phylip update

Hanspeter Niederstrasser <[email protected]> Sun, 10 Dec 2017 19:11:39 -0600
Newsgroups gmane.os.apple.fink.devel
Organization Snaggled Works
Message-ID <[email protected]> 
Hi Cyril,

Currently, Fink's phylip release 3.69.5 is unbuildable because upstream 
has removed their source file, and their license did not allow 
mirroring. They've released a new version 3.69.7 that is now open 
source. Attached are the .info and .patch files to work with the new 
phylip release. The biggest difference to current 3.69.5 is that the 
testdata is no longer included in tarball, so it's no longer installed. 
Let me know if we should go ahead and commit this new phylip release. 
Thanks,

Hanspeter

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phylip.info (text/plain, 2 KB) 
Package: phylip
Version: 3.69.7
Revision: 1
Source: http://evolution.gs.washington.edu/%n/download/%n-3.697.tar.gz
Source-MD5: 0e83d17fb4d668213603c86bc21d9012
PatchFile: %n.patch
PatchFile-MD5: 6d4ac57a09c13ae2c0391c4062b47fe1
PatchScript: <<
	#!/bin/sh -ev
	sed 's|@FINK_PREFIX@|%p|g' <%{PatchFile} | patch -p1
	export XCODE_PREFIX=`xcode-select -print-path`
	perl -pi -e "s|\/Developer|${XCODE_PREFIX}|" src/Makefile.osx
<<
BuildDepends: fink (>= 0.28)
Conflicts: coreutils-default
UseMaxBuildJobs: false
CompileScript: <<
head -n 30 src/phylip.c > Copyright
cd src && make -f Makefile.osx all
<<
InstallScript: <<
install -d -m 755 %i/Applications/phylip
cd src && make -f Makefile.osx install EXEDIR=%i/Applications/phylip
install -d -m 755 %i/share/%n
install -m 644 %i/Applications/phylip/font* %i/share/%n
install -d -m 755 %i/share/%n
ln -s font1 %i/share/%n/fontfile
rm -f %i/Applications/phylip/font*
#mv %i/Applications/phylip/testdata %i/share/%n
install -d -m 755 %i/lib
mv %i/Applications/phylip/*.dylib %i/lib
<<
Shlibs: <<
	!%p/lib/libdrawgram.dylib
	!%p/lib/libdrawtree.dylib
<<
DocFiles: doc/ %n.html Copyright
Description: Package of programs for inferring phylogenies
DescDetail: <<
PHYLIP (the PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees). 

Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.

Complete documentation is available on documentation files that come
with the package.
<<
DescPackaging: <<
nieder:
* Our versions 3.69.7 is really 3.697 upstream, but there's no guarantee
that the next version will NOT be 3.70.

nieder: changed the install script 
<<
License: BSD
Maintainer: Cyril Gallut <[email protected]>
Homepage: http://evolution.genetics.washington.edu/phylip.html
phylip.patch (text/plain, 2.9 KB) 
diff -ruN phylip-3.696.new/src/Makefile.osx phylip-3.696/src/Makefile.osx
--- phylip-3.696.new/src/Makefile.osx	2014-09-19 09:29:23.000000000 -0500
+++ phylip-3.696/src/Makefile.osx	2017-08-26 10:45:39.000000000 -0500
@@ -230,12 +230,12 @@
 	@cp $(JARS) $(EXEDIR)
 	@echo "Installing font files in $(EXEDIR)"
 	@cp font* $(EXEDIR)
-	@echo "Copying testdata to $(EXEDIR)/testdata"
-	mkdir $(EXEDIR)/testdata
-	for i in $(TESTDIR); do \
-      mkdir $(EXEDIR)/testdata/$$i; \
-      cp TestData/$$i/*.txt $(EXEDIR)/testdata/$$i; \
-    done
+#	@echo "Copying testdata to $(EXEDIR)/testdata"
+#	mkdir $(EXEDIR)/testdata
+#	for i in $(TESTDIR); do \
+#      mkdir $(EXEDIR)/testdata/$$i; \
+#      cp TestData/$$i/*.txt $(EXEDIR)/testdata/$$i; \
+#    done
 	@echo "Finished installation."
 	@echo ""
 
@@ -244,8 +244,8 @@
 	@for i in $(APPS) ; do \
       rm -rf "$(EXEDIR)/$$i" ; \
     done
-	@echo "Removing preexisting testdata"
-	@rm -rf $(EXEDIR)/testdata
+#	@echo "Removing preexisting testdata"
+#	@rm -rf $(EXEDIR)/testdata
 	@echo "Ready for new executables"
 	@echo ""
 
@@ -376,7 +376,7 @@
 	
 # needed by java	
 libdrawgram.dylib:     drawgram.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS)  -shared drawgram.o draw.o draw2.o phylip.o $(CLIBS) -o libdrawgram.dylib
+	$(CC) $(CFLAGS)  -shared -install_name @FINK_PREFIX@/lib/libdrawgram.dylib drawgram.o draw.o draw2.o phylip.o $(CLIBS) -o libdrawgram.dylib
 
 drawtree.o:     drawtree.c draw.h phylip.h
 	$(CC) $(CFLAGS) -c drawtree.c
@@ -386,7 +386,7 @@
 
 # needed by java	
 libdrawtree.dylib:     drawtree.o draw.o draw2.o phylip.o
-	$(CC) $(CFLAGS)  -shared drawtree.o draw.o draw2.o phylip.o $(CLIBS) -o libdrawtree.dylib
+	$(CC) $(CFLAGS)  -shared -install_name @FINK_PREFIX@/lib/libdrawtree.dylib drawtree.o draw.o draw2.o phylip.o $(CLIBS) -o libdrawtree.dylib
 
 factor.o:       factor.c phylip.h
 
@@ -614,11 +614,11 @@
 	mkdir $(dist_JAVADIR)
 	mkdir $(dist_SRCDIR)/mac
 	mkdir $(dist_SRCDIR)/icons
-	mkdir $(dist_EXEDIR)/testdata
-	for i in $(TESTDIR); do \
-      mkdir $(dist_EXEDIR)/testdata/$$i; \
-      cp TestData/$$i/*.txt $(dist_EXEDIR)/testdata/$$i; \
-    done
+#	mkdir $(dist_EXEDIR)/testdata
+#	for i in $(TESTDIR); do \
+#      mkdir $(dist_EXEDIR)/testdata/$$i; \
+#      cp TestData/$$i/*.txt $(dist_EXEDIR)/testdata/$$i; \
+#    done
 	for i in $(DIST_COMMON) ; do \
 	  cp -r $$i $(DISTDIR) ; \
 	done
diff -ruN phylip-3.696.new/src/phylip.h phylip-3.696/src/phylip.h
--- phylip-3.696.new/src/phylip.h	2014-09-19 09:27:09.000000000 -0500
+++ phylip-3.696/src/phylip.h	2017-08-26 10:44:23.000000000 -0500
@@ -96,7 +96,7 @@
 #define EBCDIC false
 #define INFILE "infile"
 #define OUTFILE "outfile"
-#define FONTFILE "fontfile" /* on unix this might be /usr/local/lib/fontfile */
+#define FONTFILE "@FINK_PREFIX@/share/phylip/fontfile" /* on unix this might be /usr/local/lib/fontfile */
 #define PLOTFILE "plotfile"
 #define INTREE "intree"
 #define INTREE2 "intree2"