[med-svn] r11713 - trunk/packages/norsnet/trunk/debian
Christian Mertes
mertes-guest at alioth.debian.org
Tue Jul 10 16:14:37 UTC 2012
Author: mertes-guest
Date: 2012-07-10 16:14:36 +0000 (Tue, 10 Jul 2012)
New Revision: 11713
Removed:
trunk/packages/norsnet/trunk/debian/AUTHORS
trunk/packages/norsnet/trunk/debian/COPYING
trunk/packages/norsnet/trunk/debian/ChangeLog
trunk/packages/norsnet/trunk/debian/INSTALL
trunk/packages/norsnet/trunk/debian/Makefile.am
trunk/packages/norsnet/trunk/debian/NEWS
trunk/packages/norsnet/trunk/debian/aclocal.m4
trunk/packages/norsnet/trunk/debian/configure
trunk/packages/norsnet/trunk/debian/configure.ac
trunk/packages/norsnet/trunk/debian/example/
trunk/packages/norsnet/trunk/debian/install-sh
trunk/packages/norsnet/trunk/debian/missing
trunk/packages/norsnet/trunk/debian/norsnet
trunk/packages/norsnet/trunk/debian/norsnet.pod.in
trunk/packages/norsnet/trunk/debian/scr/
Modified:
trunk/packages/norsnet/trunk/debian/changelog
Log:
Deleted: trunk/packages/norsnet/trunk/debian/AUTHORS
===================================================================
--- trunk/packages/norsnet/trunk/debian/AUTHORS 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/AUTHORS 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1 +0,0 @@
-Avner Schlessinger, Jinfeng Liu and Burkhard Rost
Deleted: trunk/packages/norsnet/trunk/debian/COPYING
===================================================================
--- trunk/packages/norsnet/trunk/debian/COPYING 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/COPYING 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,674 +0,0 @@
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- If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
-
- Later license versions may give you additional or different
-permissions. However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
- 15. Disclaimer of Warranty.
-
- THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- 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.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- <program> Copyright (C) <year> <name of author>
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
Deleted: trunk/packages/norsnet/trunk/debian/ChangeLog
===================================================================
--- trunk/packages/norsnet/trunk/debian/ChangeLog 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/ChangeLog 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,88 +0,0 @@
-norsnet (1.0.12) unstable; urgency=low
-
- * Release under GPL-3+ license.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Tue, 10 Jul 2012 13:09:57 +0200
-
-norsnet (1.0.11) unstable; urgency=low
-
- * Debianization removed.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Tue, 03 Jul 2012 19:46:27 +0200
-
-norsnet (1.0.10) stable; urgency=low
-
- * warning when pp-popcon is not installed
-
- -- Laszlo Kajan <lkajan at rostlab.org> Mon, 28 Feb 2011 18:08:50 +0100
-
-norsnet (1.0.9) stable; urgency=low
-
- * bugzilla link corrected
- * pp-popularity-contest
-
- -- Laszlo Kajan <lkajan at rostlab.org> Fri, 18 Feb 2011 16:56:41 +0100
-
-norsnet (1.0.8) stable; urgency=low
-
- * createDataFile.pl too restrictive regexp bug fixed
-
- -- Laszlo Kajan <lkajan at rostlab.org> Thu, 13 Jan 2011 15:10:44 +0100
-
-norsnet (1.0.7-1) stable; urgency=low
-
- * New upstream release
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 30 Jun 2010 13:29:07 +0200
-
-norsnet (1.0.7)
-
- * Silence in non-debug mode - correctly this time
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 30 Jun 2010 13:07:02 +0200
-
-norsnet (1.0.6)
-
- * Silence in non-debug mode
-
- -- Laszlo Kajan <lkajan at rostlab.org> Thu, 17 Jun 2010 20:32:58 +0200
-
-norsnet (1.0.5)
-
- * Example without gzip
- * Output mode 1 documented
-
- -- Laszlo Kajan <lkajan at rostlab.org> Thu, 17 Jun 2010 12:38:03 +0200
-
-norsnet (1.0.4)
-
- * Fixed __pkgdatadir__ paths
-
- -- Laszlo Kajan <lkajan at rostlab.org> Tue, 16 Mar 2010 17:55:41 +0100
-
-norsnet (1.0.3)
-
- * Fixed version, this actually produces results
- * Now calls profnet_norsnet and not profnet_bval
- * Fixed mode 6 issue - there is only mode 1, 2 and 3
- * Introduced automake + autoconf
-
- -- Laszlo Kajan <lkajan at rostlab.org> Tue, 16 Mar 2010 17:55:41 +0100
-
-norsnet (1.0.2)
-
- * Minor revision.
-
- -- Guy Yachdav <gyahcdav at rostlab.org> Thu, 10 Dec 2009 22:57:15 +0100
-
-norsnet (1.0.1)
-
- * Minor revision.
-
- -- Guy Yachdav <gyahcdav at rostlab.org> Thu, 10 Dec 2009 22:40:15 +0100
-
-norsnet (1.0.0)
-
- * Initial version.
-
- -- Guy Yachdav <gyahcdav at rostlab.org> Thu, 10 Dec 2009 22:32:15 +0100
Deleted: trunk/packages/norsnet/trunk/debian/INSTALL
===================================================================
--- trunk/packages/norsnet/trunk/debian/INSTALL 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/INSTALL 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,370 +0,0 @@
-Installation Instructions
-*************************
-
-Copyright (C) 1994-1996, 1999-2002, 2004-2011 Free Software Foundation,
-Inc.
-
- Copying and distribution of this file, with or without modification,
-are permitted in any medium without royalty provided the copyright
-notice and this notice are preserved. This file is offered as-is,
-without warranty of any kind.
-
-Basic Installation
-==================
-
- Briefly, the shell commands `./configure; make; make install' should
-configure, build, and install this package. The following
-more-detailed instructions are generic; see the `README' file for
-instructions specific to this package. Some packages provide this
-`INSTALL' file but do not implement all of the features documented
-below. The lack of an optional feature in a given package is not
-necessarily a bug. More recommendations for GNU packages can be found
-in *note Makefile Conventions: (standards)Makefile Conventions.
-
- The `configure' shell script attempts to guess correct values for
-various system-dependent variables used during compilation. It uses
-those values to create a `Makefile' in each directory of the package.
-It may also create one or more `.h' files containing system-dependent
-definitions. Finally, it creates a shell script `config.status' that
-you can run in the future to recreate the current configuration, and a
-file `config.log' containing compiler output (useful mainly for
-debugging `configure').
-
- It can also use an optional file (typically called `config.cache'
-and enabled with `--cache-file=config.cache' or simply `-C') that saves
-the results of its tests to speed up reconfiguring. Caching is
-disabled by default to prevent problems with accidental use of stale
-cache files.
-
- If you need to do unusual things to compile the package, please try
-to figure out how `configure' could check whether to do them, and mail
-diffs or instructions to the address given in the `README' so they can
-be considered for the next release. If you are using the cache, and at
-some point `config.cache' contains results you don't want to keep, you
-may remove or edit it.
-
- The file `configure.ac' (or `configure.in') is used to create
-`configure' by a program called `autoconf'. You need `configure.ac' if
-you want to change it or regenerate `configure' using a newer version
-of `autoconf'.
-
- The simplest way to compile this package is:
-
- 1. `cd' to the directory containing the package's source code and type
- `./configure' to configure the package for your system.
-
- Running `configure' might take a while. While running, it prints
- some messages telling which features it is checking for.
-
- 2. Type `make' to compile the package.
-
- 3. Optionally, type `make check' to run any self-tests that come with
- the package, generally using the just-built uninstalled binaries.
-
- 4. Type `make install' to install the programs and any data files and
- documentation. When installing into a prefix owned by root, it is
- recommended that the package be configured and built as a regular
- user, and only the `make install' phase executed with root
- privileges.
-
- 5. Optionally, type `make installcheck' to repeat any self-tests, but
- this time using the binaries in their final installed location.
- This target does not install anything. Running this target as a
- regular user, particularly if the prior `make install' required
- root privileges, verifies that the installation completed
- correctly.
-
- 6. You can remove the program binaries and object files from the
- source code directory by typing `make clean'. To also remove the
- files that `configure' created (so you can compile the package for
- a different kind of computer), type `make distclean'. There is
- also a `make maintainer-clean' target, but that is intended mainly
- for the package's developers. If you use it, you may have to get
- all sorts of other programs in order to regenerate files that came
- with the distribution.
-
- 7. Often, you can also type `make uninstall' to remove the installed
- files again. In practice, not all packages have tested that
- uninstallation works correctly, even though it is required by the
- GNU Coding Standards.
-
- 8. Some packages, particularly those that use Automake, provide `make
- distcheck', which can by used by developers to test that all other
- targets like `make install' and `make uninstall' work correctly.
- This target is generally not run by end users.
-
-Compilers and Options
-=====================
-
- Some systems require unusual options for compilation or linking that
-the `configure' script does not know about. Run `./configure --help'
-for details on some of the pertinent environment variables.
-
- You can give `configure' initial values for configuration parameters
-by setting variables in the command line or in the environment. Here
-is an example:
-
- ./configure CC=c99 CFLAGS=-g LIBS=-lposix
-
- *Note Defining Variables::, for more details.
-
-Compiling For Multiple Architectures
-====================================
-
- You can compile the package for more than one kind of computer at the
-same time, by placing the object files for each architecture in their
-own directory. To do this, you can use GNU `make'. `cd' to the
-directory where you want the object files and executables to go and run
-the `configure' script. `configure' automatically checks for the
-source code in the directory that `configure' is in and in `..'. This
-is known as a "VPATH" build.
-
- With a non-GNU `make', it is safer to compile the package for one
-architecture at a time in the source code directory. After you have
-installed the package for one architecture, use `make distclean' before
-reconfiguring for another architecture.
-
- On MacOS X 10.5 and later systems, you can create libraries and
-executables that work on multiple system types--known as "fat" or
-"universal" binaries--by specifying multiple `-arch' options to the
-compiler but only a single `-arch' option to the preprocessor. Like
-this:
-
- ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
- CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
- CPP="gcc -E" CXXCPP="g++ -E"
-
- This is not guaranteed to produce working output in all cases, you
-may have to build one architecture at a time and combine the results
-using the `lipo' tool if you have problems.
-
-Installation Names
-==================
-
- By default, `make install' installs the package's commands under
-`/usr/local/bin', include files under `/usr/local/include', etc. You
-can specify an installation prefix other than `/usr/local' by giving
-`configure' the option `--prefix=PREFIX', where PREFIX must be an
-absolute file name.
-
- You can specify separate installation prefixes for
-architecture-specific files and architecture-independent files. If you
-pass the option `--exec-prefix=PREFIX' to `configure', the package uses
-PREFIX as the prefix for installing programs and libraries.
-Documentation and other data files still use the regular prefix.
-
- In addition, if you use an unusual directory layout you can give
-options like `--bindir=DIR' to specify different values for particular
-kinds of files. Run `configure --help' for a list of the directories
-you can set and what kinds of files go in them. In general, the
-default for these options is expressed in terms of `${prefix}', so that
-specifying just `--prefix' will affect all of the other directory
-specifications that were not explicitly provided.
-
- The most portable way to affect installation locations is to pass the
-correct locations to `configure'; however, many packages provide one or
-both of the following shortcuts of passing variable assignments to the
-`make install' command line to change installation locations without
-having to reconfigure or recompile.
-
- The first method involves providing an override variable for each
-affected directory. For example, `make install
-prefix=/alternate/directory' will choose an alternate location for all
-directory configuration variables that were expressed in terms of
-`${prefix}'. Any directories that were specified during `configure',
-but not in terms of `${prefix}', must each be overridden at install
-time for the entire installation to be relocated. The approach of
-makefile variable overrides for each directory variable is required by
-the GNU Coding Standards, and ideally causes no recompilation.
-However, some platforms have known limitations with the semantics of
-shared libraries that end up requiring recompilation when using this
-method, particularly noticeable in packages that use GNU Libtool.
-
- The second method involves providing the `DESTDIR' variable. For
-example, `make install DESTDIR=/alternate/directory' will prepend
-`/alternate/directory' before all installation names. The approach of
-`DESTDIR' overrides is not required by the GNU Coding Standards, and
-does not work on platforms that have drive letters. On the other hand,
-it does better at avoiding recompilation issues, and works well even
-when some directory options were not specified in terms of `${prefix}'
-at `configure' time.
-
-Optional Features
-=================
-
- If the package supports it, you can cause programs to be installed
-with an extra prefix or suffix on their names by giving `configure' the
-option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
-
- Some packages pay attention to `--enable-FEATURE' options to
-`configure', where FEATURE indicates an optional part of the package.
-They may also pay attention to `--with-PACKAGE' options, where PACKAGE
-is something like `gnu-as' or `x' (for the X Window System). The
-`README' should mention any `--enable-' and `--with-' options that the
-package recognizes.
-
- For packages that use the X Window System, `configure' can usually
-find the X include and library files automatically, but if it doesn't,
-you can use the `configure' options `--x-includes=DIR' and
-`--x-libraries=DIR' to specify their locations.
-
- Some packages offer the ability to configure how verbose the
-execution of `make' will be. For these packages, running `./configure
---enable-silent-rules' sets the default to minimal output, which can be
-overridden with `make V=1'; while running `./configure
---disable-silent-rules' sets the default to verbose, which can be
-overridden with `make V=0'.
-
-Particular systems
-==================
-
- On HP-UX, the default C compiler is not ANSI C compatible. If GNU
-CC is not installed, it is recommended to use the following options in
-order to use an ANSI C compiler:
-
- ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
-
-and if that doesn't work, install pre-built binaries of GCC for HP-UX.
-
- HP-UX `make' updates targets which have the same time stamps as
-their prerequisites, which makes it generally unusable when shipped
-generated files such as `configure' are involved. Use GNU `make'
-instead.
-
- On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
-parse its `<wchar.h>' header file. The option `-nodtk' can be used as
-a workaround. If GNU CC is not installed, it is therefore recommended
-to try
-
- ./configure CC="cc"
-
-and if that doesn't work, try
-
- ./configure CC="cc -nodtk"
-
- On Solaris, don't put `/usr/ucb' early in your `PATH'. This
-directory contains several dysfunctional programs; working variants of
-these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
-in your `PATH', put it _after_ `/usr/bin'.
-
- On Haiku, software installed for all users goes in `/boot/common',
-not `/usr/local'. It is recommended to use the following options:
-
- ./configure --prefix=/boot/common
-
-Specifying the System Type
-==========================
-
- There may be some features `configure' cannot figure out
-automatically, but needs to determine by the type of machine the package
-will run on. Usually, assuming the package is built to be run on the
-_same_ architectures, `configure' can figure that out, but if it prints
-a message saying it cannot guess the machine type, give it the
-`--build=TYPE' option. TYPE can either be a short name for the system
-type, such as `sun4', or a canonical name which has the form:
-
- CPU-COMPANY-SYSTEM
-
-where SYSTEM can have one of these forms:
-
- OS
- KERNEL-OS
-
- See the file `config.sub' for the possible values of each field. If
-`config.sub' isn't included in this package, then this package doesn't
-need to know the machine type.
-
- If you are _building_ compiler tools for cross-compiling, you should
-use the option `--target=TYPE' to select the type of system they will
-produce code for.
-
- If you want to _use_ a cross compiler, that generates code for a
-platform different from the build platform, you should specify the
-"host" platform (i.e., that on which the generated programs will
-eventually be run) with `--host=TYPE'.
-
-Sharing Defaults
-================
-
- If you want to set default values for `configure' scripts to share,
-you can create a site shell script called `config.site' that gives
-default values for variables like `CC', `cache_file', and `prefix'.
-`configure' looks for `PREFIX/share/config.site' if it exists, then
-`PREFIX/etc/config.site' if it exists. Or, you can set the
-`CONFIG_SITE' environment variable to the location of the site script.
-A warning: not all `configure' scripts look for a site script.
-
-Defining Variables
-==================
-
- Variables not defined in a site shell script can be set in the
-environment passed to `configure'. However, some packages may run
-configure again during the build, and the customized values of these
-variables may be lost. In order to avoid this problem, you should set
-them in the `configure' command line, using `VAR=value'. For example:
-
- ./configure CC=/usr/local2/bin/gcc
-
-causes the specified `gcc' to be used as the C compiler (unless it is
-overridden in the site shell script).
-
-Unfortunately, this technique does not work for `CONFIG_SHELL' due to
-an Autoconf bug. Until the bug is fixed you can use this workaround:
-
- CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
-
-`configure' Invocation
-======================
-
- `configure' recognizes the following options to control how it
-operates.
-
-`--help'
-`-h'
- Print a summary of all of the options to `configure', and exit.
-
-`--help=short'
-`--help=recursive'
- Print a summary of the options unique to this package's
- `configure', and exit. The `short' variant lists options used
- only in the top level, while the `recursive' variant lists options
- also present in any nested packages.
-
-`--version'
-`-V'
- Print the version of Autoconf used to generate the `configure'
- script, and exit.
-
-`--cache-file=FILE'
- Enable the cache: use and save the results of the tests in FILE,
- traditionally `config.cache'. FILE defaults to `/dev/null' to
- disable caching.
-
-`--config-cache'
-`-C'
- Alias for `--cache-file=config.cache'.
-
-`--quiet'
-`--silent'
-`-q'
- Do not print messages saying which checks are being made. To
- suppress all normal output, redirect it to `/dev/null' (any error
- messages will still be shown).
-
-`--srcdir=DIR'
- Look for the package's source code in directory DIR. Usually
- `configure' can determine that directory automatically.
-
-`--prefix=DIR'
- Use DIR as the installation prefix. *note Installation Names::
- for more details, including other options available for fine-tuning
- the installation locations.
-
-`--no-create'
-`-n'
- Run the configure checks, but stop before creating any output
- files.
-
-`configure' also accepts some other, not widely useful, options. Run
-`configure --help' for more details.
-
Deleted: trunk/packages/norsnet/trunk/debian/Makefile.am
===================================================================
--- trunk/packages/norsnet/trunk/debian/Makefile.am 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/Makefile.am 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,29 +0,0 @@
-SUBDIRS = scr example
-
-man_MANS = norsnet.1
-
-dist_noinst_DATA = norsnet.pod.in
-dist_bin_SCRIPTS = norsnet
-
-norsnet.pod: norsnet.pod.in
- sed -e 's|__pkgdatadir__|$(pkgdatadir)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__bindir__|$(bindir)|g;' "$<" > "$@"
-
-norsnet.1: norsnet.pod
- pod2man -c 'User Commands' -r "$(VERSION)" $< $@
-
-distclean-local:
- rm -f norsnet.pod norsnet.1 norsnet
-
-dist-hook:
- rm -rf `find $(distdir) -name .svn`
-
-install-data-local:
-
-install-data-hook:
-
-install-exec-hook:
- sed -i -e 's|__datadir__|$(datadir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__sysconfdir__|$(sysconfdir)|g;' "$(DESTDIR)$(bindir)/norsnet"
-
-uninstall-local:
- rm -rf "$(DESTDIR)$(pkgdatadir)" "$(DESTDIR)$(docdir)"
-
Deleted: trunk/packages/norsnet/trunk/debian/NEWS
===================================================================
Deleted: trunk/packages/norsnet/trunk/debian/aclocal.m4
===================================================================
--- trunk/packages/norsnet/trunk/debian/aclocal.m4 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/aclocal.m4 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,601 +0,0 @@
-# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
-
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-m4_ifndef([AC_AUTOCONF_VERSION],
- [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],,
-[m4_warning([this file was generated for autoconf 2.67.
-You have another version of autoconf. It may work, but is not guaranteed to.
-If you have problems, you may need to regenerate the build system entirely.
-To do so, use the procedure documented by the package, typically `autoreconf'.])])
-
-# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# AM_AUTOMAKE_VERSION(VERSION)
-# ----------------------------
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Modified: trunk/packages/norsnet/trunk/debian/changelog
===================================================================
--- trunk/packages/norsnet/trunk/debian/changelog 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/changelog 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,3 +1,9 @@
+norsnet (1.0.12-1) stable; urgency=low
+
+ * packaging for debian-med
+
+ -- Christian Mertes <mertes at in.tum.de> Tue, 10 Jul 2012 17:43:00 +0100
+
norsnet (1.0.10) stable; urgency=low
* warning when pp-popcon is not installed
@@ -74,3 +80,4 @@
* Initial version.
-- Guy Yachdav <gyahcdav at rostlab.org> Thu, 10 Dec 2009 22:32:15 +0100
+
Deleted: trunk/packages/norsnet/trunk/debian/configure
===================================================================
--- trunk/packages/norsnet/trunk/debian/configure 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/configure 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,3350 +0,0 @@
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- cat
-fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
- || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
-_ACEOF
-
-# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
-# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
-# trailing colons and then remove the whole line if VPATH becomes empty
-# (actually we leave an empty line to preserve line numbers).
-if test "x$srcdir" = x.; then
- ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
-h
-s///
-s/^/:/
-s/[ ]*$/:/
-s/:\$(srcdir):/:/g
-s/:\${srcdir}:/:/g
-s/:@srcdir@:/:/g
-s/^:*//
-s/:*$//
-x
-s/\(=[ ]*\).*/\1/
-G
-s/\n//
-s/^[^=]*=[ ]*$//
-}'
-fi
-
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-fi # test -n "$CONFIG_FILES"
-
-
-eval set X " :F $CONFIG_FILES "
-shift
-for ac_tag
-do
- case $ac_tag in
- :[FHLC]) ac_mode=$ac_tag; continue;;
- esac
- case $ac_mode$ac_tag in
- :[FHL]*:*);;
- :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
- :[FH]-) ac_tag=-:-;;
- :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
- esac
- ac_save_IFS=$IFS
- IFS=:
- set x $ac_tag
- IFS=$ac_save_IFS
- shift
- ac_file=$1
- shift
-
- case $ac_mode in
- :L) ac_source=$1;;
- :[FH])
- ac_file_inputs=
- for ac_f
- do
- case $ac_f in
- -) ac_f="$tmp/stdin";;
- *) # Look for the file first in the build tree, then in the source tree
- # (if the path is not absolute). The absolute path cannot be DOS-style,
- # because $ac_f cannot contain `:'.
- test -f "$ac_f" ||
- case $ac_f in
- [\\/$]*) false;;
- *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
- esac ||
- as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
- esac
- case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
- as_fn_append ac_file_inputs " '$ac_f'"
- done
-
- # Let's still pretend it is `configure' which instantiates (i.e., don't
- # use $as_me), people would be surprised to read:
- # /* config.h. Generated by config.status. */
- configure_input='Generated from '`
- $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
- `' by configure.'
- if test x"$ac_file" != x-; then
- configure_input="$ac_file. $configure_input"
- { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
-$as_echo "$as_me: creating $ac_file" >&6;}
- fi
- # Neutralize special characters interpreted by sed in replacement strings.
- case $configure_input in #(
- *\&* | *\|* | *\\* )
- ac_sed_conf_input=`$as_echo "$configure_input" |
- sed 's/[\\\\&|]/\\\\&/g'`;; #(
- *) ac_sed_conf_input=$configure_input;;
- esac
-
- case $ac_tag in
- *:-:* | *:-) cat >"$tmp/stdin" \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
- esac
- ;;
- esac
-
- ac_dir=`$as_dirname -- "$ac_file" ||
-$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$ac_file" : 'X\(//\)[^/]' \| \
- X"$ac_file" : 'X\(//\)$' \| \
- X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$ac_file" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- as_dir="$ac_dir"; as_fn_mkdir_p
- ac_builddir=.
-
-case "$ac_dir" in
-.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
-*)
- ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
- # A ".." for each directory in $ac_dir_suffix.
- ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
- case $ac_top_builddir_sub in
- "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
- *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
- esac ;;
-esac
-ac_abs_top_builddir=$ac_pwd
-ac_abs_builddir=$ac_pwd$ac_dir_suffix
-# for backward compatibility:
-ac_top_builddir=$ac_top_build_prefix
-
-case $srcdir in
- .) # We are building in place.
- ac_srcdir=.
- ac_top_srcdir=$ac_top_builddir_sub
- ac_abs_top_srcdir=$ac_pwd ;;
- [\\/]* | ?:[\\/]* ) # Absolute name.
- ac_srcdir=$srcdir$ac_dir_suffix;
- ac_top_srcdir=$srcdir
- ac_abs_top_srcdir=$srcdir ;;
- *) # Relative name.
- ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
- ac_top_srcdir=$ac_top_build_prefix$srcdir
- ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
-esac
-ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
-
-
- case $ac_mode in
- :F)
- #
- # CONFIG_FILE
- #
-
- case $INSTALL in
- [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
- *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
- esac
- ac_MKDIR_P=$MKDIR_P
- case $MKDIR_P in
- [\\/$]* | ?:[\\/]* ) ;;
- */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
- esac
-_ACEOF
-
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-# If the template does not know about datarootdir, expand it.
-# FIXME: This hack should be removed a few years after 2.60.
-ac_datarootdir_hack=; ac_datarootdir_seen=
-ac_sed_dataroot='
-/datarootdir/ {
- p
- q
-}
-/@datadir@/p
-/@docdir@/p
-/@infodir@/p
-/@localedir@/p
-/@mandir@/p'
-case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
-*datarootdir*) ac_datarootdir_seen=yes;;
-*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
-$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
-_ACEOF
-cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
- ac_datarootdir_hack='
- s&@datadir@&$datadir&g
- s&@docdir@&$docdir&g
- s&@infodir@&$infodir&g
- s&@localedir@&$localedir&g
- s&@mandir@&$mandir&g
- s&\\\${datarootdir}&$datarootdir&g' ;;
-esac
-_ACEOF
-
-# Neutralize VPATH when `$srcdir' = `.'.
-# Shell code in configure.ac might set extrasub.
-# FIXME: do we really want to maintain this feature?
-cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-ac_sed_extra="$ac_vpsub
-$extrasub
-_ACEOF
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-:t
-/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
-s|@configure_input@|$ac_sed_conf_input|;t t
-s&@top_builddir@&$ac_top_builddir_sub&;t t
-s&@top_build_prefix@&$ac_top_build_prefix&;t t
-s&@srcdir@&$ac_srcdir&;t t
-s&@abs_srcdir@&$ac_abs_srcdir&;t t
-s&@top_srcdir@&$ac_top_srcdir&;t t
-s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
-s&@builddir@&$ac_builddir&;t t
-s&@abs_builddir@&$ac_abs_builddir&;t t
-s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
-s&@INSTALL@&$ac_INSTALL&;t t
-s&@MKDIR_P@&$ac_MKDIR_P&;t t
-$ac_datarootdir_hack
-"
-eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5
-
-test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
- { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
- { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined. Please make sure it is defined" >&5
-$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined. Please make sure it is defined" >&2;}
-
- rm -f "$tmp/stdin"
- case $ac_file in
- -) cat "$tmp/out" && rm -f "$tmp/out";;
- *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
- esac \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5
- ;;
-
-
-
- esac
-
-done # for ac_tag
-
-
-as_fn_exit 0
-_ACEOF
-ac_clean_files=$ac_clean_files_save
-
-test $ac_write_fail = 0 ||
- as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
-
-
-# configure is writing to config.log, and then calls config.status.
-# config.status does its own redirection, appending to config.log.
-# Unfortunately, on DOS this fails, as config.log is still kept open
-# by configure, so config.status won't be able to write to it; its
-# output is simply discarded. So we exec the FD to /dev/null,
-# effectively closing config.log, so it can be properly (re)opened and
-# appended to by config.status. When coming back to configure, we
-# need to make the FD available again.
-if test "$no_create" != yes; then
- ac_cs_success=:
- ac_config_status_args=
- test "$silent" = yes &&
- ac_config_status_args="$ac_config_status_args --quiet"
- exec 5>/dev/null
- $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
- exec 5>>config.log
- # Use ||, not &&, to avoid exiting from the if with $? = 1, which
- # would make configure fail if this is the last instruction.
- $ac_cs_success || as_fn_exit 1
-fi
-if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
-$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
-fi
-
Deleted: trunk/packages/norsnet/trunk/debian/configure.ac
===================================================================
--- trunk/packages/norsnet/trunk/debian/configure.ac 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/configure.ac 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,6 +0,0 @@
-AC_INIT([norsnet], [1.0.12], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=norsnet])
-AC_CONFIG_SRCDIR([scr/createDataFile.pl])
-AM_INIT_AUTOMAKE
-AC_CONFIG_FILES([Makefile scr/Makefile example/Makefile])
-
-AC_OUTPUT
Deleted: trunk/packages/norsnet/trunk/debian/install-sh
===================================================================
--- trunk/packages/norsnet/trunk/debian/install-sh 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/install-sh 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,520 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2009-04-28.21; # UTC
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
-# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
-# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-#
-# Except as contained in this notice, the name of the X Consortium shall not
-# be used in advertising or otherwise to promote the sale, use or other deal-
-# ings in this Software without prior written authorization from the X Consor-
-# tium.
-#
-#
-# FSF changes to this file are in the public domain.
-#
-# Calling this script install-sh is preferred over install.sh, to prevent
-# `make' implicit rules from creating a file called install from it
-# when there is no Makefile.
-#
-# This script is compatible with the BSD install script, but was written
-# from scratch.
-
-nl='
-'
-IFS=" "" $nl"
-
-# set DOITPROG to echo to test this script
-
-# Don't use :- since 4.3BSD and earlier shells don't like it.
-doit=${DOITPROG-}
-if test -z "$doit"; then
- doit_exec=exec
-else
- doit_exec=$doit
-fi
-
-# Put in absolute file names if you don't have them in your path;
-# or use environment vars.
-
-chgrpprog=${CHGRPPROG-chgrp}
-chmodprog=${CHMODPROG-chmod}
-chownprog=${CHOWNPROG-chown}
-cmpprog=${CMPPROG-cmp}
-cpprog=${CPPROG-cp}
-mkdirprog=${MKDIRPROG-mkdir}
-mvprog=${MVPROG-mv}
-rmprog=${RMPROG-rm}
-stripprog=${STRIPPROG-strip}
-
-posix_glob='?'
-initialize_posix_glob='
- test "$posix_glob" != "?" || {
- if (set -f) 2>/dev/null; then
- posix_glob=
- else
- posix_glob=:
- fi
- }
-'
-
-posix_mkdir=
-
-# Desired mode of installed file.
-mode=0755
-
-chgrpcmd=
-chmodcmd=$chmodprog
-chowncmd=
-mvcmd=$mvprog
-rmcmd="$rmprog -f"
-stripcmd=
-
-src=
-dst=
-dir_arg=
-dst_arg=
-
-copy_on_change=false
-no_target_directory=
-
-usage="\
-Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
- or: $0 [OPTION]... SRCFILES... DIRECTORY
- or: $0 [OPTION]... -t DIRECTORY SRCFILES...
- or: $0 [OPTION]... -d DIRECTORIES...
-
-In the 1st form, copy SRCFILE to DSTFILE.
-In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
-In the 4th, create DIRECTORIES.
-
-Options:
- --help display this help and exit.
- --version display version info and exit.
-
- -c (ignored)
- -C install only if different (preserve the last data modification time)
- -d create directories instead of installing files.
- -g GROUP $chgrpprog installed files to GROUP.
- -m MODE $chmodprog installed files to MODE.
- -o USER $chownprog installed files to USER.
- -s $stripprog installed files.
- -t DIRECTORY install into DIRECTORY.
- -T report an error if DSTFILE is a directory.
-
-Environment variables override the default commands:
- CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
- RMPROG STRIPPROG
-"
-
-while test $# -ne 0; do
- case $1 in
- -c) ;;
-
- -C) copy_on_change=true;;
-
- -d) dir_arg=true;;
-
- -g) chgrpcmd="$chgrpprog $2"
- shift;;
-
- --help) echo "$usage"; exit $?;;
-
- -m) mode=$2
- case $mode in
- *' '* | *' '* | *'
-'* | *'*'* | *'?'* | *'['*)
- echo "$0: invalid mode: $mode" >&2
- exit 1;;
- esac
- shift;;
-
- -o) chowncmd="$chownprog $2"
- shift;;
-
- -s) stripcmd=$stripprog;;
-
- -t) dst_arg=$2
- shift;;
-
- -T) no_target_directory=true;;
-
- --version) echo "$0 $scriptversion"; exit $?;;
-
- --) shift
- break;;
-
- -*) echo "$0: invalid option: $1" >&2
- exit 1;;
-
- *) break;;
- esac
- shift
-done
-
-if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
- # When -d is used, all remaining arguments are directories to create.
- # When -t is used, the destination is already specified.
- # Otherwise, the last argument is the destination. Remove it from $@.
- for arg
- do
- if test -n "$dst_arg"; then
- # $@ is not empty: it contains at least $arg.
- set fnord "$@" "$dst_arg"
- shift # fnord
- fi
- shift # arg
- dst_arg=$arg
- done
-fi
-
-if test $# -eq 0; then
- if test -z "$dir_arg"; then
- echo "$0: no input file specified." >&2
- exit 1
- fi
- # It's OK to call `install-sh -d' without argument.
- # This can happen when creating conditional directories.
- exit 0
-fi
-
-if test -z "$dir_arg"; then
- trap '(exit $?); exit' 1 2 13 15
-
- # Set umask so as not to create temps with too-generous modes.
- # However, 'strip' requires both read and write access to temps.
- case $mode in
- # Optimize common cases.
- *644) cp_umask=133;;
- *755) cp_umask=22;;
-
- *[0-7])
- if test -z "$stripcmd"; then
- u_plus_rw=
- else
- u_plus_rw='% 200'
- fi
- cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
- *)
- if test -z "$stripcmd"; then
- u_plus_rw=
- else
- u_plus_rw=,u+rw
- fi
- cp_umask=$mode$u_plus_rw;;
- esac
-fi
-
-for src
-do
- # Protect names starting with `-'.
- case $src in
- -*) src=./$src;;
- esac
-
- if test -n "$dir_arg"; then
- dst=$src
- dstdir=$dst
- test -d "$dstdir"
- dstdir_status=$?
- else
-
- # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
- # might cause directories to be created, which would be especially bad
- # if $src (and thus $dsttmp) contains '*'.
- if test ! -f "$src" && test ! -d "$src"; then
- echo "$0: $src does not exist." >&2
- exit 1
- fi
-
- if test -z "$dst_arg"; then
- echo "$0: no destination specified." >&2
- exit 1
- fi
-
- dst=$dst_arg
- # Protect names starting with `-'.
- case $dst in
- -*) dst=./$dst;;
- esac
-
- # If destination is a directory, append the input filename; won't work
- # if double slashes aren't ignored.
- if test -d "$dst"; then
- if test -n "$no_target_directory"; then
- echo "$0: $dst_arg: Is a directory" >&2
- exit 1
- fi
- dstdir=$dst
- dst=$dstdir/`basename "$src"`
- dstdir_status=0
- else
- # Prefer dirname, but fall back on a substitute if dirname fails.
- dstdir=`
- (dirname "$dst") 2>/dev/null ||
- expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$dst" : 'X\(//\)[^/]' \| \
- X"$dst" : 'X\(//\)$' \| \
- X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
- echo X"$dst" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'
- `
-
- test -d "$dstdir"
- dstdir_status=$?
- fi
- fi
-
- obsolete_mkdir_used=false
-
- if test $dstdir_status != 0; then
- case $posix_mkdir in
- '')
- # Create intermediate dirs using mode 755 as modified by the umask.
- # This is like FreeBSD 'install' as of 1997-10-28.
- umask=`umask`
- case $stripcmd.$umask in
- # Optimize common cases.
- *[2367][2367]) mkdir_umask=$umask;;
- .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
-
- *[0-7])
- mkdir_umask=`expr $umask + 22 \
- - $umask % 100 % 40 + $umask % 20 \
- - $umask % 10 % 4 + $umask % 2
- `;;
- *) mkdir_umask=$umask,go-w;;
- esac
-
- # With -d, create the new directory with the user-specified mode.
- # Otherwise, rely on $mkdir_umask.
- if test -n "$dir_arg"; then
- mkdir_mode=-m$mode
- else
- mkdir_mode=
- fi
-
- posix_mkdir=false
- case $umask in
- *[123567][0-7][0-7])
- # POSIX mkdir -p sets u+wx bits regardless of umask, which
- # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
- ;;
- *)
- tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
- if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
- then
- if test -z "$dir_arg" || {
- # Check for POSIX incompatibilities with -m.
- # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
- # other-writeable bit of parent directory when it shouldn't.
- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
- case $ls_ld_tmpdir in
- d????-?r-*) different_mode=700;;
- d????-?--*) different_mode=755;;
- *) false;;
- esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
- }
- }
- then posix_mkdir=:
- fi
- rmdir "$tmpdir/d" "$tmpdir"
- else
- # Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
- fi
- trap '' 0;;
- esac;;
- esac
-
- if
- $posix_mkdir && (
- umask $mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
- )
- then :
- else
-
- # The umask is ridiculous, or mkdir does not conform to POSIX,
- # or it failed possibly due to a race condition. Create the
- # directory the slow way, step by step, checking for races as we go.
-
- case $dstdir in
- /*) prefix='/';;
- -*) prefix='./';;
- *) prefix='';;
- esac
-
- eval "$initialize_posix_glob"
-
- oIFS=$IFS
- IFS=/
- $posix_glob set -f
- set fnord $dstdir
- shift
- $posix_glob set +f
- IFS=$oIFS
-
- prefixes=
-
- for d
- do
- test -z "$d" && continue
-
- prefix=$prefix$d
- if test -d "$prefix"; then
- prefixes=
- else
- if $posix_mkdir; then
- (umask=$mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
- # Don't fail if two instances are running concurrently.
- test -d "$prefix" || exit 1
- else
- case $prefix in
- *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
- *) qprefix=$prefix;;
- esac
- prefixes="$prefixes '$qprefix'"
- fi
- fi
- prefix=$prefix/
- done
-
- if test -n "$prefixes"; then
- # Don't fail if two instances are running concurrently.
- (umask $mkdir_umask &&
- eval "\$doit_exec \$mkdirprog $prefixes") ||
- test -d "$dstdir" || exit 1
- obsolete_mkdir_used=true
- fi
- fi
- fi
-
- if test -n "$dir_arg"; then
- { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
- { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
- test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
- else
-
- # Make a couple of temp file names in the proper directory.
- dsttmp=$dstdir/_inst.$$_
- rmtmp=$dstdir/_rm.$$_
-
- # Trap to clean up those temp files at exit.
- trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
-
- # Copy the file name to the temp name.
- (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
-
- # and set any options; do chmod last to preserve setuid bits.
- #
- # If any of these fail, we abort the whole thing. If we want to
- # ignore errors from any of these, just make sure not to ignore
- # errors from the above "$doit $cpprog $src $dsttmp" command.
- #
- { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
- { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
- { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
-
- # If -C, don't bother to copy if it wouldn't change the file.
- if $copy_on_change &&
- old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
- new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
-
- eval "$initialize_posix_glob" &&
- $posix_glob set -f &&
- set X $old && old=:$2:$4:$5:$6 &&
- set X $new && new=:$2:$4:$5:$6 &&
- $posix_glob set +f &&
-
- test "$old" = "$new" &&
- $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
- then
- rm -f "$dsttmp"
- else
- # Rename the file to the real destination.
- $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
-
- # The rename failed, perhaps because mv can't rename something else
- # to itself, or perhaps because mv is so ancient that it does not
- # support -f.
- {
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
- test ! -f "$dst" ||
- $doit $rmcmd -f "$dst" 2>/dev/null ||
- { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
- { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
- } ||
- { echo "$0: cannot unlink or rename $dst" >&2
- (exit 1); exit 1
- }
- } &&
-
- # Now rename the file to the real destination.
- $doit $mvcmd "$dsttmp" "$dst"
- }
- fi || exit 1
-
- trap '' 0
- fi
-done
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
Deleted: trunk/packages/norsnet/trunk/debian/missing
===================================================================
--- trunk/packages/norsnet/trunk/debian/missing 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/missing 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,376 +0,0 @@
-#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
-
-scriptversion=2009-04-28.21; # UTC
-
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
-# 2008, 2009 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# 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.
-
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-if test $# -eq 0; then
- echo 1>&2 "Try \`$0 --help' for more information"
- exit 1
-fi
-
-run=:
-sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
-sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
-
-# In the cases where this matters, `missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
- configure_ac=configure.ac
-else
- configure_ac=configure.in
-fi
-
-msg="missing on your system"
-
-case $1 in
---run)
- # Try to run requested program, and just exit if it succeeds.
- run=
- shift
- "$@" && exit 0
- # Exit code 63 means version mismatch. This often happens
- # when the user try to use an ancient version of a tool on
- # a file that requires a minimum version. In this case we
- # we should proceed has if the program had been absent, or
- # if --run hadn't been passed.
- if test $? = 63; then
- run=:
- msg="probably too old"
- fi
- ;;
-
- -h|--h|--he|--hel|--help)
- echo "\
-$0 [OPTION]... PROGRAM [ARGUMENT]...
-
-Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
-
-Options:
- -h, --help display this help and exit
- -v, --version output version information and exit
- --run try to run the given command, and emulate it if it fails
-
-Supported PROGRAM values:
- aclocal touch file \`aclocal.m4'
- autoconf touch file \`configure'
- autoheader touch file \`config.h.in'
- autom4te touch the output file, or create a stub one
- automake touch all \`Makefile.in' files
- bison create \`y.tab.[ch]', if possible, from existing .[ch]
- flex create \`lex.yy.c', if possible, from existing .c
- help2man touch the output file
- lex create \`lex.yy.c', if possible, from existing .c
- makeinfo touch the output file
- tar try tar, gnutar, gtar, then tar without non-portable flags
- yacc create \`y.tab.[ch]', if possible, from existing .[ch]
-
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
-
-Send bug reports to <bug-automake at gnu.org>."
- exit $?
- ;;
-
- -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
- echo "missing $scriptversion (GNU Automake)"
- exit $?
- ;;
-
- -*)
- echo 1>&2 "$0: Unknown \`$1' option"
- echo 1>&2 "Try \`$0 --help' for more information"
- exit 1
- ;;
-
-esac
-
-# normalize program name to check for.
-program=`echo "$1" | sed '
- s/^gnu-//; t
- s/^gnu//; t
- s/^g//; t'`
-
-# Now exit if we have it, but it failed. Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program). This is about non-GNU programs, so use $1 not
-# $program.
-case $1 in
- lex*|yacc*)
- # Not GNU programs, they don't have --version.
- ;;
-
- tar*)
- if test -n "$run"; then
- echo 1>&2 "ERROR: \`tar' requires --run"
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- exit 1
- fi
- ;;
-
- *)
- if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
- # We have it, but it failed.
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- # Could not run --version or --help. This is probably someone
- # running `$TOOL --version' or `$TOOL --help' to check whether
- # $TOOL exists and not knowing $TOOL uses missing.
- exit 1
- fi
- ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case $program in
- aclocal*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`acinclude.m4' or \`${configure_ac}'. You might want
- to install the \`Automake' and \`Perl' packages. Grab them from
- any GNU archive site."
- touch aclocal.m4
- ;;
-
- autoconf*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`${configure_ac}'. You might want to install the
- \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
- archive site."
- touch configure
- ;;
-
- autoheader*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`acconfig.h' or \`${configure_ac}'. You might want
- to install the \`Autoconf' and \`GNU m4' packages. Grab them
- from any GNU archive site."
- files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
- test -z "$files" && files="config.h"
- touch_files=
- for f in $files; do
- case $f in
- *:*) touch_files="$touch_files "`echo "$f" |
- sed -e 's/^[^:]*://' -e 's/:.*//'`;;
- *) touch_files="$touch_files $f.in";;
- esac
- done
- touch $touch_files
- ;;
-
- automake*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
- You might want to install the \`Automake' and \`Perl' packages.
- Grab them from any GNU archive site."
- find . -type f -name Makefile.am -print |
- sed 's/\.am$/.in/' |
- while read f; do touch "$f"; done
- ;;
-
- autom4te*)
- echo 1>&2 "\
-WARNING: \`$1' is needed, but is $msg.
- You might have modified some files without having the
- proper tools for further handling them.
- You can get \`$1' as part of \`Autoconf' from any GNU
- archive site."
-
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -f "$file"; then
- touch $file
- else
- test -z "$file" || exec >$file
- echo "#! /bin/sh"
- echo "# Created by GNU Automake missing as a replacement of"
- echo "# $ $@"
- echo "exit 0"
- chmod +x $file
- exit 1
- fi
- ;;
-
- bison*|yacc*)
- echo 1>&2 "\
-WARNING: \`$1' $msg. You should only need it if
- you modified a \`.y' file. You may need the \`Bison' package
- in order for those modifications to take effect. You can get
- \`Bison' from any GNU archive site."
- rm -f y.tab.c y.tab.h
- if test $# -ne 1; then
- eval LASTARG="\${$#}"
- case $LASTARG in
- *.y)
- SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" y.tab.c
- fi
- SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" y.tab.h
- fi
- ;;
- esac
- fi
- if test ! -f y.tab.h; then
- echo >y.tab.h
- fi
- if test ! -f y.tab.c; then
- echo 'main() { return 0; }' >y.tab.c
- fi
- ;;
-
- lex*|flex*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a \`.l' file. You may need the \`Flex' package
- in order for those modifications to take effect. You can get
- \`Flex' from any GNU archive site."
- rm -f lex.yy.c
- if test $# -ne 1; then
- eval LASTARG="\${$#}"
- case $LASTARG in
- *.l)
- SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" lex.yy.c
- fi
- ;;
- esac
- fi
- if test ! -f lex.yy.c; then
- echo 'main() { return 0; }' >lex.yy.c
- fi
- ;;
-
- help2man*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a dependency of a manual page. You may need the
- \`Help2man' package in order for those modifications to take
- effect. You can get \`Help2man' from any GNU archive site."
-
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -f "$file"; then
- touch $file
- else
- test -z "$file" || exec >$file
- echo ".ab help2man is required to generate this page"
- exit $?
- fi
- ;;
-
- makeinfo*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a \`.texi' or \`.texinfo' file, or any other file
- indirectly affecting the aspect of the manual. The spurious
- call might also be the consequence of using a buggy \`make' (AIX,
- DU, IRIX). You might want to install the \`Texinfo' package or
- the \`GNU make' package. Grab either from any GNU archive site."
- # The file to touch is that specified with -o ...
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -z "$file"; then
- # ... or it is the one specified with @setfilename ...
- infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
- file=`sed -n '
- /^@setfilename/{
- s/.* \([^ ]*\) *$/\1/
- p
- q
- }' $infile`
- # ... or it is derived from the source name (dir/f.texi becomes f.info)
- test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
- fi
- # If the file does not exist, the user really needs makeinfo;
- # let's fail without touching anything.
- test -f $file || exit 1
- touch $file
- ;;
-
- tar*)
- shift
-
- # We have already tried tar in the generic part.
- # Look for gnutar/gtar before invocation to avoid ugly error
- # messages.
- if (gnutar --version > /dev/null 2>&1); then
- gnutar "$@" && exit 0
- fi
- if (gtar --version > /dev/null 2>&1); then
- gtar "$@" && exit 0
- fi
- firstarg="$1"
- if shift; then
- case $firstarg in
- *o*)
- firstarg=`echo "$firstarg" | sed s/o//`
- tar "$firstarg" "$@" && exit 0
- ;;
- esac
- case $firstarg in
- *h*)
- firstarg=`echo "$firstarg" | sed s/h//`
- tar "$firstarg" "$@" && exit 0
- ;;
- esac
- fi
-
- echo 1>&2 "\
-WARNING: I can't seem to be able to run \`tar' with the given arguments.
- You may want to install GNU tar or Free paxutils, or check the
- command line arguments."
- exit 1
- ;;
-
- *)
- echo 1>&2 "\
-WARNING: \`$1' is needed, and is $msg.
- You might have modified some files without having the
- proper tools for further handling them. Check the \`README' file,
- it often tells you about the needed prerequisites for installing
- this package. You may also peek at any GNU archive site, in case
- some other package would contain this missing \`$1' program."
- exit 1
- ;;
-esac
-
-exit 0
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
Deleted: trunk/packages/norsnet/trunk/debian/norsnet
===================================================================
--- trunk/packages/norsnet/trunk/debian/norsnet 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/norsnet 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,45 +0,0 @@
-#!/usr/bin/perl -w
-use File::Temp;
-use Carp qw(cluck croak);
-
-# popularity contest
-if( system('pp_popcon_cnt', '-p', 'norsnet') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }
-
-$DEF_MODE=1;
-if (@ARGV<1) {
- # 0 1 2 3 4 5 6 7
- die "\nUsage: $0 [fasta] [prof] [hssp] [output_file] [target_name] [profbval_file] [mode] [debug]\n";
-}
-$seq_file=$ARGV[0];
-$rdbProf_file=$ARGV[1];
-$hssp_file=$ARGV[2];
-$output_file=$ARGV[3];
-#$target_name=$ARGV[4];
-$profbval_file=$ARGV[5];
-$mode=$ARGV[6]||$DEF_MODE;
-my $dbg = $ARGV[7] || 0;
-
-if( $mode eq '-' ){ $mode = $DEF_MODE; }
-
-if( $mode ne '1' && $mode ne '2' && $mode ne '3' ) { die( "invalid mode, must be one of 1, 2 or 3" ); }
-
-$dir = $ENV{NORSNET_ROOT} || "__pkgdatadir__";
-$resultsdir = File::Temp::tempdir( CLEANUP => !$dbg );
-
-$createDataFile_exe = "$dir/scr/createDataFile.pl";
-$norsnet_exe = "$dir/scr/NORSnet.pl";
-
-
-{
- # 0 1 2 3 4
- my @cmd = ( $createDataFile_exe, $seq_file, $rdbProf_file, $hssp_file, $resultsdir, $dbg );
- if( $dbg ){ warn( "@cmd" ); }
- system( @cmd ) && die( "@cmd failed: $!, ".( $? >> 8 ) );
-}
-{
- # 0 1 2 3 4 5 6
- my @cmd = ( $norsnet_exe, $seq_file, $output_file, $mode, $profbval_file, $resultsdir, $dir, $dbg );
- if( $dbg ){ warn( "@cmd" ); }
- system( @cmd ) && die( "@cmd failed: $!, ".( $? >> 8 ));
-}
-
Deleted: trunk/packages/norsnet/trunk/debian/norsnet.pod.in
===================================================================
--- trunk/packages/norsnet/trunk/debian/norsnet.pod.in 2012-07-10 15:44:06 UTC (rev 11712)
+++ trunk/packages/norsnet/trunk/debian/norsnet.pod.in 2012-07-10 16:14:36 UTC (rev 11713)
@@ -1,193 +0,0 @@
-=head1 NAME
-
-norsnet - identifies unstructured loops from sequence
-
-=head1 SYNOPSIS
-
-norsnet <FASTA_FILE> <RDBPROF_FILE> <HSSP_FILE> <OUTPUT_FILE> <PROTEIN_NAME> <PROFBVAL_FILE> <OUTPUT_MODE> <DEBUG>
-
-=head1 DESCRIPTION
-
-NORSnet is a neural network based method that focuses on the identification of unstructured loops.
-
-NORSnet was trained to distinguish between very long contiguous segments with non-regular secondary structure (NORS regions) and well-folded proteins. NORSnet was trained on predicted information rather than on experimental data. Therefore, it was optimized on a large data, which is not biased by today's experimental means of capturing disorder. Thus, NORSnet reached into regions in sequence space that are not covered by the specialized disorder predictors. One disadvantage of this approach is that it is not optimal for the identification of the "average" disordered region.
-
-=head2 Output format
-
-=head3 Output mode 1
-
-Tabular output, columns:
-
- pos amino acid number (1..)
- res residue 1-letter code
- node1 output of neural network node 1
- node2 output of neural network node 2
- pred node1 / ( node1 + node2 )
- n40 pred < 0.40 ? '-' : 'N'
- n40fil at least 31 AA long stretches of 'N' in n40
- n59 pred < 0.59 ? '-' : 'N'
- n59fil at least 31 AA long stretches of 'N' in n59
-
-'N' is for non-regular secondary structure.
-
-=head1 REFERENCES
-
-=over
-
-=item Schlessinger, A., Liu, J., and Rost, B. (2007). Natively unstructured loops differ from other loops. PLoS Comput Biol, 3(7), e140.
-
-=back
-
-=head1 OPTIONS
-
-=over
-
-=item FASTA_FILE
-
-file containing protein amino-acid sequence in fasta format.
-
-=item RDBPROF_FILE
-
-Secondary structure and solvent accessibility prediction by PROF in rdb format.
-
-=item HSSP_FILE
-
-PSI-BLAST alignment profile file converted to HSSP format
-
-=item OUTPUT_FILE
-
-The name of the final NORSnet output file.
-
-=item PROFBVAL_FILE
-
-Flexibile/rigid residues prediction by profbval(1) in rdb format (mode 5).
-
-=item OUTPUT_MODE
-
-NORSnet can create output files in different formats for different purposes. Valid modes are `1', `2' or `3'. Default mode: I<1>.
-
-=over
-
-=item -
-
-Default mode. Use this when you do not want to give a value here but you want to specify B<debug>.
-
-=item 1
-
-for metadisorder(1)
-
-=back
-
-=item DEBUG
-
-Set to 1 for debugging messages
-
-=back
-
-=head1 OUTPUT
-
-=over
-
-=item number -
-
-residue number
-
-=item residue -
-
-residue type
-
-=item raw -
-
-raw value of the different between the two output nodes
-
-=back
-
-=head1 EXAMPLES
-
- norsnet __pkgdatadir__/example/cad23.f __pkgdatadir__/example/cad23-fil.rdbProf __pkgdatadir__/example/cad23-fil.hssp cad23.norsnet cad23 __pkgdatadir__/example/cad23.profbval
-
-=head1 ENVIRONMENT
-
-=over
-
-=item NORSNET_ROOT
-
-Overrides __pkgdatadir__, the path to helper scripts and data files.
-
-=back
-
-=head1 FILES
-
-=over
-
-=item F<*.norsnet>
-
-default output file extension
-
-=item F<__pkgdatadir__/example>
-
-default precomputed input files directory
-
-=back
-
-=head1 NOTES
-
-=over
-
-=item 1. It is recommended to create the profiles using 3 iteration of PSI-BLAST against big database
-
-=item 2. It is also recommended to filter the hssp files using hssp_filter.pl from the Prof package using the following command: perl hssp_filter.pl hssp_file red=80
-
-=back
-
-=head1 AUTHOR
-
-A. Schlessinger <avnersch at gmail.com>
-
-=head1 COPYRIGHT AND LICENSE
-
-NON COMMERCIAL SOFTWARE LICENSE AGREEMENT
-
-1. GENERAL.
-
-THE TERMS OF THIS LICENSE APPLY TO NON-PROFIT ORGANZIATIONS AND USERS WHO ARE EMPLOYEES OF NON-PROFIT ORGANIZAIONS. FOR PROFIT ORGANIZATION AND INDIVIDIAL USERS SHOULD CONTACT L<info at bio-sof.com> TO OBTAIN A COMMERCIAL LICENSE
-
-2. OWNERSHIP OF LICENSED PRODUCT.
-
-(a) Licensee acknowledges and agrees that the ``Licensed Product'' and all copies thereof are Licensor's exclusive property. Licensee has no rights with respect to the Licensed Product except as set forth in this Agreement, and, without limiting the generality of the foregoing, may not distribute, resell, sublicense, assign or transfer the ``Licensed Product'' or any portion thereof, or modify, decompile, disassemble or otherwise change the Licensed Software without Licensor's prior written consent.
-
-(b) Upon any termination, cancellation, or expiration hereof, Licensee shall immediately delete the Licensed Software from all of its computer systems and destroy any copies of the Licensed Documentation in its possession.
-
-3. GRANT OF LICENSE.
-
-a. Licensor hereby grants to Licensee, and Licensee hereby accepts, a personal, Non-exclusive and non-transferable license to Use the Licensed Software at the Licensed Site during the term hereof, and to use the Licensed Documentation during such term in support of the Use of the Licensed Software. Additionally individuals who are employees or contractors of Licensee who log into computers at the Licensed Site from their personal home or while traveling, are entitled to Use the Licensed Software at such remote locations, provided that such Use is undertaken for and on behalf of the Licensee and that such employees or contractors report directly to employees of the Licensee whose usual and regular place of work is the Licensed Site.
-
-b. Other than as set forth in paragraph 3(a) above, a separate license shall be required, together with the payment of additional annual license fees and charges, to use the Licensed Software at any location other than the Licensed Site.
-
-4. REPRODUCTION OF LICENSED PRODUCT.
-
-Licensee may reproduce the Software for Use in accordance with the terms of the limited License granted to the Licensee in Section 2. Reproduction of the Licensed Software for any other reason is strictly prohibited. All copies of the Software, in whole or in part, shall contain the Licensor's restrictive and proprietary notices as they appear on the copies of Software provided by Licensor.
-
-5. LIMITATION OF LIABILITY.
-
-a. IN NO EVENT SHALL LICENSOR BE LIABLE TO LICENSEE FOR ANY INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES OR LOST PROFITS, ARISING OUT OF OR RELATED TO THIS LICENSE AGREEMENT OR THE PERFORMANCE OR BREACH THEREOF, EVEN IF THE LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY THEREOF.
-
-b. IN NO EVENT SHALL LICENSOR BE LIABLE TO LICENSEE FOR ANY DAMAGES RESULTING FROM OR RELATED TO ANY FAILURE OF THE SOFTWARE PRODUCTS, INCLUDING, BUT NOT LIMITED TO LOSS OF DATA, OR DELAY OF THE LICENSOR IN THE DELIVERY OF THE LICENSED PRODUCT OR IN THE PERFORMANCE OF SERVICES UNDER THIS LICENSE AGREEMENT.
-
-c. IN NO EVENT SHALL LICENSEE BE LIABLE TO LICENSOR FOR ANY LOST PROFITS, LOST OPPORTUNITY COSTS OR ANY SPECIAL, INDIRECT, CONSEQUENTIAL OR INCIDENTAL DAMAGES, HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY.
-
-=head1 SEE ALSO
-
-=over
-
-=item profbval(1), prof(1).
-
-=item Main website
-
-L<http://www.predictprotein.org/>
-
-=back
-
-=cut
-
-# vim:et:
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