Commit 7d972ed7 authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.0.20

parent 4c613cc1
Laszlo Kajan <lkajan@rostlab.org>
This diff is collapsed.
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
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This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
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You may convey a Combined Work under terms of your choice that,
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5. Combined Libraries.
You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
choice, if you do both of the following:
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Each version is given a distinguishing version number. If the
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librostlab (1.0.20) unstable; urgency=low
* Moved blast parser out into librostlab-blast.
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 28 Mar 2012 16:53:34 +0200
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ACLOCAL_AMFLAGS = -I m4
SUBDIRS = lib
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/* config.hin. Generated from configure.ac by autoheader. */
/* Define to 1 if you have the <dlfcn.h> header file. */
#undef HAVE_DLFCN_H
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
/* Define to 1 if you have the <stdint.h> header file. */
#undef HAVE_STDINT_H
/* Define to 1 if you have the <stdlib.h> header file. */
#undef HAVE_STDLIB_H
/* Define to 1 if you have the <strings.h> header file. */
#undef HAVE_STRINGS_H
/* Define to 1 if you have the <string.h> header file. */
#undef HAVE_STRING_H
/* Define to 1 if you have the <sys/stat.h> header file. */
#undef HAVE_SYS_STAT_H
/* Define to 1 if you have the <sys/types.h> header file. */
#undef HAVE_SYS_TYPES_H
/* Define to 1 if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define to the sub-directory in which libtool stores uninstalled libraries.
*/
#undef LT_OBJDIR
/* Name of package */
#undef PACKAGE
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the home page for this package. */
#undef PACKAGE_URL
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
/* Version number of package */
#undef VERSION
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AC_INIT([librostlab], [1.0.20], [https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librostlab])
AC_CONFIG_MACRO_DIR([m4])
AC_CONFIG_SRCDIR([lib/rostlab/aux_functions.h])
AC_CONFIG_HEADERS([config.h:config.hin])
AM_INIT_AUTOMAKE
AC_PROG_CC
AC_PROG_CXX
AC_PROG_LIBTOOL
AC_LANG([C++])
DX_PDF_FEATURE(OFF)
DX_PS_FEATURE(OFF)
DX_INIT_DOXYGEN([librostlab], [Doxyfile], [../doxygen-doc])
AC_CONFIG_FILES([Makefile] [lib/Makefile] [lib/Doxyfile])
AC_OUTPUT
Notes on how this package can be tested.
────────────────────────────────────────
This package can be tested by executing
sh installation-test
in order to confirm its integrity.
To test manually, compile /usr/share/doc/librostlab3-dev/examples/blosum62_test.cpp:
g++ -Wall -lrostlab blosum62_test.cpp -o blosum62_test
After that run:
./blosum62_test
As a result, blosum62 matrix contents will be written to stdout.
This is simplest possible test which demonstrates that librostlab's header
files are installed and can be found.
If you wish to use library for more advanced cases, address to documentation
available in package `librostlab-doc`.
librostlab (1.0.20-6) unstable; urgency=medium
* Team upload.
* small fix - add build-essential dependency in debian/tests/control
-- Tatiana Malygina <merlettaia@gmail.com> Sat, 16 Jul 2016 03:28:22 +0300
librostlab (1.0.20-5) unstable; urgency=medium
[ Tatiana Malygina ]
* Team upload.
* add hardening
* add simplest test
* add examples/ to librostlab-dev
* cme fix dpkg-control
* add debian/README.test, debian/librostlab3-dev.docs,
cosmetic fixes in debian/examples/blosum62_test.cpp
[ Andreas Tille ]
* cleanup d/rules
* Do not install useless autogenerated doxygen files
* Link to jquery.js provided by sphinx-common
* DEP5
-- Tatiana Malygina <merlettaia@gmail.com> Sun, 26 Jun 2016 09:06:16 +0300
librostlab (1.0.20-4) unstable; urgency=medium
* use dh-autoreconf instead of autotools-dev to fix FTBFS on ppc64el
(thanks for the patch to Logan Rosen <logan@ubuntu.com>)
Closes: #735956
* cme fix dpkg-control
-- Andreas Tille <tille@debian.org> Tue, 13 May 2014 15:10:15 +0200
librostlab (1.0.20-3) unstable; urgency=low
* debian/control:
- cme fix dpkg-control
- debhelper 9
- canonical Vcs fields
* debian/rules: --with autotools_dev
Closes: #727433
* debian/*.install: Multi-Arch locations
-- Andreas Tille <tille@debian.org> Thu, 24 Oct 2013 08:49:13 +0200
librostlab (1.0.20-2) unstable; urgency=low
* Added handening flags.
* Added symbols file for shared library dependency information.
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 19 Sep 2012 14:03:45 +0200
librostlab (1.0.20-1) unstable; urgency=low
[ Laszlo Kajan ]
* Moved blast parser out into librostlab-blast.
* Initial release in Debian (Closes: #666192)
[ Andreas Tille ]
* debian/control:
- Enhanced long description - Joe Debian-User might possibly
not know what rostlab is and from the explanation it did not
became clear that the library is useful in computational
biology
- Priority: optional (just leave the debug package extra)
- Short descriptions should be different
* debian/librostlab-doc.doc-base: Add doc-base file for the included
documentation
-- Andreas Tille <tille@debian.org> Fri, 30 Mar 2012 15:21:06 +0200
librostlab (1.0.19) unstable; urgency=low
* Added trace_scanning() and changed trace_scanning( bool )
* Fixed multi-result file parsing
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 21 Mar 2012 14:47:50 +0100
librostlab (1.0.18) unstable; urgency=low
* Fixed more std::.
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 21 Mar 2012 14:41:19 +0100
librostlab (1.0.17) unstable; urgency=low
* No using namespace std; any more in headers
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 21 Mar 2012 13:50:03 +0100
librostlab (1.0.16) unstable; urgency=low
* changed library license to LGPL
* Changed package name to librostlab0, librostlab0-dbg and librostlab0-dev.
* Provides librostlab-dev.
* Hit is now a template with hsp type as parameter.
* Added NCBI BLOSUM62 matrix data.
* Cleaned up grammar for rounds.
* Added rostlab_stdio.h
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 14 Oct 2011 20:41:57 +0200
librostlab (1.0.15) unstable; urgency=low
* better description
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 14 Oct 2011 20:34:30 +0200
librostlab (1.0.14) unstable; urgency=low
* added documentation
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 14 Oct 2011 20:12:30 +0200
librostlab (1.0.13) unstable; urgency=low
* parser::parse now returns result_type
* cast of result_type to bool is done
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 14 Oct 2011 19:34:04 +0200
librostlab (1.0.12) unstable; urgency=low
* more headers installed
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 14 Oct 2011 19:18:42 +0200
librostlab (1.0.11) unstable; urgency=low
* headers are now installed
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 14 Oct 2011 19:02:15 +0200
librostlab (1.0.10) unstable; urgency=low
* Removed libzerg-based blast parser
* Added bison/flex based LGPL blast parser
-- Laszlo Kajan <lkajan@rostlab.org> Thu, 06 Oct 2011 19:57:29 +0200
librostlab (1.0.9) unstable; urgency=low
* flock_resource -> file_lock_resource
* locking now with fcntl: also works on NFS
-- Laszlo Kajan <lkajan@rostlab.org> Mon, 26 Sep 2011 18:50:22 +0200
librostlab (1.0.8) unstable; urgency=low
* added missing -dev dependency on librostlab0
* removed private members from doxygen documentation
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 23 Sep 2011 21:45:02 +0200
librostlab (1.0.7) unstable; urgency=low
* renamed _map_split_in_2 to map_split_in_2
* added blastpgp parser
* cdbs
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 23 Sep 2011 21:43:11 +0200
librostlab (1.0.6) unstable; urgency=low
* added mapAA2int.h
Maximilian Hecht <hecht@rostlab.org> Wed, 29 Jun 2011 09:50:51 +0200
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 29 Jun 2011 10:50:51 +0200
librostlab (1.0.5) unstable; urgency=low
* added throw() definitions to interface of flock_resource
-- Laszlo Kajan <lkajan@rostlab.org> Mon, 20 Jun 2011 10:52:36 +0200
librostlab (1.0.4) unstable; urgency=low
* FASTA format checking improved
-- Laszlo Kajan <lkajan@rostlab.org> Fri, 10 Jun 2011 10:29:22 +0200
librostlab (1.0.3) stable; urgency=low
* flock debugging added
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 02 Feb 2011 14:53:19 +0100
librostlab (1.0.2) stable; urgency=low
* does not touch lock file any more
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 02 Feb 2011 13:44:10 +0100
librostlab (1.0.1) stable; urgency=low
* now closes lock file before throwing an exception if locking fails
* added cwd_resource
-- Laszlo Kajan <lkajan@rostlab.org> Thu, 20 Jan 2011 23:57:04 +0100
librostlab (1.0.0) stable; urgency=low
* Initial release
-- Laszlo Kajan <lkajan@rostlab.org> Wed, 15 Sep 2010 15:28:53 +0200
Source: librostlab
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan@rostlab.org>,
Andreas Tille <tille@debian.org>
Section: libs
Priority: optional
Build-Depends: debhelper (>= 9),
dh-autoreconf,
doxygen,
graphviz,
latex-xcolor,
texlive-fonts-recommended,
texlive-latex-extra,
dh-linktree,
sphinx-common
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/librostlab/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/librostlab/trunk/
Homepage: http://rostlab.org/
Package: librostlab3
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Description: C++ library for computational biology
This library was developed by the Rost Lab. The lab's research is
driven by a conviction that protein and DNA sequences encode a
significant core of information about the ultimate structure and
function of genetic material and its gene products.
.
The library provides the following facilities:
* current working directory resource
* exception with stack backtrace
* file lock resource
* passwd and group structures for C++
* effective uid and gid resource
* rostlab::bio::seq class with stream input operator for FASTA format
* umask resource
.
This package contains the shared library.
Package: librostlab3-dev
Architecture: any
Section: libdevel
Depends: librostlab3 (= ${binary:Version}),
${misc:Depends}
Suggests: librostlab-doc
Provides: librostlab-dev
Replaces: librostlab0-dev
Description: C++ library for computational biology (development)
This library was developed by the Rost Lab. The lab's research is
driven by a conviction that protein and DNA sequences encode a
significant core of information about the ultimate structure and
function of genetic material and its gene products.
.
The library provides the following facilities:
* current working directory resource
* exception with stack backtrace
* file lock resource
* passwd and group structures for C++
* effective uid and gid resource
* rostlab::bio::seq class with stream input operator for FASTA format
* umask resource
.
This package contains files necessary for developing applications with
librostlab.
Package: librostlab-doc
Architecture: all
Section: doc
Depends: ${shlibs:Depends},
${misc:Depends},
${js:Depends}
Description: C++ library for computational biology (documentation)
This library was developed by the Rost Lab. The lab's research is
driven by a conviction that protein and DNA sequences encode a
significant core of information about the ultimate structure and
function of genetic material and its gene products.
.
The library provides the following facilities:
* current working directory resource
* exception with stack backtrace
* file lock resource
* passwd and group structures for C++
* effective uid and gid resource
* rostlab::bio::seq class with stream input operator for FASTA format
* umask resource
.
This package contains html documentation.
Package: librostlab3-dbg
Architecture: any
Section: debug
Priority: extra
Depends: librostlab3 (= ${binary:Version}),
${misc:Depends}
Description: debugging symbols for librostlab
The library provides the following facilities:
* current working directory resource
* exception with stack backtrace
* file lock resource
* passwd and group structures for C++
* effective uid and gid resource
* rostlab::bio::seq class with stream input operator for FASTA format
* umask resource
.
This package provides the detached debug symbols for librostlab.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: librostlab
Upstream-Contact: Laszlo Kajan <lkajan@rostlab.org>
Source: http://rostlab.org/
Files: *
Copyright: 2012 Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
License: LGPL-3+
Files: debian/*
Copyright: 2012 Laszlo Kajan <lkajan@rostlab.org>, Technical University of Munich, Germany
License: GPL-3+
License: GPL-3+
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/>.
.
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
License: LGPL-3+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This package 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 Lesser General Public License for more details.
.
You should have received a copy of the GNU Lesser General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
.
On Debian systems, the complete text of the GNU Lesser General
Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'.
// Simple example file for autopkgtest:
// loads blosum62 matrix from librostlab and prints it.
// Author: Tatiana Malygina <merlettaia@gmail.com>
#include <iostream>
#include <rostlab/blosum62.h>
int main() {
for (int i = 0; i < 27; i++) {
for (int j = 0; j < 27; j++) {
std::cout << int(rostlab::blosum62[i][j]) << " ";
}
std::cout << std::endl;
}
return 0;
}
// Compile with:
// g++ -Wall -lrostlab blosum62_test.cpp -o blosum62_test
Document: librostlab
Title: librostlab Documentation
Author: Laszlo Kajan <lkajan@rostlab.org>
Abstract: C++ library for computational biology
This library was developed by the Rost Lab. The lab's research is
driven by a conviction that protein and DNA sequences encode a
significant core of information about the ultimate structure and
function of genetic material and its gene products.
.
The library provides the following facilities:
* current working directory resource
* exception with stack backtrace
* file lock resource
* passwd and group structures for C++
* effective uid and gid resource
* rostlab::bio::seq class with stream input operator for FASTA format
* umask resource
Section: Science/Biology
Format: html
Files: /usr/share/doc/librostlab-doc/html/*.html
Index: /usr/share/doc/librostlab-doc/html/index.html
Format: PDF
Files: /usr/share/doc/librostlab-doc/librostlab.pdf.gz
doxygen-doc/html/
doxygen-doc/librostlab.pdf
lib/librostlab.tag
replace usr/share/sphinx/themes/basic/static/jquery.js usr/share/doc/librostlab-doc/html/jquery.js
debian/README.test
debian/tests/installation-test
usr/include/*
usr/lib/*/librostlab.a
usr/lib/*/librostlab.la
usr/lib/*/librostlab.so
usr/lib/*/librostlab.so.*
librostlab.so.3 librostlab3 #MINVER#
_ZN7rostlab8blosum62E@Base 1.0.20
#!/usr/bin/make -f
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@ --with autoreconf --with linktree --parallel
override_dh_auto_configure:
dh_auto_configure --parallel -- --enable-doxygen-dot --enable-doxygen-pdf
override_dh_auto_build:
dh_auto_build --parallel
$(MAKE) -C lib doxygen-doc
override_dh_installdocs:
dh_installdocs
find debian -name "*_*.md5" -delete
override_dh_strip:
dh_strip --dbg-package=librostlab3-dbg
override_dh_compress:
dh_compress -Xlibrostlab.tag
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs