Hi Alexander and Dan, Thank you for checking into this. I noticed it since I'm teaching a class in several weeks that includes installing EMBOSS via Fink. Having these unrequired (from past experiences) dependencies is a significant burden relative to past installs (considering that building directly from source files to /usr/local/ is relative straightforward for EMBOSS).
While having the extra dependencies are a plus, most (from my experiences, no *sql, higher-level plotting, etc) everyday useage does not require them. Might it be better to have "full" and "slim" packages available in the repository depending on need? I understand its more work maintaining two packages, but such a situation could be easier for future end users. Cheers, 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: san...@auburn.edu Lab Website: http://www.auburn.edu/~santosr/ ********************************************************************** fink-users-requ...@lists.sourceforge.net wrote: > Send Fink-users mailing list submissions to > fink-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/fink-users > or, via email, send a message with subject or body 'help' to > fink-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > fink-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Fink-users digest..." > > > Today's Topics: > > 1. Re: DCMTK and xmedcon unstable package install... (Abe, Sumiko) > 2. Re: EMBOSS update - new dependencies? (Daniel E. Macks) > 3. Re: EMBOSS update - new dependencies? (Alexander Hansen) > 4. Re: EMBOSS update - new dependencies? (Scott R. Santos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Aug 2010 13:52:08 -0700 > From: "Abe, Sumiko" <sumi...@uci.edu> > Subject: Re: [Fink-users] DCMTK and xmedcon unstable package > install... > To: Alexander Hansen <alexanderk.han...@gmail.com>, > "fink-users@lists.sourceforge.net" <fink-users@lists.sourceforge.net>, > Core Group <fink-c...@lists.sourceforge.net> > Message-ID: > <5ff7dfb23ed16044be8ea5f4d637fff6050222a...@msx03.hs.uci.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, I am running fink configure with downloading unstable packages options. > And run fink selfupdate. The following errors happened: > cp ./match.c _match.S > gcc -std=gnu99 -E -I/sw/include _match.S > _match.i > sed '/^ * < _match.i > match_.s > /bin/sh: -c: line 0: unexpected EOF while looking for matching `'' > /bin/sh: -c: line 1: syntax error: unexpected end of file > make[3]: *** [match.o] Error 2 > make[2]: *** [all-recursive] Error 1 > make[1]: *** [all] Error 2 > make: *** [all-recursive] Error 1 > ### execution of make failed, exit code 2 > Removing runtime build-lock... > Removing build-lock package... > /sw/bin/dpkg-lockwait -r fink-buildlock-gzip-1.4-2 > (Reading database ... 6073 files and directories currently installed.) > Removing fink-buildlock-gzip-1.4-2 ... > Failed: phase compiling: gzip-1.4-2 failed > > Before reporting any errors, please run "fink selfupdate" and > try again. If you continue to have issues, please check to see if the > FAQ on fink's website solves the problem. If not, ask on the fink-users > or fink-beginners mailing lists, with a carbon copy to the maintainer: > > Fink Core Group <fink-c...@lists.sourceforge.net> > > Note that this is preferable to emailing the maintainer directly, since > most fink package maintainers do not have access to all possible > hardware and software configurations. > > > Any advice? > My Mac is running on 10.6.3. > Thank you, > > Sumiko > > -----Original Message----- > From: Abe, Sumiko > Sent: Tuesday, August 10, 2010 12:01 PM > To: Lichtner, Peter C; fink-users@lists.sourceforge.net > Subject: DCMTK and xmedcon unstable package install... > > Hi, > > I am porting DCMTK package to Mac OS. The unstable version is available on > the web site. I am trying to find the information for how to enable the > unstable packabe but could not find the information...Might be I am missing > something.. > That would be great appreciated if any advice. > > My Mac is running on 10.6.3 > > Bests, > > Sumiko > > This message contains confidential information and is intended only for the > individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail by mistake and delete > this e-mail from your system. E-mail transmission cannot be guaranteed to be > secure or error-free as information could be intercepted, corrupted, lost, > destroyed, arrive late or incomplete, or contain viruses. The sender > therefore does not accept liability for any errors or omissions in the > contents of this message, which arise as a result of e-mail transmission. > > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Aug 2010 21:37:08 +0000 (UTC) > From: "Daniel E. Macks" <dma...@netspace.org> > Subject: Re: [Fink-users] EMBOSS update - new dependencies? > To: fink-users@lists.sourceforge.net > Message-ID: <slrni63hk4.7ql.dma...@macks-factor.home> > Content-Type: text/plain; charset=us-ascii > > 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 > > > > > ------------------------------ > > Message: 3 > Date: Tue, 10 Aug 2010 19:30:14 -0400 > From: Alexander Hansen <alexanderk.han...@gmail.com> > Subject: Re: [Fink-users] EMBOSS update - new dependencies? > To: fink-users@lists.sourceforge.net > Message-ID: <4c61e106.2080...@gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On 8/10/10 5:37 PM, Daniel E. Macks wrote: > > Alexander Hansen <alexanderk.han...@gmail.com> said: > <snip> > > >>> > >>> 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 > > > plplot builds against octave, so it brings that into the mix, too. > > - -- > Alexander Hansen > Fink User Liaison > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (Darwin) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEYEARECAAYFAkxh4QYACgkQB8UpO3rKjQ8NqQCfR92T2L+4Y/QKA3iViL6IWAq/ > 21AAn04lndHnjkEAbFWIXiLtGkozt+IC > =U7Wc > -----END PGP SIGNATURE----- > > > > ------------------------------ > > Message: 4 > Date: Tue, 10 Aug 2010 14:11:10 -0500 > From: "Scott R. Santos" <san...@auburn.edu> > Subject: Re: [Fink-users] EMBOSS update - new dependencies? > To: fink-users mailing list <Fink-users@lists.sourceforge.net> > Message-ID: <d2ee1d9a-ff27-4869-9ad3-da7df8779...@auburn.edu> > Content-Type: text/plain; charset=us-ascii > > > 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: san...@auburn.edu > 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: san...@auburn.edu > >> 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 > Fink-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/fink-users > > > End of Fink-users Digest, Vol 52, Issue 10 > ****************************************** ------------------------------------------------------------------------------ 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
