Author: tille Date: 2013-07-30 12:03:17 +0000 (Tue, 30 Jul 2013) New Revision: 14268
Added: trunk/packages/mafft/trunk/debian/patches/ trunk/packages/mafft/trunk/debian/patches/hardening.patch trunk/packages/mafft/trunk/debian/patches/series Modified: trunk/packages/mafft/trunk/debian/changelog trunk/packages/mafft/trunk/debian/control Log: hardening patch; anonscm Modified: trunk/packages/mafft/trunk/debian/changelog =================================================================== --- trunk/packages/mafft/trunk/debian/changelog 2013-07-30 11:39:40 UTC (rev 14267) +++ trunk/packages/mafft/trunk/debian/changelog 2013-07-30 12:03:17 UTC (rev 14268) @@ -6,6 +6,9 @@ [ Andreas Tille ] * New upstream version * debian/README.source: removed because redundant + * debian/patches/hardening.patch: Enable propagation of hardening + options + * debian/control: use anonscm in Vcs fields -- Andreas Tille <[email protected]> Tue, 30 Jul 2013 13:39:43 +0200 Modified: trunk/packages/mafft/trunk/debian/control =================================================================== --- trunk/packages/mafft/trunk/debian/control 2013-07-30 11:39:40 UTC (rev 14267) +++ trunk/packages/mafft/trunk/debian/control 2013-07-30 12:03:17 UTC (rev 14268) @@ -6,8 +6,8 @@ Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mafft/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mafft/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mafft/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mafft/trunk/ Homepage: http://mafft.cbrc.jp/alignment/software/ XS-Testsuite: autopkgtest Added: trunk/packages/mafft/trunk/debian/patches/hardening.patch =================================================================== --- trunk/packages/mafft/trunk/debian/patches/hardening.patch (rev 0) +++ trunk/packages/mafft/trunk/debian/patches/hardening.patch 2013-07-30 12:03:17 UTC (rev 14268) @@ -0,0 +1,207 @@ +Author: Andreas Tille <[email protected]> +LastChanged: Tue, 30 Jul 2013 13:49:02 +0200 +Description: Propagate hardening options + +--- a/core/Makefile ++++ b/core/Makefile +@@ -145,151 +145,151 @@ mltaln.h : functions.h + touch mltaln.h + + version : version.c mltaln.h +- $(CC) -o $@ version.c $(MYCFLAGS) ++ $(CC) -o $@ version.c $(MYCFLAGS) $(LDFLAGS) + + tbfast : $(OBJTBFAST) +- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + addsingle : $(OBJADDSINGLE) +- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + makedirectionlist : $(OBJMAKEDIRECTIONLIST) +- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + setdirection : $(OBJSETDIRECTION) +- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + replaceu : $(OBJREPLACEU) +- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + restoreu : $(OBJRESTOREU) +- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) ++ $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LDFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(MYCFLAGS) -c gapfill.c Added: trunk/packages/mafft/trunk/debian/patches/series =================================================================== --- trunk/packages/mafft/trunk/debian/patches/series (rev 0) +++ trunk/packages/mafft/trunk/debian/patches/series 2013-07-30 12:03:17 UTC (rev 14268) @@ -0,0 +1 @@ +hardening.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
