commit: 22a501fd359a8b2d18b88806f0c94a1694bc0c7d Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Feb 13 11:07:18 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Feb 13 11:07:18 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=22a501fd
sci-biology/last: clean up unused patches Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> .../last/files/last-852-fix-build-system.patch | 54 --------------------- .../last/files/last-852-portable-shebangs.patch | 56 ---------------------- 2 files changed, 110 deletions(-) diff --git a/sci-biology/last/files/last-852-fix-build-system.patch b/sci-biology/last/files/last-852-fix-build-system.patch deleted file mode 100644 index 6ee4f5a67..000000000 --- a/sci-biology/last/files/last-852-fix-build-system.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- last-852/makefile.ori 2016-12-13 07:22:11.000000000 +0100 -+++ last-852/makefile 2017-05-10 11:04:14.610665834 +0200 -@@ -1,6 +1,7 @@ --CXXFLAGS = -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -+CXXFLAGS ?= -O3 -+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS - all: -- @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)" -+ $(MAKE) -C src - - progs = src/lastdb src/lastal src/last-split src/last-merge-batches \ - src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8 -@@ -13,17 +14,17 @@ - cp $(progs) scripts/* $(bindir) - - clean: -- @cd src && $(MAKE) clean -+ $(MAKE) -C src clean - - html: -- @cd doc && $(MAKE) -+ $(MAKE) -C doc - - distdir = last-`hg id -n` - - RSYNCFLAGS = -aC --exclude '*8' --exclude 'last??' --exclude last-split --exclude last-merge-batches --exclude last-pair-probs - - dist: log html -- @cd src && $(MAKE) version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh -+ $(MAKE) -C src version.hh CyclicSubsetSeedData.hh ScoreMatrixData.hh - rsync $(RSYNCFLAGS) build doc examples makefile scripts src data *.txt $(distdir) - zip -qrm $(distdir) $(distdir) - ---- last-852/src/makefile.ori 2016-12-13 06:53:24.000000000 +0100 -+++ last-852/src/makefile 2017-05-10 11:05:22.792501835 +0200 -@@ -1,12 +1,13 @@ --CXX = g++ --CC = gcc -+CXX ?= g++ -+CC ?= gcc - --CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ ---Wcast-align -pedantic -g -std=c++11 -pthread -DHAS_CXX_THREADS -+CXXFLAGS ?= -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ -+-Wcast-align -pedantic -g -+CXXFLAGS += -std=c++11 -pthread -DHAS_CXX_THREADS - # -Wconversion - # -fomit-frame-pointer ? - --CFLAGS = -Wall -O2 -+CFLAGS ?= -Wall -O2 - - alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o \ - alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o \ diff --git a/sci-biology/last/files/last-852-portable-shebangs.patch b/sci-biology/last/files/last-852-portable-shebangs.patch deleted file mode 100644 index c2131da63..000000000 --- a/sci-biology/last/files/last-852-portable-shebangs.patch +++ /dev/null @@ -1,56 +0,0 @@ ---- last-852/scripts/last-dotplot.ori 2017-05-10 11:14:05.206748593 +0200 -+++ last-852/scripts/last-dotplot 2017-05-10 11:15:31.009058957 +0200 -@@ -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. ---- last-852/scripts/last-map-probs.ori 2017-05-10 11:14:11.856927669 +0200 -+++ last-852/scripts/last-map-probs 2017-05-10 11:15:35.139288498 +0200 -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#! /usr/bin/env python2 - - # Copyright 2010, 2011, 2012, 2014 Martin C. Frith - ---- last-852/scripts/last-postmask.ori 2017-05-10 11:14:19.817142021 +0200 -+++ last-852/scripts/last-postmask 2017-05-10 11:15:44.939556158 +0200 -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#! /usr/bin/env python2 - - # Copyright 2014 Martin C. Frith - ---- last-852/scripts/last-train.ori 2017-05-10 11:14:27.687353953 +0200 -+++ last-852/scripts/last-train 2017-05-10 11:15:48.679658384 +0200 -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#! /usr/bin/env python2 - # Copyright 2015 Martin C. Frith - - import math, optparse, os, random, signal, subprocess, sys, tempfile ---- last-852/scripts/maf-convert.ori 2017-05-10 11:14:34.267531142 +0200 -+++ last-852/scripts/maf-convert 2017-05-10 11:15:52.439761157 +0200 -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#! /usr/bin/env python2 - # Copyright 2010, 2011, 2013, 2014 Martin C. Frith - # Read MAF-format alignments: write them in other formats. - # Seems to work with Python 2.x, x>=6 ---- last-852/scripts/maf-join.ori 2017-05-10 11:14:41.407723414 +0200 -+++ last-852/scripts/maf-join 2017-05-10 11:15:56.699877600 +0200 -@@ -1,4 +1,4 @@ --#! /usr/bin/env python -+#! /usr/bin/env python2 - - # Copyright 2009, 2010, 2011 Martin C. Frith - ---- last-852/scripts/maf-swap.ori 2017-05-10 11:14:48.417912185 +0200 -+++ last-852/scripts/maf-swap 2017-05-10 11:16:02.300030669 +0200 -@@ -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.
