[med-svn] [paml] 01/01: Re-add debian/ dir
Andreas Tille
tille at debian.org
Mon May 2 13:54:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/4.8+dfsg-1
in repository paml.
commit e1c25a4c0c91dab1ed23da373d80acf982909f51
Author: Andreas Tille <tille at debian.org>
Date: Mon May 2 15:35:51 2016 +0200
Re-add debian/ dir
---
debian/README.Debian | 20 ++++++++
debian/README.source | 9 ++++
debian/changelog | 87 ++++++++++++++++++++++++++++++++
debian/compat | 1 +
debian/control | 29 +++++++++++
debian/copyright | 22 ++++++++
debian/paml-doc.docs | 1 +
debian/paml-doc.examples | 1 +
debian/paml.docs | 3 ++
debian/paml.install | 8 +++
debian/paml.links | 8 +++
debian/patches/fix_format_security.patch | 26 ++++++++++
debian/patches/hardening.patch | 15 ++++++
debian/patches/makefile.patch | 30 +++++++++++
debian/patches/series | 3 ++
debian/profile.d/paml | 3 ++
debian/rules | 16 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++
debian/watch | 3 ++
20 files changed, 298 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..27c2aab
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,20 @@
+paml for Debian
+---------------
+
+*** Renamed executable: evolver ***
+
+A different package in Debian (namely evolver) ships a binary with the
+very same name and to avoid name space pollution the binary from the
+paml package needed to be renamed to /usr/bin/paml-evolver (if you
+disagree with this choice of name please help us to make Debian better
+and make a more appropriate suggestion.)
+
+If you are using this exectuable in scripts and you need to relay on the
+original name there is another option: Copy the directory
+/usr/share/doc/paml/profile.d to /etc/profile.d and by doing so enable
+setting the PATH variable to prefer the PATH /usr/lib/debian-med/bin
+over /usr/bin. There the original name is conserved. Please note that
+this might hide the binary contained in the evolver package from all
+users of your computer.
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 May 2012 11:10:59 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..88baf42
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,9 @@
+paml for Debian
+---------------
+
+The source code ships with PDFs that have their sources
+not shipped with the sources code. Given that the package
+is non-free anyway, those have been left in.
+
+The Windows binaries have been removed from the source tree by
+using Files-Excluded.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..38769b0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,87 @@
+paml (4.8+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * d/rules: Adapt get-orig-source to new uscan syntax
+ * d/watch: uversionmangle to get correct download file name
+ * d/README.*: Updated
+ * d/control:
+ - Priority: optional
+ - cme fix dpkg-control
+ - XS-Autobuild: yes
+ * d/patches/fix_format_security.patch: Fix some format security issues
+
+ -- Andreas Tille <tille at debian.org> Wed, 30 Jul 2014 14:30:38 +0200
+
+paml (4.7-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/control:
+ - cme fix dpkg-control
+ - use anonscm in Vcs fields
+ * debian/rules: provide get-orig-source target to make use of new uscan
+ to remove windows binaries
+
+ -- Andreas Tille <tille at debian.org> Thu, 08 Aug 2013 22:07:27 +0200
+
+paml (4.5-1) unstable; urgency=low
+
+ [ Pjotr Prins ]
+ * Improved long description.
+
+ [ Andreas Tille ]
+ * New upstream version
+ * Fixed watch file
+ * debian/control: Standards-Version: 3.9.3 (no changes needed)
+ * debian/rules: remove useless dh-make template
+ * debian/paml.dirs: removed because unneeded
+ * debian/{install,links}: install all binaries to
+ /usr/lib/debian-med/bin and symlink to /usr/bin with the
+ exception of evolver which has a name space conflict. This
+ is renamed to /usr/bin/paml-evolver
+ Closes: #661519
+ * debian/{paml.docs,paml-doc.docs}:
+ - Adapted to new names
+ - do not duplicate the same files into both packages (paml and
+ paml-doc)
+ * debian/profile.d/paml: Set PATH to find paml executables under
+ their expected names
+ * debian/README.Debian: Document the name space conflict solution
+ * debian/upstream: Citation information
+ * debhelper 9 (control+compat)
+ * debian/patches/hardening.patch: Enable propagation of hardening
+ flags
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 May 2012 11:10:59 +0200
+
+paml (4.4e-1) unstable; urgency=low
+
+ * Team upload.
+ * New upstream release.
+ * Upload to unstable (Closes: #643843).
+ * Corrected debian/watch for downloading sources with uscan.
+ * Removed links to inexsistant Git repositories in debian/README.source.
+ * Corrected VCS URLs (debian/control).
+ * Conforms to Policy 3.9.2 (debian/control, no other changes needed).
+ * Use Debhelper 8 (debian/control, debian/compat).
+ * Converted debian/copyright to machine readable format version 1.0.
+ * Compress binary packages with xz.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 30 Sep 2011 21:48:20 +0900
+
+paml (4.4c-3) experimental; urgency=low
+
+ * doc -> non-free/doc (Closes: #608530).
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 01 Jan 2011 13:56:50 +0100
+
+paml (4.4c-2) experimental; urgency=low
+
+ * Adjusting for non-free section.
+
+ -- Pjotr Prins <pjotr.debian at thebird.nl> Sat, 11 Sep 2010 23:01:37 +0200
+
+paml (4.4c-1) experimental; urgency=low
+
+ * Initial release (Closes: #595958).
+
+ -- Pjotr Prins <pjotr.debian at thebird.nl> Tue, 07 Sep 2010 21:09:02 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..6df46f7
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: paml
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>,
+ Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: non-free/science
+XS-Autobuild: yes
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/paml/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/paml/trunk/
+Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
+
+Package: paml
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Phylogenetic Analysis by Maximum Likelihood (PAML)
+ PAML is a package of programs for phylogenetic analyses of DNA or
+ protein sequences using maximum likelihood.
+
+Package: paml-doc
+Architecture: all
+Section: non-free/doc
+Depends: ${misc:Depends}
+Description: Documentation for PAML
+ The source code comes with a series of PDF files to help with
+ further insights for the working of, and with, PAML.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..614c0e4
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,22 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Ziheng Yang <z.yang at ucl.ac.uk>
+Source: http://abacus.gene.ucl.ac.uk/software/paml.html
+Files-Excluded:
+ bin/*.exe
+ Technical/Simulation/*.exe
+ Technical/Simulation/Codon/*.exe
+
+Files: *
+Copyright: © 1992-2013 Ziheng Yang
+License: PAML-From-the-home-page-2010-09-08
+ PAML is a package of programs for phylogenetic analyses of DNA or
+ protein sequences using maximum likelihood. It is maintained and
+ distributed for academic use free of charge by Ziheng Yang.
+Comment: The author and copyright holder has agreed to the redistribution
+ of PAML by Debian.
+
+Files: debian/*
+Copyright: © 2010 Pjotr Prins <pjotr.debian at thebird.nl>
+License: GPL-3
+ see "/usr/share/common-licenses/GPL-3".
+
diff --git a/debian/paml-doc.docs b/debian/paml-doc.docs
new file mode 100644
index 0000000..30d29de
--- /dev/null
+++ b/debian/paml-doc.docs
@@ -0,0 +1 @@
+doc/*
diff --git a/debian/paml-doc.examples b/debian/paml-doc.examples
new file mode 100644
index 0000000..e39721e
--- /dev/null
+++ b/debian/paml-doc.examples
@@ -0,0 +1 @@
+examples/*
diff --git a/debian/paml.docs b/debian/paml.docs
new file mode 100644
index 0000000..43038c1
--- /dev/null
+++ b/debian/paml.docs
@@ -0,0 +1,3 @@
+GeneticCode.txt
+README.txt
+debian/profile.d
diff --git a/debian/paml.install b/debian/paml.install
new file mode 100644
index 0000000..abfc9b6
--- /dev/null
+++ b/debian/paml.install
@@ -0,0 +1,8 @@
+usr/bin/baseml usr/lib/debian-med/bin
+usr/bin/basemlg usr/lib/debian-med/bin
+usr/bin/chi2 usr/lib/debian-med/bin
+usr/bin/codeml usr/lib/debian-med/bin
+usr/bin/evolver usr/lib/debian-med/bin
+usr/bin/pamp usr/lib/debian-med/bin
+usr/bin/yn00 usr/lib/debian-med/bin
+
diff --git a/debian/paml.links b/debian/paml.links
new file mode 100644
index 0000000..d1b4f7d
--- /dev/null
+++ b/debian/paml.links
@@ -0,0 +1,8 @@
+usr/lib/debian-med/bin/baseml usr/bin/baseml
+usr/lib/debian-med/bin/basemlg usr/bin/basemlg
+usr/lib/debian-med/bin/chi2 usr/bin/chi2
+usr/lib/debian-med/bin/codeml usr/bin/codeml
+usr/lib/debian-med/bin/evolver usr/bin/paml-evolver
+usr/lib/debian-med/bin/pamp usr/bin/pamp
+usr/lib/debian-med/bin/yn00 usr/bin/yn00
+
diff --git a/debian/patches/fix_format_security.patch b/debian/patches/fix_format_security.patch
new file mode 100644
index 0000000..c4e7c7a
--- /dev/null
+++ b/debian/patches/fix_format_security.patch
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 30 Jul 2014 14:30:38 +0200
+Description: Fix some format security issues
+
+--- a/src/mcmctree.c
++++ b/src/mcmctree.c
+@@ -324,7 +324,7 @@ int GetMem (void)
+ error2("oom conP");
+
+ com.conPin[1] = com.conPin[0] + com.sconP/sizeof(double);
+- printf("\n%u bytes for conP\n", 2*com.sconP);
++ printf("\n%u bytes for conP\n", 2*(unsigned)com.sconP);
+
+ /* set gnodes[locus][].conP for tips and internal nodes */
+ com.curconP = 0;
+--- a/src/treesub.c
++++ b/src/treesub.c
+@@ -158,7 +158,7 @@ int ReadMorphology (FILE *fout, FILE *fi
+ }
+
+ for(i=0; i<com.ns; i++) {
+- fprintf(fout, com.spname[i]);
++ fprintf(fout, "%s", com.spname[i]);
+ for(j=0; j<com.ls; j++)
+ fprintf(fout, " %8.5f", data.zmorph[locus][i][j]);
+ FPN(fout);
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..6b5a1ba
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,15 @@
+Description: Enable propagation of hardening flags
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 15 May 2012 11:10:59 +0200
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,7 +1,7 @@
+ PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2
+ CC = cc # cc, gcc, cl
+
+-CFLAGS = -O4 -funroll-loops -fomit-frame-pointer -finline-functions
++CFLAGS += -O4 -funroll-loops -fomit-frame-pointer -finline-functions
+
+ #MAC OSX G5:
+ #CFLAGS = -mcpu=G5 -O4 -funroll-loops -fomit-frame-pointer -finline-functions
diff --git a/debian/patches/makefile.patch b/debian/patches/makefile.patch
new file mode 100644
index 0000000..63c98dc
--- /dev/null
+++ b/debian/patches/makefile.patch
@@ -0,0 +1,30 @@
+Description: Simplify building by creating main Makefile and install target for src/Makefile
+Author: Pjotr Prins <pjotr.debian at thebird.nl>
+Date: Tue, 07 Sep 2010 21:09:02 +0200
+
+--- /dev/null
++++ b/Makefile
+@@ -0,0 +1,9 @@
++
++all install build:
++ echo "Executing make $@ in src directory, instead."
++ make -C src $@
++
++clean:
++ echo "Cleaning binaries"
++ rm -f $(find src -name "*.c" | sed -e 's/.c$//')
++
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -36,3 +36,11 @@ yn00: yn00.c tools.c paml.h
+ $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+ chi2 : chi2.c
+ $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++
++PREFIX=/usr
++DESTDIR=/
++
++install:
++ if [ ! -d "$(DESTDIR)/$(PREFIX)/bin" ]; then mkdir -p "$(DESTDIR)/$(PREFIX)/bin"; fi
++ cp $(PRGS) $(DESTDIR)/$(PREFIX)/bin/
++
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..151a986
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+fix_format_security.patch
+makefile.patch
+hardening.patch
diff --git a/debian/profile.d/paml b/debian/profile.d/paml
new file mode 100644
index 0000000..f4357da
--- /dev/null
+++ b/debian/profile.d/paml
@@ -0,0 +1,3 @@
+# set PATH to enable finding paml executables with original name
+# install this file to /etc/profile.d
+export PATH="/usr/lib/debian-med/bin:$PATH"
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7ef6030
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+override_dh_installexamples:
+ dh_installexamples
+ for d in `find debian -name examples -a -type d`; do \
+ find $$d \! -type d | xargs -r chmod -x ; \
+ done
+
+%:
+ dh $@
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..0d68370
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Ziheng Yang
+ Title: "PAML 4: phylogenetic analysis by maximum likelihood"
+ Journal: Molecular Biology and Evolution
+ Year: 2007
+ Volume: 24
+ Number: 8
+ Pages: 1586-91
+ DOI: 10.1093/molbev/msm088
+ PMID: 17483113
+ URL: http://mbe.oxfordjournals.org/content/24/8/1586
+ eprint: http://mbe.oxfordjournals.org/content/24/8/1586.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..afa8a1e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=uversionmangle=s/$/+dfsg/ \
+ http://abacus.gene.ucl.ac.uk/software/paml.html paml([0-9a-z.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip)
--
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