Author: tille Date: 2013-08-08 16:16:08 +0000 (Thu, 08 Aug 2013) New Revision: 14390
Added: trunk/packages/phylip/trunk/debian/README.source trunk/packages/phylip/trunk/debian/patches/hardening.patch trunk/packages/phylip/trunk/debian/patches/install_fonts_data.patch trunk/packages/phylip/trunk/debian/phylip.lintian-overrides trunk/packages/phylip/trunk/debian/source/lintian-overrides Removed: trunk/packages/phylip/trunk/debian/patches/01_src_Makefile.patch Modified: trunk/packages/phylip/trunk/debian/changelog trunk/packages/phylip/trunk/debian/control trunk/packages/phylip/trunk/debian/patches/01_src_phylip_h trunk/packages/phylip/trunk/debian/patches/series trunk/packages/phylip/trunk/debian/phylip.examples trunk/packages/phylip/trunk/debian/phylip.install trunk/packages/phylip/trunk/debian/rules Log: Using stable network connection to commit some mass changes basically to adapt to the new build system and lintian overrides Added: trunk/packages/phylip/trunk/debian/README.source =================================================================== --- trunk/packages/phylip/trunk/debian/README.source (rev 0) +++ trunk/packages/phylip/trunk/debian/README.source 2013-08-08 16:16:08 UTC (rev 14390) @@ -0,0 +1,4 @@ +This packages uses the quilt patch system. Please read +/usr/share/doc/quilt/README.source for more information. + + -- Andreas Tille <[email protected]> Mon, 31 Aug 2009 14:50:19 +0200 Modified: trunk/packages/phylip/trunk/debian/changelog =================================================================== --- trunk/packages/phylip/trunk/debian/changelog 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/changelog 2013-08-08 16:16:08 UTC (rev 14390) @@ -6,6 +6,9 @@ - cme fix dpkg-control - debhelper 9 - debian/source/format: 3.0 (quilt) + * Upstream changed build system - this chance was used to switch from + cdbs to dh (patches were changed) + * Lintian overrides -- Andreas Tille <[email protected]> Wed, 07 Aug 2013 22:17:03 +0200 Modified: trunk/packages/phylip/trunk/debian/control =================================================================== --- trunk/packages/phylip/trunk/debian/control 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/control 2013-08-08 16:16:08 UTC (rev 14390) @@ -4,10 +4,7 @@ Manuel Prinz <[email protected]> Section: non-free/science Priority: optional -Build-Depends: cdbs, - patchutils, - debhelper (>= 9), - quilt, +Build-Depends: debhelper (>= 9), libx11-dev, libxt-dev, libxaw7-dev @@ -19,7 +16,6 @@ Package: phylip Architecture: any -Section: non-free/science Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: phylip-doc @@ -37,7 +33,7 @@ Section: non-free/doc Depends: ${misc:Depends} Suggests: phylip -Description: package of programs for inferring phylogenies +Description: package of programs for inferring phylogenies (documentation) The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. Methods that are available in the package include parsimony, distance Deleted: trunk/packages/phylip/trunk/debian/patches/01_src_Makefile.patch =================================================================== --- trunk/packages/phylip/trunk/debian/patches/01_src_Makefile.patch 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/patches/01_src_Makefile.patch 2013-08-08 16:16:08 UTC (rev 14390) @@ -1,42 +0,0 @@ -Author: Andreas Tille <[email protected]> -Forwarded: No -Description: Debian keeps the font files in a different location than normal installer; - distclean target needed by cdbs was missing -License: see debian/copyright ---- phylip-3.67.orig/src/Makefile -+++ phylip-3.67/src/Makefile -@@ -45,6 +45,7 @@ - # - # the following specifies the directory where the executables will be placed - EXEDIR = ../exe -+DATADIR = ../exe - # - # ---------------------------------------------------------------------------- - # -@@ -189,8 +190,10 @@ - @echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)" - @mkdir -p $(EXEDIR) - @cp $(PROGS) $(EXEDIR) -- @echo "Installing font files in $(EXEDIR)" -- @cp font* $(EXEDIR) -+ @echo "Installing font files in $(DATADIR)" -+ @mkdir -p $(DATADIR) -+ @cp font* $(DATADIR) -+ @cd $(DATADIR) && ln -s font1 fontfile - @echo "Finished installation." - @echo "" - -@@ -207,6 +210,13 @@ - @echo "Finished cleanup." - @echo "" - -+distclean: -+ @make clean -+ @echo "Removing executables" -+ @rm -rf $(EXEDIR) $(DATADIR) -+ @echo "Finaly removed all executable files." -+ @echo "" -+ - # - # compile object files shared between programs - # (make's implicit rule for %.o will take care of these) Modified: trunk/packages/phylip/trunk/debian/patches/01_src_phylip_h =================================================================== --- trunk/packages/phylip/trunk/debian/patches/01_src_phylip_h 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/patches/01_src_phylip_h 2013-08-08 16:16:08 UTC (rev 14390) @@ -2,9 +2,9 @@ Forwarded: No Description: Debian keeps the font files in a different location than normal installer License: see debian/copyright ---- phylip-3.67.orig/src/phylip.h -+++ phylip-3.67/src/phylip.h -@@ -72,7 +72,7 @@ +--- a/src/phylip.h ++++ b/src/phylip.h +@@ -72,7 +72,7 @@ void phyFillScreenColor(void); #define EBCDIC false #define INFILE "infile" #define OUTFILE "outfile" Added: trunk/packages/phylip/trunk/debian/patches/hardening.patch =================================================================== --- trunk/packages/phylip/trunk/debian/patches/hardening.patch (rev 0) +++ trunk/packages/phylip/trunk/debian/patches/hardening.patch 2013-08-08 16:16:08 UTC (rev 14390) @@ -0,0 +1,15 @@ +Author: Andreas Tille <[email protected]> +LastChanged: Wed, 07 Aug 2013 22:17:03 +0200 +Description: Let hardening flags sneek in + +--- a/src/Makefile.unx ++++ b/src/Makefile.unx +@@ -126,7 +126,7 @@ DFLAGS = $(CFLAGS) + # + # Most of the programs need only the math libraries, specified like this; + # +-LIBS = -lm ++LIBS = -lm $(LDFLAGS) + # + # The drawing programs may also need access to the graphics libraries. This is + # specified with the DLIBS variable. Added: trunk/packages/phylip/trunk/debian/patches/install_fonts_data.patch =================================================================== --- trunk/packages/phylip/trunk/debian/patches/install_fonts_data.patch (rev 0) +++ trunk/packages/phylip/trunk/debian/patches/install_fonts_data.patch 2013-08-08 16:16:08 UTC (rev 14390) @@ -0,0 +1,41 @@ +Author: Andreas Tille <[email protected]> +Forwarded: No +Description: Debian keeps the font files in a different location than normal installer; + distclean target makes sure everything will be cleaned up + +--- a/src/Makefile.unx ++++ b/src/Makefile.unx +@@ -51,6 +51,7 @@ VERSION=3.695 + # + # the following specifies the directory where the executables will be placed + EXEDIR = ../exe ++DATADIR = ../exe + # + # ---------------------------------------------------------------------------- + # +@@ -235,8 +236,10 @@ put: + @cp $(DYLIBS) $(EXEDIR) + @echo "Installing jar files in $(EXEDIR)" + @cp $(JARS) $(EXEDIR) +- @echo "Installing font files in $(EXEDIR)" +- @cp font* $(EXEDIR) ++ @echo "Installing font files in $(DATADIR)" ++ @mkdir -p $(DATADIR) ++ @cp font* $(DATADIR) ++ @cd $(DATADIR) && ln -s font1 fontfile + @echo "Copying testdata files to $(EXEDIR)/testdata/..." + mkdir $(EXEDIR)/testdata + for i in $(TESTDIR); do \ +@@ -259,6 +262,12 @@ clean: + @echo "Finished cleanup." + @echo "" + ++distclean: clean ++ @echo "Removing executables" ++ @rm -rf $(EXEDIR) $(DATADIR) ++ @echo "Finaly removed all executable files." ++ @echo "" ++ + # + # compile object files shared between programs + # (make's implicit rule for %.o will take care of these) Modified: trunk/packages/phylip/trunk/debian/patches/series =================================================================== --- trunk/packages/phylip/trunk/debian/patches/series 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/patches/series 2013-08-08 16:16:08 UTC (rev 14390) @@ -1,3 +1,3 @@ -01_src_Makefile.patch +install_fonts_data.patch +hardening.patch 01_src_phylip_h -02_fix_treedist Modified: trunk/packages/phylip/trunk/debian/phylip.examples =================================================================== --- trunk/packages/phylip/trunk/debian/phylip.examples 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/phylip.examples 2013-08-08 16:16:08 UTC (rev 14390) @@ -1 +1,2 @@ debian/examples/* +src/testdata \ No newline at end of file Modified: trunk/packages/phylip/trunk/debian/phylip.install =================================================================== --- trunk/packages/phylip/trunk/debian/phylip.install 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/phylip.install 2013-08-08 16:16:08 UTC (rev 14390) @@ -1,4 +1,4 @@ -exe/[a-eg-z]* usr/lib/phylip/bin -exe/f[a-mp-z]* usr/lib/phylip/bin -exe/font* usr/share/phylip -debian/bin/phylip usr/bin +exe/[a-su-z]* usr/lib/phylip/bin +exe/t[a-df-z]* usr/lib/phylip/bin +fonts/* usr/share/phylip +debian/bin/phylip usr/bin Added: trunk/packages/phylip/trunk/debian/phylip.lintian-overrides =================================================================== --- trunk/packages/phylip/trunk/debian/phylip.lintian-overrides (rev 0) +++ trunk/packages/phylip/trunk/debian/phylip.lintian-overrides 2013-08-08 16:16:08 UTC (rev 14390) @@ -0,0 +1,54 @@ +# Seems to be false positives - options are properly set +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/clique +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/consense +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/contml +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/contrast +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnacomp +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnadist +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnainvar +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnaml +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnamlk +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnamove +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnapars +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnapenny +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dollop +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dolmove +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dolpenny +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/drawgram +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/drawtree +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/factor +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/fitch +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/gendist +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/kitsch +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/libdrawgram.so +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/libdrawtree.so +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/mix +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/move +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/neighbor +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/pars +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/penny +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/proml +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/promlk +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/protdist +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/protpars +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/restdist +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/restml +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/retree +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/seqboot +phylip: hardening-no-fortify-functions usr/lib/phylip/bin/treedist +# No idea why upstream is providing duplicated files - they are small in any case +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dollop/dollopinfile.txt usr/share/doc/phylip/examples/testdata/mix/mixinfile.txt usr/share/doc/phylip/examples/testdata/pars/parsinfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/fitch/fitchinfile.txt usr/share/doc/phylip/examples/testdata/kitsch/kitschinfile.txt usr/share/doc/phylip/examples/testdata/neighbor/neighborinfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnacomp/dnacompinfile.txt usr/share/doc/phylip/examples/testdata/dnapars/dnaparsinfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/mammal.txt usr/share/doc/phylip/examples/testdata/drawtree/mammal.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/14tip.txt usr/share/doc/phylip/examples/testdata/drawtree/14tip.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlcats.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkcats.txt usr/share/doc/phylip/examples/testdata/proml/promlcats.txt usr/share/doc/phylip/examples/testdata/promlk/promlkcats.txt usr/share/doc/phylip/examples/testdata/protdist/protdistcats.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape2.txt usr/share/doc/phylip/examples/testdata/drawtree/ape2.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlweights.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkweights.txt usr/share/doc/phylip/examples/testdata/proml/promlweights.txt usr/share/doc/phylip/examples/testdata/promlk/promlkweights.txt usr/share/doc/phylip/examples/testdata/protdist/protdistweights.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/contml/contmlinfile.txt usr/share/doc/phylip/examples/testdata/gendist/gendistinfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlinfile.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkinfile.txt usr/share/doc/phylip/examples/testdata/proml/promlinfile.txt usr/share/doc/phylip/examples/testdata/promlk/promlkinfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistoutfile.txt usr/share/doc/phylip/examples/testdata/restml/restmloutfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/clique/cliqueinfile.txt usr/share/doc/phylip/examples/testdata/dolmove/dolmoveinfile.txt usr/share/doc/phylip/examples/testdata/move/moveinfile.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/cats.txt usr/share/doc/phylip/examples/testdata/drawtree/cats.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape1.txt usr/share/doc/phylip/examples/testdata/drawtree/ape1.txt +phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistinfile.txt usr/share/doc/phylip/examples/testdata/restml/restmlinfile.txt Modified: trunk/packages/phylip/trunk/debian/rules =================================================================== --- trunk/packages/phylip/trunk/debian/rules 2013-08-08 11:46:00 UTC (rev 14389) +++ trunk/packages/phylip/trunk/debian/rules 2013-08-08 16:16:08 UTC (rev 14390) @@ -1,15 +1,20 @@ #!/usr/bin/make -f -# debian/rules for phylip using cdbs +# debian/rules for phylip using dh # Andreas Tille <[email protected]>, GPL -include /usr/share/cdbs/1/rules/patchsys-quilt.mk -include /usr/share/cdbs/1/rules/debhelper.mk -include /usr/share/cdbs/1/class/makefile.mk +%: + dh $@ -DEB_MAKE_BUILD_TARGET := all -DEB_MAKE_INSTALL_TARGET := install +override_dh_auto_build: + dh_auto_build --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx all -DEB_BUILDDIR := src +override_dh_auto_install: + dh_auto_install --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx install DATADIR=../fonts -clean:: - rm -fr exe/* fonts/ +override_dh_installexamples: + dh_installexamples + find debian -type f -name "*.txt" -exec chmod a-x \{\} \; + +override_dh_auto_clean: + dh_auto_clean --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx clean + rm -fr exe/* fonts/ src/*.so Added: trunk/packages/phylip/trunk/debian/source/lintian-overrides =================================================================== --- trunk/packages/phylip/trunk/debian/source/lintian-overrides (rev 0) +++ trunk/packages/phylip/trunk/debian/source/lintian-overrides 2013-08-08 16:16:08 UTC (rev 14390) @@ -0,0 +1,3 @@ +# The package is non-free anyway - so why bothering touching the source +phylip: source-contains-prebuilt-windows-binary src/javajars/DrawGramJava.exe +phylip: source-contains-prebuilt-windows-binary src/javajars/DrawTreeJava.exe _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
