[med-svn] [Git][med-team/freecontact][master] 7 commits: Raising d/watch version to 4
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Tue Oct 12 10:53:10 BST 2021
Pierre Gruet pushed to branch master at Debian Med / freecontact
Commits:
eea69eb9 by Pierre Gruet at 2021-10-12T10:38:03+02:00
Raising d/watch version to 4
- - - - -
43f79070 by Pierre Gruet at 2021-10-12T10:57:11+02:00
Refreshing d/copyright
- - - - -
248c5aab by Pierre Gruet at 2021-10-12T10:57:52+02:00
Raising Standards version to 4.6.0 (no change needed)
- - - - -
8c90dc9d by Pierre Gruet at 2021-10-12T11:19:25+02:00
Adding Multi-Arch fields in d/control
- - - - -
e9921f2e by Pierre Gruet at 2021-10-12T11:19:55+02:00
Removing exception specifications to comply with C++17
- - - - -
ef364733 by Pierre Gruet at 2021-10-12T11:20:27+02:00
Updating changelog
- - - - -
628cb820 by Pierre Gruet at 2021-10-12T11:52:49+02:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/avoid_exception_specification.patch
- + debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+freecontact (1.0.21-10) unstable; urgency=medium
+
+ * Team upload
+ * Remove exception specifications, removed in C++17 (Closes: #984107)
+ * Raising Standards version to 4.6.0 (no change needed)
+ * Raising d/watch version to 4
+ * Refreshing d/copyright
+ * Adding Multi-Arch fields in d/control
+
+ -- Pierre Gruet <pgt at debian.org> Tue, 12 Oct 2021 11:20:41 +0200
+
freecontact (1.0.21-9) unstable; urgency=medium
* Fix override in d-shlibmove
=====================================
debian/control
=====================================
@@ -17,7 +17,7 @@ Build-Depends: debhelper-compat (= 12),
perl,
xsdcxx
Build-Depends-Indep: doxygen
-Standards-Version: 4.5.0
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/freecontact
Vcs-Git: https://salsa.debian.org/med-team/freecontact.git
Homepage: http://rostlab.org/
@@ -58,6 +58,7 @@ Depends: libfreecontact0v5 (= ${binary:Version}),
Suggests: libfreecontact-doc
Conflicts: libfreecontact-dev
Provides: libfreecontact-dev
+Multi-Arch: same
Description: fast protein contact predictor library - development files
${Description}
.
@@ -69,6 +70,7 @@ Architecture: all
Section: doc
Depends: ${misc:Depends},
libjs-jquery
+Multi-Arch: foreign
Description: documentation for libfreecontact
${Description}
.
=====================================
debian/copyright
=====================================
@@ -4,15 +4,69 @@ Upstream-Contact: Laszlo Kajan <lkajan at rostlab.org>
Source: ftp://rostlab.org/free/
Files: *
-Copyright: 2013 Laszlo Kajan <lkajan at rostlab.org>, Technical University of Munich, Germany
+Copyright: 2012-2013 Laszlo Kajan <lkajan at rostlab.org> Rost Lab, Technical University of Munich, Germany
License: GPL-3+
+Files: INSTALL
+Copyright: 1994-2009 Free Software Foundation, Inc.
+License: FSFAP
+
+Files: compile
+Copyright: 1999-2013 Free Software Foundation, Inc.
+License: GPL-2+ with Autoconf-data exception
+
Files: lib/glassofast-real.f90
Copyright: 2012 M. A. Sustik <msustik at gmail.com>
2012 B. Calderhead
2013 L. Kajan <lkajan at rostlab.org>
License: GPL-3+
+Files: m4/*
+Copyright: 2004-2009 Free Software Foundation, Inc.
+License: FSFULLR
+
+Files: m4/ax_blas.m4
+ m4/ax_lapack.m4
+ m4/ax_openmp.m4
+Copyright: 2008-2009 Steven G. Johnson <stevenj at alum.mit.edu>
+License: GPL-3+ with Autoconf-2.0~Archive exception
+
+Files: m4/ax_boost_base.m4
+Copyright: 2009 Peter Adolphs
+ 2008 Thomas Porschberg <thomas at randspringer.de>
+License: FSFAP
+
+Files: m4/ax_boost_program_options.m4
+Copyright: 2009 Thomas Porschberg <thomas at randspringer.de>
+License: FSFAP
+
+Files: m4/ax_check_compile_flag.m4
+Copyright: 2011 Maarten Bosmans <mkbosmans at gmail.com>
+ 2008 Guido U. Draheim <guidod at gmx.de>
+License: GPL-3+ with Autoconf-2.0~Archive exception
+
+Files: m4/ax_ext.m4
+Copyright: 2007 Christophe Tournayre <turn3r at users.sourceforge.net>
+License: FSFAP
+
+Files: m4/ax_gcc_x86_cpuid.m4
+Copyright: 2008 Steven G. Johnson <stevenj at alum.mit.edu>
+ 2008, Matteo Frigo
+License: GPL-3+ with Autoconf-2.0~Archive exception
+
+Files: m4/ax_lib_xerces.m4
+Copyright: 2008 Mateusz Loskot <mateusz at loskot.net>
+License: FSFAP
+
+Files: m4/ax_pthread.m4
+Copyright: 2011, Daniel Richard G. <skunk at iSKUNK.ORG>
+ 2008, Steven G. Johnson <stevenj at alum.mit.edu>
+License: GPL-3+
+
+Files: m4/ax_xsdcxx.m4
+Copyright: 2013 Laszlo Kajan <lkajan at rostlab.org> Rost Lab, Technical University of Munich, Germany
+License: FSFAP
+
Files: debian/*
Copyright: 2013-2015 Laszlo Kajan <lkajan at rostlab.org>
2014-2018 Andreas Tille <tille at debian.org>
@@ -34,3 +88,70 @@ License: GPL-3+
.
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: FSFAP
+ Copying and distribution of this file and the accompanying media
+ files, with or without modification, are permitted in any medium
+ without royalty provided the copyright notice and this notice are
+ preserved. These files are offered as-is, without any warranty.
+
+License: GPL-2+ with Autoconf-data exception
+ 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.
+ .
+ This file is maintained in Automake, please report
+ bugs to <bug-automake at gnu.org> or send patches to
+ <automake-patches at gnu.org>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
+License: FSFULLR
+ 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.
+
+License: GPL-3+ with Autoconf-2.0~Archive exception
+ 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/>.
+ .
+ As a special exception, the respective Autoconf Macro's copyright owner
+ gives unlimited permission to copy, distribute and modify the configure
+ scripts that are the output of Autoconf when processing the Macro. You
+ need not follow the terms of the GNU General Public License when using
+ or distributing such scripts, even though portions of the text of the
+ Macro appear in them. The GNU General Public License (GPL) does govern
+ all other use of the material that constitutes the Autoconf Macro.
+ .
+ This special exception to the GPL applies to versions of the Autoconf
+ Macro released by the Autoconf Archive. When you make and distribute a
+ modified version of the Autoconf Macro, you may extend this special
+ exception to the GPL to apply to your modified version as well.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
=====================================
debian/patches/avoid_exception_specification.patch
=====================================
@@ -0,0 +1,94 @@
+Description: avoid exception specifications, removed in C++17
+Author: Pierre Gruet <pgt at debian.org>
+Bug-Debian: https://bugs.debian.org/984107
+Forwarded: lkajan at rostlab.org
+Last-Update: 2021-10-12
+
+--- a/lib/freecontact.cpp
++++ b/lib/freecontact.cpp
+@@ -237,7 +237,7 @@
+ freq_vec_t &__aliw, double &__wtot,
+ const ali_t& __ali, double __cp,
+ bool __veczw, int __num_threads
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
++ ) //throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
+ {
+ if (__ali.seqcnt < 2) throw alilen_error(bo::str(bo::format("alignment size (%d) < 2") % __ali.seqcnt));
+ // lkajan: the present implementation is limited to alilen 4080.
+@@ -436,7 +436,7 @@
+ double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda,
+ bool __cov20, bool __apply_gapth, double __rho,
+ int __num_threads, time_t __icme_timeout, time_res_t *__timing
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
++ ) //throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
+ {
+ if (__ali.seqcnt < 2) throw alilen_error(bo::str(bo::format("alignment size (%d) < 2") % __ali.seqcnt));
+ if (__ali.seqcnt != __aliw.size()) throw alilen_error(bo::str(bo::format("alignment size (%d) != alignment weight vector size (%d)") % __ali.seqcnt % __aliw.size()));
+@@ -973,7 +973,7 @@
+ double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda,
+ bool __cov20, bool __apply_gapth, double __rho,
+ bool __veczw, int __num_threads, time_t __icme_timeout, time_res_t *__timing
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
++ ) //throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
+ {
+ timeval t_top; gettimeofday(&t_top, NULL);
+ timeval t_before; gettimeofday(&t_before, NULL);
+@@ -998,7 +998,7 @@
+ }
+
+
+-ali_t& ali_t::push(const std::vector<uint8_t>& __al) throw (alilen_error)
++ali_t& ali_t::push(const std::vector<uint8_t>& __al) //throw (alilen_error)
+ {
+ if( __al.size() != alilen ) throw alilen_error(bo::str(bo::format("alignment length mismatch, expected %d, got %d") % alilen % __al.size() ));
+ resize( ++seqcnt*alilen16, _mm_setzero_si128() );
+--- a/lib/freecontact.h
++++ b/lib/freecontact.h
+@@ -110,10 +110,10 @@
+ }
+
+ /// Push a sequence to the alignment.
+- ali_t& push(const std::vector<uint8_t>& __al) throw (alilen_error);
++ ali_t& push(const std::vector<uint8_t>& __al);// throw (alilen_error);
+
+ /// Push a sequence to the alignment.
+- inline ali_t& push(const std::string& __l) throw (alilen_error)
++ inline ali_t& push(const std::string& __l) //throw (alilen_error)
+ {
+ return push(read_a_seq(__l));
+ }
+@@ -182,7 +182,7 @@
+ freq_vec_t &__aliw, double &__wtot,
+ const ali_t& __ali, double __clustpc,
+ bool __veczw = true, int __num_threads = 0
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error);
++ );// throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error);
+
+ /// Predict residue contacts.
+ /** \param [in] __ali Input alignment.
+@@ -216,7 +216,7 @@
+ double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda,
+ bool __cov20, bool __apply_gapth, double __rho,
+ int __num_threads = 0, time_t __icme_timeout = 1800, time_res_t *__timing = NULL
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error);
++ );// throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error);
+
+ /// Predict residue contacts.
+ cont_res_t run(const ali_t& __ali, double __clustpc,
+@@ -224,14 +224,14 @@
+ double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda,
+ bool __cov20, bool __apply_gapth, double __rho,
+ bool __veczw = true, int __num_threads = 0, time_t __icme_timeout = 1800, time_res_t *__timing = NULL
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error);
++ );// throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error);
+
+ /// Predict residue contacts.
+ inline
+ cont_res_t run(const ali_t& __ali,
+ const parset_t& __parset,
+ bool __veczw = true, int __num_threads = 0, time_t __icme_timeout = 1800, time_res_t *__timing = NULL
+- ) throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
++ )// throw (alilen_error, icme_timeout_error, std::range_error, std::runtime_error)
+ {
+ return run(__ali, __parset.clustpc,
+ __parset.density, __parset.gapth, __parset.mincontsep,
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+avoid_exception_specification.patch
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=3
+version=4
opts=passive \
ftp://rostlab.org/free/freecontact-([0-9.]+)\.tar\..z debian
View it on GitLab: https://salsa.debian.org/med-team/freecontact/-/compare/8fb081477511cb1b3947489e5f4deebd3cd10eec...628cb820a9da16eb8fc045d41b151a413befea44
--
View it on GitLab: https://salsa.debian.org/med-team/freecontact/-/compare/8fb081477511cb1b3947489e5f4deebd3cd10eec...628cb820a9da16eb8fc045d41b151a413befea44
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