diff options
Diffstat (limited to 'sci-biology/last/files')
| -rw-r--r-- | sci-biology/last/files/last-299-fix-build-system.patch | 74 | ||||
| -rw-r--r-- | sci-biology/last/files/last-299-portable-shebangs.patch | 99 |
2 files changed, 0 insertions, 173 deletions
diff --git a/sci-biology/last/files/last-299-fix-build-system.patch b/sci-biology/last/files/last-299-fix-build-system.patch deleted file mode 100644 index 0a89cea60278..000000000000 --- a/sci-biology/last/files/last-299-fix-build-system.patch +++ /dev/null @@ -1,74 +0,0 @@ -Make build system respect user flags - ---- a/makefile -+++ b/makefile -@@ -1,6 +1,5 @@ --CXXFLAGS = -O3 - all: -- @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)" -+ $(MAKE) -C src - - prefix = /usr/local - exec_prefix = $(prefix) -@@ -10,15 +9,15 @@ - cp src/last?? scripts/*.?? $(bindir) - - clean: -- @cd src && $(MAKE) clean -+ $(MAKE) -C src clean - - html: -- @cd doc && $(MAKE) -+ $(MAKE) -C doc - - distdir = last-`hg id -n` - - dist: log html -- @cd src && $(MAKE) version.hh -+ $(MAKE) -C src version.hh - rsync -rC --exclude 'last??' doc examples makefile s* *.txt $(distdir) - zip -qrm $(distdir) $(distdir) - ---- a/src/makefile -+++ b/src/makefile -@@ -1,12 +1,9 @@ --CXX = g++ --CC = gcc -- --CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ ---Wcast-align -Wno-long-long -ansi -pedantic -+last_CXXFLAGS = -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ -+-Wcast-align -Wno-long-long -pedantic - # -Wconversion - # -fomit-frame-pointer ? - --CFLAGS = -Wall -+last_CFLAGS = -Wall - - DBSRC = Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc \ - SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc \ -@@ -49,17 +46,20 @@ - - all: lastdb lastal lastex - -+.cpp.o: -+ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) -c -o $@ $< -+ - lastdb: $(DBSRC) $(DBINC) makefile -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC) -+ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC) - - lastal: $(ALSRC) $(ALINC) makefile $(OBJ) -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ) -+ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ) - - lastex: $(EXSRC) $(EXINC) makefile -- $(CXX) -Igumbel_params $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC) -+ $(CXX) $(CPPFLAGS) -Igumbel_params $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC) - - $(OBJ): CA_code/*.c CA_code/*.h makefile -- $(CC) $(CPPFLAGS) $(CFLAGS) -c CA_code/lambda_calculator.c -+ $(CC) $(CPPFLAGS) $(last_CFLAGS) $(CFLAGS) -c -o $@ CA_code/lambda_calculator.c - - clean: - rm -f lastdb lastal lastex $(OBJ) diff --git a/sci-biology/last/files/last-299-portable-shebangs.patch b/sci-biology/last/files/last-299-portable-shebangs.patch deleted file mode 100644 index 03ecbdcbde20..000000000000 --- a/sci-biology/last/files/last-299-portable-shebangs.patch +++ /dev/null @@ -1,99 +0,0 @@ -Make shebangs portable and prefix friendly -See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ - ---- a/scripts/last-dotplot.py -+++ b/scripts/last-dotplot.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read pair-wise alignments in MAF or LAST tabular format: write an - # "Oxford grid", a.k.a. dotplot. ---- a/scripts/last-map-probs.py -+++ b/scripts/last-map-probs.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2010, 2011, 2012 Martin C. Frith - ---- a/scripts/last-merge-batches.py -+++ b/scripts/last-merge-batches.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2010, 2011 Martin C. Frith - ---- a/scripts/last-pair-probs.py -+++ b/scripts/last-pair-probs.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2011, 2012, 2013 Martin C. Frith - ---- a/scripts/last-reduce-alignments.sh -+++ b/scripts/last-reduce-alignments.sh -@@ -1,4 +1,4 @@ --#! /bin/sh -+#!/usr/bin/env sh - - # This script reads MAF-format alignments with lastal header - # information, removes "uninteresting" alignments, and writes the ---- a/scripts/last-remove-dominated.py -+++ b/scripts/last-remove-dominated.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read MAF-format alignments, and write those are not "dominated" by - # any other one. X dominates Y if they overlap on the top sequence, ---- a/scripts/last-split-probs.py -+++ b/scripts/last-split-probs.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2012 Martin C. Frith - ---- a/scripts/maf-convert.py -+++ b/scripts/maf-convert.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - # Copyright 2010, 2011 Martin C. Frith - # Read MAF-format alignments: write them in other formats. - # Seems to work with Python 2.x, x>=4 ---- a/scripts/maf-cull.py -+++ b/scripts/maf-cull.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read MAF-format alignments. Write them, omitting alignments whose - # coordinates in the top-most sequence are contained in those of >= ---- a/scripts/maf-join.py -+++ b/scripts/maf-join.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Copyright 2009, 2010, 2011 Martin C. Frith - ---- a/scripts/maf-sort.sh -+++ b/scripts/maf-sort.sh -@@ -1,4 +1,4 @@ --#! /bin/sh -+#!/usr/bin/env sh - - # Sort MAF-format alignments by sequence name, then strand, then start - # position, then end position, of the top sequence. Also, merge ---- a/scripts/maf-swap.py -+++ b/scripts/maf-swap.py -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#!/usr/bin/env python2 - - # Read MAF-format alignments, and write them, after moving the Nth - # sequence to the top in each alignment. |