Hi Alexander, Thanks for the quick reply. Yes, EMBOSS is the _only_ package being updated. Same result if I do a "fink update emboss":
fink update emboss Password: Information about 9508 packages read in 2 seconds. fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) octave: Matlab-like language for computations (2) octave-atlas: Matlab-like language for computations Pick one: [1] fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) gnuplot: Command-driven interactive plotting program (2) gnuplot-nox: Command-driven interactive plotting program (3) gnuplot-nogtk: Command-driven interactive plotting program Pick one: [1] fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) help2man-perl588: Generates man pages from program output (2) help2man-perl5100: Generates man pages from program output Pick one: [1] fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) ptex-base: ASCII publishing TeX (2) ptex-nox-base: ASCII publishing TeX (3) tetex-nox-base: Base programs for a teTeX installation (4) tetex-base: Base programs for a teTeX installation (5) texlive-nox-base: Base programs for a TeX Live installation (6) texlive-base: Base programs for a TeX Live installation Pick one: [1] fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) texlive-base: Base programs for a TeX Live installation (2) texlive-nox-base: Base programs for a TeX Live installation Pick one: [1] 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 Failed: Package requirements not satisfied >From the Fink "Recent Package Updates" for EMBOSS: 2010-08-06: emboss-6.3.1-101 (Molecular Biology Open Software Suite) EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. commit log from dmacks: completely overhaul package layout, with new lib package-names and root dir; now with more externalized support libs too! I noticed that there has been a "completely overhaul package layout". My guess is that something didn't go well with the overall, thus invoking these new (and non-essential) dependencies. Thanks again, Scott ********************************************************************** Scott R. Santos Department of Biological Sciences & Cell and Molecular Biosciences Peak Program Auburn University 101 Life Science Building, Rm. 128 Auburn, AL 36849 Tele # (334) 844-7410 Fax # (334) 844-1645 Email: [email protected] Lab Website: http://www.auburn.edu/~santosr/ ********************************************************************** On Aug 10, 2010, at 2:00 PM, Alexander Hansen wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Removing now-former emboss maintainer. > > On 8/10/10 2:30 PM, Scott R. Santos wrote: >> >> Hi everyone, >> >> Following a "sudo fink update-all", I was greeted with the following (which >> left me scratching my head): >> > > Don't use "sudo fink". > >> Information about 9508 packages read in 3 seconds. >> >> fink needs help picking an alternative to satisfy a virtual dependency. The >> candidates: >> >> (1) octave: Matlab-like language for computations >> (2) octave-atlas: Matlab-like language for computations >> >> Pick one: [1] >> >> fink needs help picking an alternative to satisfy a virtual dependency. The >> candidates: >> >> (1) gnuplot: Command-driven interactive plotting program >> (2) gnuplot-nox: Command-driven interactive plotting program >> (3) gnuplot-nogtk: Command-driven interactive plotting program >> >> Pick one: [1] >> >> fink needs help picking an alternative to satisfy a virtual dependency. The >> candidates: >> >> (1) help2man-perl588: Generates man pages from program output >> (2) help2man-perl5100: Generates man pages from program output >> >> Pick one: [1] >> >> fink needs help picking an alternative to satisfy a virtual dependency. The >> candidates: >> >> (1) ptex-base: ASCII publishing TeX >> (2) ptex-nox-base: ASCII publishing TeX >> (3) tetex-nox-base: Base programs for a teTeX installation >> (4) tetex-base: Base programs for a teTeX installation >> (5) texlive-nox-base: Base programs for a TeX Live installation >> (6) texlive-base: Base programs for a TeX Live installation >> >> Pick one: [1] >> >> fink needs help picking an alternative to satisfy a virtual dependency. The >> candidates: >> >> (1) texlive-base: Base programs for a TeX Live installation >> (2) texlive-nox-base: Base programs for a TeX Live installation >> >> Pick one: [1] >> 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? >> >> Thanks in advance for insight into this. >> >> Scott >> >> ********************************************************************** >> Scott R. Santos >> Department of Biological Sciences & >> Cell and Molecular Biosciences Peak Program >> Auburn University >> 101 Life Science Building, Rm. 128 >> Auburn, AL 36849 >> Tele # (334) 844-7410 >> Fax # (334) 844-1645 >> Email: [email protected] >> Lab Website: http://www.auburn.edu/~santosr/ >> ********************************************************************** >> >> >> > > Is emboss the _only_ outdated package you had? If not, then don't use > "fink update-all" if you don't want to build anything not related to it. > > The all-of-gnome thing probably came from gnuplot. You can use > gnuplot-nogtk to avoid that. > > - -- > Alexander Hansen > Fink User Liaison > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (Darwin) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEUEARECAAYFAkxhob8ACgkQB8UpO3rKjQ9xXgCXXpzmCxtEVVsTBSPP1vp3J9I+ > 1wCcDvAYHiL+zj23BWHFtouBxPiuV08= > =9JLO > -----END PGP SIGNATURE----- ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/fink-users
