnome-weather
*** TODO iagno
*** TODO lightsoff
*** TODO nautilus-sendto
*** TODO nemiver
*** TODO orca
*** TODO quadrapassel
*** TODO rygel
*** TODO seahorse
*** TODO swell-foop
*** TODO tali
*** TODO vinagre
** Other
*** DONE gconf
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE gnome-vfs
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE gnumeric
    CLOSED: [2012-12-16 Sun 20:12]
*** DEFERRED gtk+ 1
would be useful as a dependency for old packages
*** DONE intltool
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE libbonobo
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE libbonoboui
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE libglade
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE libgnome
    CLOSED: [2012-12-16 Sun 20:12]
*** DONE libgnomecanvas
    CLOSED: [2012-12-16 Sun 20:12]
* GNUstep packages [22/28] [78%]
** DONE enterprise
   CLOSED: [2012-12-16 Sun 20:12]
** TODO examples
** DONE gnumail
   CLOSED: [2013-04-10 Wed 22:20]
** DONE gnustep-backend
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnustep-base
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnustep-corebase
   CLOSED: [2012-12-16 Sun 20:12]
** TODO gnustep-examples
** DONE gnustep-gui
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE gnustep-guile
   CLOSED: [2012-12-16 Sun 20:16]
*** unsupported by upstream
** DONE gnustep-libobjc2
   CLOSED: [2013-08-17 Sat 16:51]
** DONE gnustep-make
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gnustep-ppd
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gorm
   CLOSED: [2012-12-16 Sun 20:12]
** DONE gworkspace
   CLOSED: [2012-12-16 Sun 20:12]
** TODO jigs
** IGNORE nib2gmodel
   CLOSED: [2012-12-16 Sun 20:16]
*** obsolete
** IGNORE openstep-2gnu-converter
   CLOSED: [2012-12-16 Sun 20:16]
*** obsolete
** DONE pantomime
   CLOSED: [2013-04-10 Wed 22:08]
** DONE performance
   CLOSED: [2012-12-16 Sun 20:12]
** DONE project-center
   CLOSED: [2012-12-16 Sun 20:12]
** DONE renaissance
   CLOSED: [2012-12-16 Sun 20:12]
** TODO rpmviewer
** DONE sqlclient
   CLOSED: [2012-12-16 Sun 20:12]
** IGNORE steptalk
   CLOSED: [2012-12-16 Sun 20:16]
*** unsupported by upstream
** TODO system-preferences
** DONE webserver
   CLOSED: [2012-12-16 Sun 20:12]
** DONE webservices
   CLOSED: [2012-12-16 Sun 20:12]
** TODO wrappers
# -*- org -*-
#+TITLE: BioSRC TODO List
#+AUTHOR: Brandon Invergo
#+EMAIL: brandon@invergo.net
#+DESCRIPTION: This file tracks all of the TODO items for BioSRC, primarily for
#+DESCRIPTION: adding new packages but also for improvements to the system.
#+TODO: TODO CANTADD ADDDEPS PROBLEM | DONE

* System
** DONE Add rule for checking for existence of upstream updates
   CLOSED: [2014-05-21 Wed 11:58]
* Packages
** bio [53/134]
*** CANTADD abyss
    http://www.bcgsc.ca/platform/bioinfo/software/abyss
    Has contradictory license terms: "GPL for non-commercial use"
*** TODO arachne
[[http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page]]
*** TODO awty
http://ceb.scs.fsu.edu/awty
*** TODO axtchain
http://genomewiki.ucsc.edu/index.php/The_source_tree
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
http://genomewiki.cse.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
The axtChain program is in the kent source tree:
/kent/src/hg/mouseStuff/axtChain
*** DONE bamtools
    CLOSED: [2014-03-13 Thu 21:30]
*** TODO bcftools
http://sourceforge.net/projects/samtools/files/samtools/1.0/
https://github.com/samtools/bcftools
*** TODO beast
https://code.google.com/p/beast-mcmc/
*** TODO bedops
https://github.com/bedops/bedops
*** DONE bedtools
    CLOSED: [2014-02-27 Thu 22:08]
*** DONE bfast
    CLOSED: [2014-03-13 Thu 21:38]
*** DONE bismark
    CLOSED: [2014-03-13 Thu 21:45]
*** CANTADD blat
    Academic-use-only license
*** DONE bowtie
    CLOSED: [2014-02-27 Thu 22:32]
*** DONE breakway
    CLOSED: [2014-03-13 Thu 22:02]
*** DONE bwa
    CLOSED: [2014-04-07 Mon 15:31]
*** TODO cafe
http://sites.bio.indiana.edu/~hahnlab/Software.html
*** TODO ccat
http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm
*** DONE cd-hit
    CLOSED: [2014-07-21 Mon 18:12]
*** TODO cegma
http://korflab.ucdavis.edu/Datasets/cegma/
*** DONE clustal-omega
    CLOSED: [2014-02-24 Mon 10:34]
*** DONE clustalw
    CLOSED: [2014-02-24 Mon 10:34]
*** TODO consed
http://www.phrap.org/phredphrapconsed.html#block_consed
*** TODO coseg
http://www.repeatmasker.org/COSEGDownload.html
*** DONE csblast
    CLOSED: [2014-07-17 Thu 15:53]
*** DONE cufflinks
    CLOSED: [2014-02-27 Thu 23:18]
*** TODO cutadapt
https://code.google.com/p/cutadapt/
*** DONE dnaa
    CLOSED: [2014-04-07 Mon 17:00]
*** TODO dnasp
http://www.ub.edu/dnasp/
*** TODO dustmasker
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker
*** DONE e-pcr
    CLOSED: [2014-04-08 Tue 15:10]
*** PROBLEM eautils
    https://code.google.com/p/ea-utils/
    Uses Google Drive to distribute files, so no direct download link
    Use SVN checkout (no tags available for releases)
*** DONE emboss
    CLOSED: [2014-02-24 Mon 14:40]
*** TODO eponine
https://www.sanger.ac.uk/resources/software/eponine/
*** TODO exonerate
https://www.ebi.ac.uk/~guy/exonerate/
*** TODO fastcodeml
*** TODO fastqc
    http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    GPL
    Check if can be built without GUI
*** DONE fasttree
    CLOSED: [2014-02-24 Mon 15:08]
*** DONE fastx-toolkit
    CLOSED: [2014-02-28 Fri 10:40]
*** CANTADD foldx
    proprietary; no source or executable freely available
*** DONE fsa
    CLOSED: [2014-02-24 Mon 15:22]
*** TODO fundi
*** TODO gphocs
http://compgen.bscb.cornell.edu/GPhoCS/
*** TODO gatk
https://www.broadinstitute.org/gatk/
*** TODO garli
https://www.nescent.org/wg_garli/Main_Page
*** CANTADD gblocks
    Proprietary (no source, no license)
*** TODO glfprogs
http://maq.sourceforge.net/glfProgs.shtml
*** TODO hapsembler
http://compbio.cs.toronto.edu/hapsembler/
*** DONE hmmer
    CLOSED: [2014-02-19 Wed 20:15]
*** DONE hyphy
    CLOSED: [2014-03-03 Mon 16:12]
*** TODO interproscan
    https://code.google.com/p/interproscan/
    Apache license
*** TODO ispcr
http://users.soe.ucsc.edu/~kent/src/
in-silico pcr
*** CANTADD iupred
    proprietary
*** DONE jellyfish
    CLOSED: [2014-05-23 Fri 18:15]
    http://www.genome.umd.edu/jellyfish.html
*** TODO jmodeltest2
https://code.google.com/p/jmodeltest2/
*** DONE kraken
    CLOSED: [2014-05-23 Fri 18:34]
    http://ccb.jhu.edu/software/kraken/
*** TODO lastz
http://www.bx.psu.edu/~rsharris/lastz/
*** DONE macs
    CLOSED: [2014-03-05 Wed 22:19]
*** DONE mafft
    CLOSED: [2014-02-24 Mon 16:24]
*** TODO maq
http://maq.sourceforge.net/maq-man.shtml
*** CANTADD mega
    Proprietary license (and not available for GNU/Linux?)
*** DONE melting
    CLOSED: [2014-02-19 Wed 20:15]
*** CANTADD meme
    http://meme.ebi.edu.au/meme/intro.html
    Restrictive (academic-only) license
*** CANTADD modeller
    proprietary
*** CANTADD modpipe
    free software, but has a hard dependency on Modeller
*** TODO monocle
http://monocle-bio.sourceforge.net/
*** DONE moods
    CLOSED: [2014-03-05 Wed 22:49]
*** DONE mrbayes
    CLOSED: [2014-03-06 Thu 20:21]
*** TODO mrfast
http://sourceforge.net/projects/mrfast/
*** TODO mrsfast
http://mrsfast.sourceforge.net/Home
*** TODO ms
http://home.uchicago.edu/~rhudson1/source/mksamples.html
*** TODO multiz
http://www.bx.psu.edu/miller_lab/
*** DONE mummer
    CLOSED: [2014-04-07 Mon 16:01]
*** CANTADD muscle
    proprietary (no license available)
*** DONE ncbi-blast
    CLOSED: [2014-02-24 Mon 10:34]
*** DONE newick-utils
    CLOSED: [2014-02-24 Mon 11:03]
*** DONE oma
    CLOSED: [2014-02-19 Wed 20:49]
*** ADDDEPS pagan-msa
    boost
*** CANTADD paml
    restrictive academic-use-only clause
*** CANTADD paup
    proprietary?
    http://paup.csit.fsu.edu/
*** ADDDEPS pfamscan
*** TODO phast
http://compgen.bscb.cornell.edu/phast/
*** TODO phrap
http://www.phrap.org/phredphrapconsed.html#block_phrap
*** TODO phred
http://www.phrap.org/phredphrapconsed.html#block_phred
*** CANTADD phylip
    Restrictive license (can't use commercially)
*** TODO picard
    http://picard.sourceforge.net/
*** TODO pinstripe
    http://pinstripe.matticklab.com/
*** DONE phyml
    CLOSED: [2014-02-24 Mon 11:35]
*** DONE primer3
    CLOSED: [2014-04-07 Mon 15:45]
*** DONE prank-msa
    CLOSED: [2014-02-24 Mon 11:23]
*** PROBLEM prottest
    https://code.google.com/p/prottest3/
    Uses Google Drive to distribute files, so no direct download.
    Use Hg checkout?
*** DONE provean
    CLOSED: [2014-07-22 Tue 12:28]
    http://provean.jcvi.org/index.php
    GPLv3
*** DONE pscan
    CLOSED: [2014-05-23 Fri 18:47]
*** TODO psmc
*** DONE qmmraxml
    CLOSED: [2014-02-26 Wed 22:57]
*** DONE quake
    CLOSED: [2014-04-07 Mon 13:44]
*** TODO quicktree
https://www.sanger.ac.uk/resources/software/quicktree/
*** DONE raxml
    CLOSED: [2014-02-19 Wed 22:25]
*** TODO repeatmasker
http://www.repeatmasker.org/
*** DONE reapr
    CLOSED: [2014-04-07 Mon 15:24]
*** CANTADD rnaprofile
    No license
*** DONE rnaz
    CLOSED: [2014-04-07 Mon 15:52]
*** DONE samtoools
    CLOSED: [2014-02-27 Thu 23:11]
*** DONE seqsuite
    CLOSED: [2014-02-24 Mon 16:25]
*** DONE seqtk
    CLOSED: [2014-06-23 Mon 22:43]
    https://github.com/lh3/seqtk
*** CANTADD sift
    Restrictive license (non-commercial)
*** TODO sff2fastq
    https://github.com/indraniel/sff2fastq
    no official release...
*** TODO slimcodeml
*** DONE slimsuite
    CLOSED: [2014-09-19 Fri 14:35]
*** DONE smalt
    CLOSED: [2014-06-26 Thu 19:20]
    https://www.sanger.ac.uk/resources/software/smalt/
*** TODO snpeff
    http://sourceforge.net/projects/snpeff/
*** DONE snpomatic
    CLOSED: [2014-04-07 Mon 14:17]
*** TODO soapdenovo
    http://soap.genomics.org.cn/
*** TODO soapaligner/soap2
    http://soap.genomics.org.cn/
*** TODO soapsplice
    http://soap.genomics.org.cn/
*** TODO soapsnp
    http://soap.genomics.org.cn/
*** TODO soapindel
    http://soap.genomics.org.cn/
*** TODO soapsv
    http://soap.genomics.org.cn/
*** TODO sra-toolkit
    https://www.ncbi.nlm.nih.gov/Traces/sra/?view=software
    Massive pain to build...try again some other time    
*** TODO srma
    http://sourceforge.net/projects/srma/
*** TODO ssaha2
    https://www.sanger.ac.uk/resources/software/ssaha2/
*** TODO stampy
*** DONE t-coffee
    CLOSED: [2014-02-19 Wed 20:16]
*** DONE tabix
    CLOSED: [2014-04-07 Mon 14:08]
*** TODO tdg09
    https://github.com/tamuri/tdg09
*** TODO tdg12
    https://github.com/tamuri/tdg12
*** TODO tophat
    http://tophat.cbcb.umd.edu/
    Boost, probably, like cufflinks
*** DONE treebest
    CLOSED: [2014-04-02 Wed 14:02]
*** TODO treesoft
http://sourceforge.net/projects/treesoft/
*** DONE trimal
    CLOSED: [2014-02-19 Wed 21:08]
*** TODO trinity
    http://trinityrnaseq.sourceforge.net/
    BSD
*** TODO velvet
    https://www.ebi.ac.uk/~zerbino/velvet/
*** TODO viennarna
    http://www.tbi.univie.ac.at/~ronny/RNA/
*** DONE weeder
    CLOSED: [2014-05-23 Fri 18:57]
    GPLv3
*** DONE weederh
    CLOSED: [2014-05-23 Fri 19:09]
** dev [3/7]
*** TODO apache-ant
    dep of melting
*** DONE gcc
    CLOSED: [2014-05-14 Wed 12:38]
*** TODO lua
*** TODO perl
*** DONE python
    CLOSED: [2014-03-03 Mon 14:18]
*** DONE python2
    CLOSED: [2014-03-03 Mon 14:47]
*** TODO ruby
** libs [20/33]
*** DONE bambamc
    CLOSED: [2014-06-26 Thu 19:18]
    https://github.com/gt1/bambamc
*** DONE glpk
    CLOSED: [2014-02-19 Wed 20:17]
*** TODO gmp
*** DONE gsl
    CLOSED: [2014-02-19 Wed 20:17]
*** DONE beagle-lib
    CLOSED: [2014-03-06 Thu 20:06]
*** TODO boost
    dep of pagan-msa
*** DONE eigen
    CLOSED: [2014-02-27 Thu 23:11]
*** DONE gdbm
    CLOSED: [2014-03-05 Wed 15:45]
*** DONE htslib
    CLOSED: [2014-09-19 Fri 14:34]
*** DONE libgtextutils
    CLOSED: [2014-02-28 Fri 10:41]
*** TODO mpc
*** TODO mpfr
*** DONE perl-bioperl
    CLOSED: [2014-02-19 Wed 20:17]
*** TODO perl-ensembl
*** TODO perl-moose [0/22]
    pre-req for pfamscan
**** TODO perl-class-load
**** TODO perl-class-load-xs
**** TODO perl-data-optlist
**** TODO perl-devel-globaldestruction
**** TODO perl-dist-checkconflicts
**** TODO perl-eval-closure
**** TODO perl-list-moreutils
**** TODO perl-mro-compat
**** TODO perl-package-deprecationmanager
**** TODO perl-package-stash
**** TODO perl-package-stash-xs
**** TODO perl-params-util
**** TODO perl-sub-exporter
**** TODO perl-sub-name
**** TODO perl-task-weaken
**** TODO perl-test-checkdeps
**** TODO perl-try-tiny
**** TODO perl-devel-stacktrace
**** TODO perl-dist-checkconflicts
**** TODO perl-test-fatal
**** TODO perl-test-requires
**** TODO perl-test-without-module
*** DONE python-biopython
    CLOSED: [2014-02-19 Wed 20:17]
*** DONE python-dateutil
    CLOSED: [2014-05-14 Wed 11:27]
*** DONE python-htseq
    CLOSED: [2014-02-28 Fri 11:01]
*** TODO python-matplotlib
*** DONE python-networkx
    CLOSED: [2014-03-06 Thu 10:50]
*** TODO python-nose
*** DONE python-numpy
    CLOSED: [2014-03-05 Wed 15:34]
*** DONE python-pandas
    CLOSED: [2014-05-14 Wed 11:26]
*** TODO python-pybedtools
https://pypi.python.org/pypi/pybedtools
*** TODO python-pycogent
*** TODO python-scikit-learn
*** DONE python-scipy
    CLOSED: [2014-03-05 Wed 15:34]
*** DONE python-setuptools
    CLOSED: [2014-04-23 Wed 17:09]
*** DONE python-sqlalchemy
    CLOSED: [2014-04-23 Wed 17:09]
*** TODO python-sympy
*** TODO r-cummerbund
http://compbio.mit.edu/cummeRbund/
*** DONE seqan
    CLOSED: [2014-06-26 Thu 23:04]
*** DONE sparsehash
    CLOSED: [2014-07-17 Thu 14:14]
** tools [7/8]
*** DONE datamash
    CLOSED: [2014-05-21 Wed 22:46]
*** TODO ipython
*** DONE mcsim
    CLOSED: [2014-02-19 Wed 20:18]
*** DONE parallel
    CLOSED: [2014-02-26 Wed 22:31]
*** DONE plotutils
    CLOSED: [2014-02-19 Wed 20:18]
*** DONE units
    CLOSED: [2014-02-19 Wed 20:18]
*** DONE wdiff
    CLOSED: [2014-02-19 Wed 20:18]
*** DONE zeptodb
    CLOSED: [2014-02-26 Wed 22:31]
