bash-2.05b$ fink index Reading package info... Updating package index... done. bash-2.05b$ date Thu Mar 24 08:50:22 CST 2005 bash-2.05b$ fink -V Package manager version: 0.24.1 Distribution version: 0.6.3.rsync
Copyright (c) 2001 Christoph Pfisterer
Copyright (c) 2001-2005 The Fink Package Manager Team
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
bash-2.05b$ fink install hmmer
Information about 3326 packages read in 2 seconds.
The package 'hmmer' will be built and installed.
The following package will be installed or updated:
hmmer
The following package will be removed:
fink
Do you want to continue? [Y/n] n
Failed: Package requirements not satisfied
bash-2.05b$ fink dumpinfo hmmer
Information about 3326 packages read in 2 seconds.
infofile: /sw/fink/dists/unstable/main/finkinfo/sci/hmmer-2.2g-3.info
package: hmmer
version: 2.2g
revision: 3
family: hmmer
status: latest
allversions:
2.2g-3
description: Profile HMMs for biological sequence analysis
type: [undefined]
license: GPL
maintainer: Richard Graul <[EMAIL PROTECTED]>
buildconflicts: fink (>= 0.23.5.cvs-20050120.0000)
essential: [undefined]
builddependsonly: [undefined]
source: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.2g/hmmer-2.2g.tar.gz
source-md5: d7def2007a0aaf2eafb9a96a07986b8c
nosourcedirectory: [undefined]
source2: http://pfam.wustl.edu/cgi-bin/gethmm?name=7tm_1\&type=fs
source2rename: 7tm_1
source2-md5: 2267b9803e79806141fd17116e4cb560
source3: http://us.expasy.org/cgi-bin/get-sprot-fasta?P08908
source3rename: P08908.fasta
source3-md5: 30eac186ce169f3156bf64bae97a286c
updateconfigguess: [undefined]
updatelibtool: [undefined]
updatepomakefile: [undefined]
patch: hmmer-2.2g-3.patch
env:
ANT_HOME=/sw/lib/ant
CCACHE_DIR=/sw/var/ccacheCLASSPATH=/sw/share/java/commons-collections/commons-collections-3.1.jar:/sw/share/java/commons-collections/commons-collections-testframework-3.1.jar:/sw/share/java/commons-logging/commons-logging-api.jar:/sw/share/java/commons-logging/commons-logging.jar:/sw/share/java/db42-ssl-java/db.jar:/sw/share/java/junit/junit.jar:/sw/share/java/log4j/log4j-1.2.8.jar:. CPPFLAGS=-I/sw/include FLTK_DOCDIR=/sw/share/doc/fltk-x11-43/html GDK_USE_XFT=1 GNOME_DISABLE_CRASH_DIALOG=1 HOME=/Users/rgrtw INFOPATH=/sw/share/info:/sw/info:/usr/share/info LDFLAGS=-L/sw/lib LD_PREBIND=1 LD_PREBIND_ALLOW_OVERLAP=1 LD_SEG_ADDR_TABLE=/sw/var/lib/fink/prebound/seg_addr_table LESS=--RAW-CONTROL-CHARS LESSOPEN=| /sw/bin/lesspipe.sh %s MACOSX_DEPLOYMENT_TARGET=10.1 MAGIC=/sw/share/lesspipe/magic:/private/etc/magic
MANPATH=/sw/share/man:/sw/man:/usr/share/man:/usr/X11R6/man:/sw/lib/perl5-core/5.6.0/man:/sw/lib/perl5/5.6.0/man:/sw/lib/perl5-core/5.8.0/man:/sw/lib/perl5/5.8.0/man
PATH=/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin
PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin
PWD=/sw/src
QMAKESPEC=/sw/share/qt3/mkspecs/darwin-g++
QTDIR=/sw
SGML_CATALOG_FILES=/sw/etc/sgml/catalog
SHLVL=2
XAPPLRESDIR=/sw/etc/app-defaults/
XML_CATALOG_FILES=/sw/etc/xml/catalog
configureparams: --prefix=/sw --bindir=/sw/src/root-hmmer-2.2g-3/sw/bin --mandir=/sw/src/root-hmmer-2.2g-3/sw/share/man
compilescript:
./configure --prefix=/sw --bindir=/sw/src/root-hmmer-2.2g-3/sw/bin --mandir=/sw/src/root-hmmer-2.2g-3/sw/share/man
make
make check
chmod a+r documentation/man/*
chmod a+r squid/Man/*
noperltests: [undefined]
updatepod: [undefined]
installscript:
install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/bin
install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/share/man/man1
mv INSTALL INSTALL.sav
make install prefix=/sw/src/root-hmmer-2.2g-3/sw
mv INSTALL.sav INSTALL
install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/include/hmmer-2.2g
install -c -p -m 644 version.h src/*.h /sw/src/root-hmmer-2.2g-3/sw/include/hmmer-2.2g
ln -s hmmer-2.2g /sw/src/root-hmmer-2.2g-3/sw/include/hmmer
install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/lib
install -c -p -m 644 src/libhmmer.a /sw/src/root-hmmer-2.2g-3/sw/lib/libhmmer-2.2g.a
ln -s libhmmer-2.2g.a /sw/src/root-hmmer-2.2g-3/sw/lib/libhmmer.a
install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo
install -c -p -m 644 ../7tm_1 /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo
install -c -p -m 644 ../P08908.fasta /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo
echo "#!/bin/sh" > /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh
echo "hmmsearch /sw/share/hmmer/demo/7tm_1 /sw/share/hmmer/demo/P08908.fasta" >> /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh
chmod 755 /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh
docfiles: 00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
runtimevars:
HMMERDB: /data/hmmerdb
postinstscript:
echo "****************************************"
echo "To demonstrate hmmer, run:"
echo "/sw/share/hmmer/demo/hmmsearch.sh"
echo "****************************************"
echo "You may manually download any HMM libraries to /data/hmmerdb from:"
echo "ftp://ftp.genetics.wustl.edu/pub/eddy/Pfam/";
echo ""
echo "If you want to use another location for your databases set"
echo "the environment variable HMMERDB."
echo ""
echo "For more information, see:"
echo "http://hmmer.wustl.edu/";
echo "http://pfam.wustl.edu/";
homepage: http://hmmer.wustl.edu/
descdetail:
HMMER - profile hidden Markov models for biological sequence analysis
Version 2.2 (August 2001)
Copyright (C) 1992-2001 Washington University School of Medicine
------------------------------------------------------------------
.
o About this software...
HMMER is an implementation of profile HMM methods for
sensitive database searches using multiple sequence alignments as queries.
.
Basically, you give HMMER a multiple sequence alignment as input;
it builds a statistical model called a "hidden Markov model"
which you can then use as a query into a sequence database
to find (and/or align) additional homologues of the sequence family.
descusage:
To demonstrate hmmer, run:
/sw/share/hmmer/demo/hmmsearch.sh
.
You may manually download any HMM libraries to /data/hmmerdb from:
ftp://ftp.genetics.wustl.edu/pub/eddy/Pfam/
.
If you want to use another location for your databases set
the environment variable HMMERDB.
.
For more information, see:
http://hmmer.wustl.edu/
http://pfam.wustl.edu/
bash-2.05b$
Martin Costabel wrote:
Robert Wyatt wrote:
Do y'all know why I am getting this? Thanks, Robert
Did you look at the file to see whether you have the new version? If yes, maybe you need to run "fink index".
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