[med-svn] r14390 - in trunk/packages/phylip/trunk/debian: . patches source

Andreas Tille tille at alioth.debian.org
Thu Aug 8 16:16:08 UTC 2013 

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 <tille at debian.org>  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 <tille at debian.org>  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 <manuel at debian.org>
 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 <tille at debian.org>
-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 <tille at debian.org>
+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 <tille at debian.org>
+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 <tille at debian.org>, 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

More information about the debian-med-commit mailing list