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author | David Seifert <soap@gentoo.org> | 2016-10-03 01:07:43 +0200 |
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committer | David Seifert <soap@gentoo.org> | 2016-10-03 22:21:05 +0200 |
commit | 655a8a83559815e73e6e09f6b83fa0905dffee28 (patch) | |
tree | acca00e672c7ab09a2e88678cd7fca6b72607097 /sci-biology/phrap/files | |
parent | sci-biology/phred: Revbump to EAPI=6 (diff) | |
download | gentoo-655a8a83559815e73e6e09f6b83fa0905dffee28.tar.gz gentoo-655a8a83559815e73e6e09f6b83fa0905dffee28.tar.bz2 gentoo-655a8a83559815e73e6e09f6b83fa0905dffee28.zip |
sci-biology/phrap: Revbump to EAPI=6
Package-Manager: portage-2.3.1
Diffstat (limited to 'sci-biology/phrap/files')
-rw-r--r-- | sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch | 100 |
1 files changed, 100 insertions, 0 deletions
diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch new file mode 100644 index 000000000000..6d30c2ce326a --- /dev/null +++ b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch @@ -0,0 +1,100 @@ +* Fix perl shebang to be portable +* Make build system honour LDFLAGS + +--- a/makefile ++++ b/makefile +@@ -25,9 +25,8 @@ + # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) + #CC= icc + #CFLAGS= -O2 -wd266,880 +-CC= cc +-CFLAGS= -O2 +-LFLAGS= -lm ++CC ?= cc ++LIBS = -lm + + SWATOBJS= swat.o weibull.o + +@@ -96,46 +95,46 @@ + chmod a+x phrapview + + swat: makefile $(SWATOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS) + chmod o-r swat + + alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) + chmod o-r alpha_swat + + swat_counts: makefile $(COUNOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) + chmod o-r swat_counts + + swprobs: makefile $(PROBOBJS) +- $(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS) + + phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r phrap + + gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) +- $(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) + chmod o-r gcphrap + + cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r cross_match + + gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) +- $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) + chmod o-r gccross_match + + cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r cluster + + loco: makefile $(LOCOOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS) + chmod o-r loco + + erf_test: $(ERFOBJS) +- $(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS) + + loco.o: swat.h + +@@ -228,7 +227,7 @@ + anomalies.o: swat.h + + fast_smith_wat.s: fast_smith_wat.c +- cc -S -machine_code -source_listing -O3 fast_smith_wat.c ++ $(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c + #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!! + + tig_node.o: swat.h +--- a/phrapview ++++ b/phrapview +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl + + + #/***************************************************************************** +@@ -25,6 +25,7 @@ + # + #*****************************************************************************/ + ++use warnings; + use strict; + use Tk; + #phrapview version 0.960731 |