[med-svn] [Git][med-team/hisat2][master] 2 commits: Refresh the patches
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Jan 27 10:01:01 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / hisat2
Commits:
53a23cf6 by Michael R. Crusoe at 2020-08-11T13:36:54+02:00
Refresh the patches
- - - - -
ef149b86 by Michael R. Crusoe at 2020-08-11T13:42:47+02:00
2.2.1-1
- - - - -
5 changed files:
- debian/changelog
- debian/patches/fix-manual
- debian/patches/hardening
- debian/patches/python3
- debian/patches/reproducibile
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,14 @@
-hisat2 (2.2.1-1) UNRELEASED; urgency=medium
+hisat2 (2.2.1-1) unstable; urgency=medium
+ [ Steffen Moeller ]
* Team upload.
* New upstream version
* debhelper-compat 13 (routine-update)
- -- Steffen Moeller <moeller at debian.org> Mon, 10 Aug 2020 16:06:18 +0200
+ [ Michael R. Crusoe ]
+ * Refresh the patches
+
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 11 Aug 2020 13:42:31 +0200
hisat2 (2.2.0-2) unstable; urgency=medium
=====================================
debian/patches/fix-manual
=====================================
@@ -2,7 +2,7 @@ From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Update manual path
--- hisat2.orig/Makefile
+++ hisat2/Makefile
-@@ -550,16 +550,16 @@
+@@ -548,16 +548,16 @@
rm -rf .bin.tmp
.PHONY: doc
=====================================
debian/patches/hardening
=====================================
@@ -12,7 +12,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-@@ -308,7 +308,7 @@
+@@ -306,7 +306,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
@@ -21,7 +21,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -317,7 +317,7 @@
+@@ -315,7 +315,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
@@ -30,7 +30,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
#
# hisat2-repeat targets
-@@ -329,7 +329,7 @@
+@@ -327,7 +327,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_REPEAT_CPPS_MAIN) \
@@ -39,7 +39,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-repeat-debug: hisat2_repeat.cpp $(REPEAT_CPPS) $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -337,7 +337,7 @@
+@@ -335,7 +335,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_REPEAT_CPPS_MAIN) \
@@ -48,7 +48,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
#
-@@ -350,7 +350,7 @@
+@@ -348,7 +348,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -57,7 +57,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-@@ -358,7 +358,7 @@
+@@ -356,7 +356,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -66,7 +66,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -366,7 +366,7 @@
+@@ -364,7 +364,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -75,7 +75,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -374,7 +374,7 @@
+@@ -372,7 +372,7 @@
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -84,7 +84,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
#
# hisat2 targets
-@@ -386,7 +386,7 @@
+@@ -384,7 +384,7 @@
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -93,7 +93,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-@@ -394,7 +394,7 @@
+@@ -392,7 +392,7 @@
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -102,7 +102,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -403,7 +403,7 @@
+@@ -401,7 +401,7 @@
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -111,7 +111,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -412,7 +412,7 @@
+@@ -410,7 +410,7 @@
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -120,7 +120,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
#
# hisat2-inspect targets
-@@ -425,7 +425,7 @@
+@@ -423,7 +423,7 @@
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -129,7 +129,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
-@@ -434,7 +434,7 @@
+@@ -432,7 +432,7 @@
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -138,7 +138,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -443,7 +443,7 @@
+@@ -441,7 +441,7 @@
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -147,7 +147,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -452,7 +452,7 @@
+@@ -450,7 +450,7 @@
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
=====================================
debian/patches/python3
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/reproducibile
=====================================
@@ -21,28 +21,24 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/250
VERSION = $(shell cat VERSION)
# Convert BITS=?? to a -m flag
-@@ -234,13 +234,13 @@
+@@ -234,11 +234,11 @@
$(HT2LIB_DIR)/pymodule/ht2example.py
-GENERAL_LIST = $(wildcard scripts/*.sh) \
- $(wildcard scripts/*.pl) \
- $(wildcard *.py) \
-- $(wildcard hisatgenotype_modules/*.py) \
-- $(wildcard hisatgenotype_scripts/*.py) \
- $(wildcard example/index/*.ht2) \
- $(wildcard example/reads/*.fa) \
+GENERAL_LIST = $(sort $(wildcard scripts/*.sh)) \
+ $(sort $(wildcard scripts/*.pl)) \
+ $(sort $(wildcard *.py)) \
-+ $(sort $(wildcard hisatgenotype_modules/*.py)) \
-+ $(sort $(wildcard hisatgenotype_scripts/*.py)) \
+ $(sort $(wildcard example/index/*.ht2)) \
+ $(sort $(wildcard example/reads/*.fa)) \
example/reference/22_20-21M.fa \
example/reference/22_20-21M.snp \
$(PTHREAD_PKG) \
-@@ -263,10 +263,10 @@
+@@ -261,10 +261,10 @@
# the Windows FIND tool instead.
FIND=$(shell which find)
@@ -57,7 +53,7 @@ Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/250
$(HT2LIB_PKG_SRC) \
Makefile \
CMakeLists.txt \
-@@ -288,15 +288,20 @@
+@@ -286,15 +286,20 @@
repeat-debug: hisat2-repeat-debug
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/c535c449c109e1427baee0169313948cc680291b...ef149b86ac639fd8bafcd909f62ad912a8124e1a
--
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/c535c449c109e1427baee0169313948cc680291b...ef149b86ac639fd8bafcd909f62ad912a8124e1a
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