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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Fri, 30 Sep 2011 21:48:20 +0900 + +paml (4.4c-3) experimental; urgency=low + + * doc -> non-free/doc (Closes: #608530). + + -- Steffen Moeller <[email protected]> Sat, 01 Jan 2011 13:56:50 +0100 + +paml (4.4c-2) experimental; urgency=low + + * Adjusting for non-free section. + + -- Pjotr Prins <[email protected]> Sat, 11 Sep 2010 23:01:37 +0200 + +paml (4.4c-1) experimental; urgency=low + + * Initial release (Closes: #595958). + + -- Pjotr Prins <[email protected]> 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 <[email protected]> +Uploaders: Pjotr Prins <[email protected]>, + Steffen Moeller <[email protected]>, + Andreas Tille <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/paml.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
