--- jags-4.2.0.orig/debian/watch +++ jags-4.2.0/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://www-fis.iarc.fr/~martyn/software/jags/JAGS-(.+)\.tar\.gz --- jags-4.2.0.orig/debian/jags.lintian-overrides +++ jags-4.2.0/debian/jags.lintian-overrides @@ -0,0 +1,13 @@ +jags: non-dev-pkg-with-shlib-symlink usr/lib/libjrmath.so.0.0.0 usr/lib/libjrmath.so +jags: hardening-no-relro usr/lib/jags/jags-terminal +jags: package-name-doesnt-match-sonames libjags4 libjrmath0 +jags: hardening-no-relro usr/lib/JAGS/modules-4/basemod.so +jags: hardening-no-relro usr/lib/JAGS/modules-4/bugs.so +jags: hardening-no-relro usr/lib/JAGS/modules-4/dic.so +jags: hardening-no-relro usr/lib/JAGS/modules-4/glm.so +jags: hardening-no-relro usr/lib/JAGS/modules-4/lecuyer.so +jags: hardening-no-relro usr/lib/JAGS/modules-4/mix.so +jags: hardening-no-relro usr/lib/JAGS/modules-4/msm.so +jags: hardening-no-relro usr/lib/libjrmath.so.0.0.0 +jags: hardening-no-relro usr/lib/libjags.so.4.0.1 +jags: non-dev-pkg-with-shlib-symlink usr/lib/libjags.so.4.0.1 usr/lib/libjags.so --- jags-4.2.0.orig/debian/copyright +++ jags-4.2.0/debian/copyright @@ -0,0 +1,60 @@ +This is the Debian GNU/Linux jags package. Jags is 'Just Another Gibbs +Sampler', a program for analysis of Bayesian Graphical models by Gibbs +Sampling. Jags was written by Martyn Plummer. + +This package was created by Dirk Eddelbuettel . +The sources were downloaded from the sources + http://www-fis.iarc.fr/~martyn/software/jags/ + +Copyright and License information: + +1) JAGS itself: +Copyright (C) 2002 - 2008 Martyn Plummer +License: GPL + +2) The libltdl/ directory containing GNU libltdl (a system independent +dlopen wrapper for GNU libtool): +Copyright (C) 1998 - 2000, 2004 - 2007 Free Software Foundation, Inc. +Originally by Thomas Tanner +License: LGPL + +3) The src/jrmath/ directory containing a modified interface to GNU R +(where Martyn Plummer is a member of the R Core Development Team) +Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka +Copyright (C) 1998-2004 Ross Ihaka and the R Development Core Team +Copyright (C) 1998-2004 The R Development Core Team +Copyright (C) 1998--2005 The R Development Core Team +Copyright (C) 1998 Ross Ihaka +Copyright (C) 1999-2000 The R Development Core Team +Copyright (C) 2000-2001 The R Core Development Team +Copyright (C) 2000-2002 The R Development Core Team +Copyright (C) 2000, 2003 The R Development Core Team +Copyright (C) 2000-2005 The R Development Core Team +Copyright (C) 2000-2006 The R Development Core Team +Copyright (C) 2000-2006 The R Development Core Team +Copyright (C) 2000-2006 The R Development Core Team +Copyright (C) 2000 The R Core Development Team +Copyright (C) 2000 The R Development Core Team +Copyright (C) 2002-2004 The R Foundation +Copyright (C) 2003-2004 The R Foundation +Copyright (C) 2003-2004 The R Foundation +Copyright (C) 2003 The R Foundation +Copyright (C) 2004 Morten Welinder +Copyright (C) 2004 The R Foundation +Copyright (C) 2004 The R Foundation +Copyright (C) 2005-6 Morten Welinder +Copyright (C) 2005-6 The R Foundation +Copyright (C) 2005 The R Foundation +Copyright (C) 2006 The R Core Development Team +Copyright (C) 2006 The R Development Core Team +License: GPL + +4) For the src/modules/base/rngs/MersenneTwisterRNG.cc +Copyright (C) 1997, 1999 Makoto Matsumoto and Takuji Nishimura. +License: GPL + + +On a Debian GNU/Linux system, the GPL and LGPL licenses are included +in the files /usr/share/common-licenses/GPL and +/usr/share/common-licenses/LGPL. + --- jags-4.2.0.orig/debian/control +++ jags-4.2.0/debian/control @@ -0,0 +1,24 @@ +Source: jags +Section: math +Priority: optional +Maintainer: Dirk Eddelbuettel +Build-Depends: debhelper (>= 7.0.50~), gfortran, liblapack-dev, libltdl-dev (>= 2.2.6b), texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, texinfo, autotools-dev, faketime, g++, libcppunit-dev +Standards-Version: 3.9.6 +Homepage: http://www-fis.iarc.fr/~martyn/software/jags/ + +Package: jags +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Just Another Gibbs Sampler for Bayesian MCMC - binary + JAGS is Just Another Gibbs Sampler. It is a program for analysis of + Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) + simulation not wholly unlike BUGS. + . + JAGS was written with three aims in mind: + * To have an engine for the BUGS language that runs on Unix + * To be extensible, allowing users to write their own functions, + distributions and samplers. + * To be a plaftorm for experimentation with ideas in Bayesian modelling + . + This package contains the 'jags' binary as well as the associated + shared library modules loaded by the binary. --- jags-4.2.0.orig/debian/compat +++ jags-4.2.0/debian/compat @@ -0,0 +1 @@ +5 --- jags-4.2.0.orig/debian/rules +++ jags-4.2.0/debian/rules @@ -0,0 +1,28 @@ +#!/usr/bin/make -f + +## cf https://wiki.debian.org/ReproducibleBuilds/TimestampsInPDFGeneratedByLaTeX +DEB_DATE_RFC_2822 := $(shell dpkg-parsechangelog -S date) +DEB_DATE_RFC_3339 := $(shell date -u "--rfc-3339=seconds" -d "$(DEB_DATE_RFC_2822)") + +override_dh_auto_configure: + dh_auto_configure -- --without-included-ltdl + +override_dh_auto_build: + make + ## cf https://wiki.debian.org/ReproducibleBuilds/TimestampsInPDFGeneratedByLaTeX + ## and override current time with time in changelog for indentical pdf docs + ## also see #https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778462 for the chmod + #(cd doc/manual && faketime -f "$(DEB_DATE_RFC_3339)" make docs && ls) + (cd doc/manual && make docs) + +override_dh_auto_install: + dh_auto_install + # + # edd 08 May 2011 + # empty dependency_lib in .la files (cf #621213) + find debian/$(package) -name \*.la | \ + xargs perl -p -i -e "s/dependency_libs='.*'/dependency_libs=''/" + +%: + dh $@ + --- jags-4.2.0.orig/debian/jags.docs +++ jags-4.2.0/debian/jags.docs @@ -0,0 +1,3 @@ +doc/manual/jags_installation_manual.pdf +doc/manual/jags_user_manual.pdf +doc/manual/jags_developer_manual.pdf --- jags-4.2.0.orig/debian/jags.postinst +++ jags-4.2.0/debian/jags.postinst @@ -0,0 +1,6 @@ + +#DEBHELPER# + +if [ "$1" = "configure" ]; then + ldconfig +fi --- jags-4.2.0.orig/debian/changelog +++ jags-4.2.0/debian/changelog @@ -0,0 +1,155 @@ +jags (4.2.0-1precise0) precise; urgency=low + + * Compilation for Ubuntu 12.04.5 LTS + * debian/control, revert to a version of gfortran that is available + * debian/control, revert to a version of g++ that is available + + -- Michael Rutter Mon, 22 Feb 2016 12:32:24 +0000 + +jags (4.2.0-1) unstable; urgency=medium + + * New upstream release + + -- Dirk Eddelbuettel Sun, 21 Feb 2016 22:09:31 -0600 + +jags (4.1.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Sun, 17 Jan 2016 15:49:52 -0600 + +jags (4.0.0-1) unstable; urgency=low + + * New upstream release + + * debian/control: Add new Build-Depends: libcppunit-dev + + -- Dirk Eddelbuettel Wed, 07 Oct 2015 09:45:54 -0500 + +jags (3.4.0-3) unstable; urgency=low + + * debian/control: Build-Depends on 'g++ (>= 4:5.2)'; ditto for gfortran + (Closes: #791081) + + -- Dirk Eddelbuettel Sat, 08 Aug 2015 12:21:27 -0500 + +jags (3.4.0-2) unstable; urgency=low + + [ never released, changes later reverted ] + * debian/rules: Use faketime along with the changelog timestamp to + enforce reproducible builds + + * debian/control: Add faketime to Build-Depends + + -- Dirk Eddelbuettel Sun, 10 May 2015 13:28:49 -0500 + +jags (3.4.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Wed, 04 Sep 2013 09:13:25 -0500 + +jags (3.3.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Tue, 02 Oct 2012 06:06:54 -0500 + +jags (3.2.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Tue, 03 Jan 2012 09:48:37 -0600 + +jags (3.1.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Mon, 08 Aug 2011 19:55:32 -0500 + +jags (3.0.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Wed, 06 Jul 2011 15:31:43 -0500 + +jags (2.2.0-2) unstable; urgency=low + + * debian/rules: Add short find and perl snippet to process .la files + in order to empty dependency_libs (Closes: #621593) + + -- Dirk Eddelbuettel Sun, 08 May 2011 17:16:41 -0500 + +jags (2.2.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Wed, 10 Nov 2010 10:51:17 -0600 + +jags (2.1.0-2) unstable; urgency=low + + * configure: Once again patched for sh4. + + * debian/rules: Also run make docs inside doc/manual/ + * debian/control: Added Build-Depends: for manual creation + * debian/jags.doc: Install the three pdf manuals + + -- Dirk Eddelbuettel Tue, 18 May 2010 14:46:08 -0500 + +jags (2.1.0-1) unstable; urgency=low + + * New upstream release + + -- Dirk Eddelbuettel Wed, 12 May 2010 11:11:24 -0500 + +jags (2.0.0-1) unstable; urgency=low + + * New upstream release + + * debian/control: Updated Standards-Version: to current version + + -- Dirk Eddelbuettel Mon, 26 Apr 2010 11:05:20 -0500 + +jags (1.0.4-4) unstable; urgency=low + + * configure: Applied patch by Nobuhiro Iwamatsu to support the + SH architecture (Closes: #561050) + + -- Dirk Eddelbuettel Sun, 13 Dec 2009 19:26:57 -0600 + +jags (1.0.4-3) unstable; urgency=low + + * debian/control: Tighten Build-Depends to libltdl-dev (>= 2.2.6b) + + -- Dirk Eddelbuettel Sat, 12 Dec 2009 16:34:46 -0600 + +jags (1.0.4-2) unstable; urgency=low + + * debian/control: Add Build-Depends: on libltdl3-dev + * debian/rules: call configure with '--without-included-ltdl' to enforce + use of the system ltdl (Closes: #560864) + + -- Dirk Eddelbuettel Sat, 12 Dec 2009 16:18:24 -0600 + +jags (1.0.4-1) unstable; urgency=low + + * New upstream release containing new libltdl/ from libtool 2.2.6b + in regards to CVE-2009-3736[0] (Closes: #559816) + + -- Dirk Eddelbuettel Thu, 10 Dec 2009 22:41:47 -0600 + +jags (1.0.3-2) unstable; urgency=low + + * configure: Applied one-line patch to allow builds on sh architecture. + Thanks to Nobuhiro Iwamatsu for the patch. (Closes: #554347) + + * debian/watch: Addded watch file + + -- Dirk Eddelbuettel Tue, 03 Nov 2009 22:10:31 -0600 + +jags (1.0.3-1) unstable; urgency=low + + * Initial build + + -- Dirk Eddelbuettel Mon, 01 Sep 2008 20:04:18 -0500 + --- jags-4.2.0.orig/debian/source/format +++ jags-4.2.0/debian/source/format @@ -0,0 +1 @@ +1.0 --- jags-4.2.0.orig/debian/unused/jags.1 +++ jags-4.2.0/debian/unused/jags.1 @@ -0,0 +1,26 @@ +.\" Man page contributed by Dirk Eddelbuettel and GPL'ed +.TH JAGS 1 "15 September 2008" "IARC" +.SH NAME +jags - just another gibbs sampler +.SH SYNOPSIS +.BR jags\ [--debugger]\ scriptfile +.SH DESCRIPTION +.PP +\fIjags\fP is a program for analysis of Bayesian hierarchical models using +Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. It expects +the model to be described in +.IR scriptfile . +.SH OPTIONS +\fIjags\fP accepts the following options: +.TP 8 +.I \-\-debugger +to run under the default debugger +.RE +.SH SEE ALSO +.IR http://www-fis.iarc.fr/~martyn/software/jags/ +.SH AUTHORS +Martyn Plummer + +This manual page was contributed by Dirk Eddelbuettel + for the Debian GNU/Linux distribution but +may be used by others. --- jags-4.2.0.orig/debian/unused/jags.manpages +++ jags-4.2.0/debian/unused/jags.manpages @@ -0,0 +1 @@ +debian/jags.1 --- jags-4.2.0.orig/debian/unused/control +++ jags-4.2.0/debian/unused/control @@ -0,0 +1,61 @@ +Source: jags +Section: math +Priority: optional +Maintainer: Dirk Eddelbuettel +Build-Depends: debhelper (>= 7.0.50~), gfortran (>= 4:5.2), liblapack-dev, libltdl-dev (>= 2.2.6b), texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, texinfo, autotools-dev, faketime, g++ (>= 4:5.2) +Standards-Version: 3.9.6 +Homepage: http://www-fis.iarc.fr/~martyn/software/jags/ + +Package: jags +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Just Another Gibbs Sampler for Bayesian MCMC - binary + JAGS is Just Another Gibbs Sampler. It is a program for analysis of + Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) + simulation not wholly unlike BUGS. + . + JAGS was written with three aims in mind: + * To have an engine for the BUGS language that runs on Unix + * To be extensible, allowing users to write their own functions, + distributions and samplers. + * To be a plaftorm for experimentation with ideas in Bayesian modelling + . + This package contains the 'jags' binary as well as the associated + shared library modules loaded by the binary. + +Package: libjags +Section: libs +Architecture: any +Multi-Arch: same +Pre-Depends: ${misc:Pre-Depends} +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Just Another Gibbs Sampler for Bayesian MCMC - library + JAGS is Just Another Gibbs Sampler. It is a program for analysis of + Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) + simulation not wholly unlike BUGS. + . + JAGS was written with three aims in mind: + * To have an engine for the BUGS language that runs on Unix + * To be extensible, allowing users to write their own functions, + distributions and samplers. + * To be a plaftorm for experimentation with ideas in Bayesian modelling + . + This package contains the run-time libraries. + +Package: libjags-dev +Section: libdevel +Multi-Arch: same +Architecture: any +Depends: libjags (= ${binary:Version}), ${misc:Depends} +Description: Just Another Gibbs Sampler for Bayesian MCMC - development + JAGS is Just Another Gibbs Sampler. It is a program for analysis of + Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) + simulation not wholly unlike BUGS. + . + JAGS was written with three aims in mind: + * To have an engine for the BUGS language that runs on Unix + * To be extensible, allowing users to write their own functions, + distributions and samplers. + * To be a plaftorm for experimentation with ideas in Bayesian modelling + . + This package contains the development header and libray links. --- jags-4.2.0.orig/debian/unused/libjags-dev.install +++ jags-4.2.0/debian/unused/libjags-dev.install @@ -0,0 +1,4 @@ +usr/include/ +usr/lib/*.so +usr/lib/*.la +usr/lib/pkgconfig/ --- jags-4.2.0.orig/debian/unused/libjags.install +++ jags-4.2.0/debian/unused/libjags.install @@ -0,0 +1,2 @@ +usr/lib/libjags.so.* +usr/lib/libjrmath.so.*