Author: tille Date: 2012-05-22 12:27:58 +0000 (Tue, 22 May 2012) New Revision: 10942
Added: trunk/packages/paml/trunk/debian/patches/hardening.patch Modified: trunk/packages/paml/trunk/debian/README.Debian trunk/packages/paml/trunk/debian/changelog trunk/packages/paml/trunk/debian/compat trunk/packages/paml/trunk/debian/control trunk/packages/paml/trunk/debian/paml.docs trunk/packages/paml/trunk/debian/patches/makefile.patch trunk/packages/paml/trunk/debian/patches/series Log: Enable hardening using debhelper 9 + Makefile patch; upload to unstable Modified: trunk/packages/paml/trunk/debian/README.Debian =================================================================== --- trunk/packages/paml/trunk/debian/README.Debian 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/README.Debian 2012-05-22 12:27:58 UTC (rev 10942) @@ -9,4 +9,22 @@ description of the documentation has not yet been addressed. Help from the community would be much appreciated on those issues. - -- Pjotr Prins <[email protected]> Wed, 08 Sep 2010 09:44:46 +0200 + +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 Modified: trunk/packages/paml/trunk/debian/changelog =================================================================== --- trunk/packages/paml/trunk/debian/changelog 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/changelog 2012-05-22 12:27:58 UTC (rev 10942) @@ -1,4 +1,4 @@ -paml (4.5-1) UNRELEASED; urgency=low +paml (4.5-1) unstable; urgency=low [ Pjotr Prins ] * Improved long description. @@ -20,7 +20,11 @@ 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 Modified: trunk/packages/paml/trunk/debian/compat =================================================================== --- trunk/packages/paml/trunk/debian/compat 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/compat 2012-05-22 12:27:58 UTC (rev 10942) @@ -1 +1 @@ -8 +9 Modified: trunk/packages/paml/trunk/debian/control =================================================================== --- trunk/packages/paml/trunk/debian/control 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/control 2012-05-22 12:27:58 UTC (rev 10942) @@ -6,7 +6,7 @@ Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> DM-Upload-Allowed: yes -Build-Depends: debhelper (>= 8) +Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/paml/trunk Modified: trunk/packages/paml/trunk/debian/paml.docs =================================================================== --- trunk/packages/paml/trunk/debian/paml.docs 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/paml.docs 2012-05-22 12:27:58 UTC (rev 10942) @@ -1,2 +1,3 @@ GeneticCode.txt README.txt +debian/profile.d Added: trunk/packages/paml/trunk/debian/patches/hardening.patch =================================================================== --- trunk/packages/paml/trunk/debian/patches/hardening.patch (rev 0) +++ trunk/packages/paml/trunk/debian/patches/hardening.patch 2012-05-22 12:27:58 UTC (rev 10942) @@ -0,0 +1,45 @@ +Description: Enable propagation of hardening flags +Author: Andreas Tille <[email protected]> +Date: Tue, 15 May 2012 11:10:59 +0200 + +--- paml4.5.orig/src/Makefile ++++ paml4.5/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 +@@ -20,21 +20,21 @@ + all : $(PRGS) + + baseml : baseml.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.c tools.c $(LIBS) + basemlg : basemlg.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.c tools.c $(LIBS) + codeml : codeml.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.c tools.c $(LIBS) + evolver : evolver.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.c tools.c $(LIBS) + pamp : pamp.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.c tools.c $(LIBS) + mcmctree : mcmctree.c tools.c treesub.c treespace.c paml.h +- $(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.c $(LIBS) + yn00: yn00.c tools.c paml.h +- $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.c tools.c $(LIBS) + chi2 : chi2.c +- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS) + + PREFIX=/usr + DESTDIR=/ Modified: trunk/packages/paml/trunk/debian/patches/makefile.patch =================================================================== --- trunk/packages/paml/trunk/debian/patches/makefile.patch 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/patches/makefile.patch 2012-05-22 12:27:58 UTC (rev 10942) @@ -1,7 +1,9 @@ -Index: paml-4.4c/Makefile -=================================================================== ---- /dev/null 1970-01-01 00:00:00.000000000 +0000 -+++ paml-4.4c/Makefile 2010-09-11 17:33:04.957524695 +0200 +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 ++++ paml4.5/Makefile @@ -0,0 +1,9 @@ + +all install build: @@ -12,10 +14,8 @@ + echo "Cleaning binaries" + rm -f $(find src -name "*.c" | sed -e 's/.c$//') + -Index: paml-4.4c/src/Makefile -=================================================================== ---- paml-4.4c.orig/src/Makefile 2010-09-08 09:29:29.810248323 +0200 -+++ paml-4.4c/src/Makefile 2010-09-11 18:01:01.116529194 +0200 +--- paml4.5.orig/src/Makefile ++++ paml4.5/src/Makefile @@ -35,3 +35,11 @@ $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS) chi2 : chi2.c Modified: trunk/packages/paml/trunk/debian/patches/series =================================================================== --- trunk/packages/paml/trunk/debian/patches/series 2012-05-22 11:37:31 UTC (rev 10941) +++ trunk/packages/paml/trunk/debian/patches/series 2012-05-22 12:27:58 UTC (rev 10942) @@ -1 +1,2 @@ makefile.patch +hardening.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
