Alexander Hansen <alexanderk.han...@gmail.com> said: > On 8/10/10 2:30 PM, Scott R. Santos wrote: >> >> The following package will be installed or updated: >> emboss >> The following 263 additional packages will be installed: >> app-defaults appleotffonts applesystemfonts aquaterm aquaterm-dev >> aquaterm-shlibs atk1 atk1-shlibs audiofile audiofile-bin audiofile-shlibs >> autoconf avahi avahi-dev bison cairo cairo-shlibs cloog cloog-shlibs cmake >> compress-raw-bzip2-pm5100 compress-raw-zlib-pm5100 crypt-ssleay-pm5100 >> cyrus-sasl2-dev cyrus-sasl2-shlibs daemonic dbus dbus-dev dbus-glib1.2-dev >> dbus-glib1.2-shlibs dbus-shlibs dbus1.3-dev dbus1.3-shlibs >> default-icon-theme docbook-dsssl-nwalsh docbook-dtd docbook-utils >> docbook-xsl doxygen emboss-libajax6-shlibs emboss-libnucleus6-shlibs esound >> esound-bin esound-common esound-shlibs fftw3 fftw3-shlibs >> fink-obsolete-packages flex-devel fondu freeglut freeglut-shlibs gcc44 >> gcc44-compiler gcc44-shlibs gconf2 gconf2-dev gconf2-shlibs getoptbin >> glib2-dev glib2-shlibs glitz glitz-shlibs glpk-dev glpk-shlibs gmp gmp-shlibs >> gnome-base gnome-common gnome-doc-utils gnome-icon-theme gnome-keyring-dev >> gnome-keyring-shlibs gnome-mime-data gnome-vfs2-unified >> gnome-vfs2-unified-dev gnome-vfs2-unified-shlibs gnuplot >> gst-plugins-base-0.10 >> gst-plugins-base-0.10-dev gst-plugins-base-0.10-shlibs gstreamer-0.10 >> gstreamer-0.10-dev gstreamer-0.10-shlibs gtk+2 gtk+2-dev gtk+2-shlibs >> gtk-doc hdf5 hdf5-bin hdf5-shlibs help2man-perl588 html-parser-pm5100 >> html-tagset-pm icon-naming-utils intltool40 io-compress-pm5100 jadetex >> lasi-dev lasi-shlibs libart2 libart2-shlibs libavahi-client3-shlibs >> libavahi-common3-shlibs libavahi-core6-shlibs libavahi-glib1-dev >> libavahi-glib1-shlibs libbonobo2 libbonobo2-dev libbonobo2-shlibs >> libbonoboui2-dev libbonoboui2-shlibs libcdparanoia0-dev >> libcdparanoia0-shlibs libcurl4 libdaemon libdaemon-shlibs libdatrie1 >> libdatrie1-shlibs libgcrypt >> libgcrypt-shlibs libgettext3-dev libglade2 libglade2-shlibs libgmpxx-shlibs >> libgnome2 libgnome2-dev libgnome2-shlibs libgnomecanvas2 libgnomecanvas2-dev >> libgnomecanvas2-shlibs libgnomecups-dev libgnomecups-shlibs >> libgnomeprint2.2-dev libgnomeprint2.2-shlibs libgnomeprintui2.2-dev >> libgnomeprintui2.2-shlibs libgnomeui2-dev libgnomeui2-shlibs libgpg-error >> libgpg-error-shlibs libidl2 libidl2-shlibs libidn libidn-shlibs libjasper.1 >> libjasper.1-shlibs libjpeg8 libkpathsea4 libkpathsea4-shlibs liblzma-shlibs >> libmpc2 libmpc2-shlibs libmpfr1 libmpfr1-shlibs libogg libogg-shlibs >> liboil-0.3 liboil-0.3-shlibs libpng14 libpng14-shlibs librarian.08-shlibs >> libtasn1-3 libtasn1-3-shlibs libthai libthai-dev libthai-shlibs >> libtheora0-shlibs libtiff libtiff-bin libtiff-shlibs libtool14 >> libtool14-shlibs libvorbis0-shlibs libwww libwww-bin libwww-pm5100 >> libwww-shlibs libxml2 >> libxml2-bin libxml2-py26 libxml2-shlibs libxslt libxslt-bin libxslt-shlibs >> locale-gettext-pm588 make mysql-unified-dev mysql-unified-shlibs nkf ocaml >> octave openjade openldap24-dev openldap24-shlibs openmotif3 >> openmotif3-shlibs opensp4 opensp4-dev opensp4-shlibs orbit2 orbit2-dev >> orbit2-shlibs pango1-xft2-ft219 pango1-xft2-ft219-dev >> pango1-xft2-ft219-shlibs passwd pdflib6 pdflib6-shlibs perl588-core pixman >> pixman-shlibs >> plotutils plotutils-dev plotutils-shlibs plplot-dev plplot-shlibs >> postgresql84 postgresql84-dev postgresql84-shlibs ppl ppl-shlibs ptex-base >> ptex-texmf ptexenc ptexenc-shlibs python26 python26-shlibs pyxml-py26 qhull >> rarian rarian-compat sdl sdl-shlibs sed sgml-entities-iso8879 sgmls-pm >> shared-mime-info suitesparse swig szip szip-shlibs t1lib5-nox >> t1lib5-nox-shlibs t1lib5-x11 t1lib5-x11-shlibs texlive-base texlive-texmf >> uri-pm5100 >> wxgtk2.8 wxgtk2.8-shlibs xdg-base xfontpath xft2-dev xft2-shlibs xinitrc >> xmkmf xml-namespacesupport-pm xml-parser-pm5100 xml-sax-expat-pm5100 >> xml-sax-pm5100 xml-simple-pm5100 xz >> Do you want to continue? [Y/n] n >> >> This is an EMBOSS update: >> >> (i) emboss 6.3.1-101 >> Molecular Biology Open Software Suite >> >> on: >> >> Darwin 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; >> root:xnu-1504.7.4~1/RELEASE_I386 i386 i386 >> >> Question: when (or more importantly, why) did EMBOSS suddenly require the >> installation of (all of) 263 dependencies, including what appears to be all >> of GNOME? > > The all-of-gnome thing probably came from gnuplot. You can use > gnuplot-nogtk to avoid that.
Also the latest (as of -101) emboss package relies on external (separate packages) of several things that used to be internal. In particular, plplot is a huge library that is no longer build within emboss itself. The plplot packaging is itself using lots of gnome things that emboss doesn't need. To quote a note in the emboss packaging file: # plplot's -nognome varianting is a disaster (adding/removing can # change who if anyone supplies various headers and libs). It's fixable (tease apart the non-gnome stuff into a clean independent package set) but not yet fixed. The plplot that comes with emboss is its own packaging disaster that's *not* fixable and had led to all sorts of other breakage in the previous packaging of the emboss suite. So until I finish cleaning up plplot, "users of plplot" (i.e., you, if you update emboss) are stuck getting gnome stuff. If the previous emboss you had installed (I assume you had it, because update-all saw it was present-and-old) was working fine, there's no urgency to updating it. The changes are *just* to the packaging layout: shifting lots of things to external and solving lots of binary compatibility problems in its included libraries. Updates to plplot, which should trim out most of the gnome stuff, will probably take another week or so. dan -- Daniel Macks dma...@netspace.org ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
