3:12 p.m.
The package rpms/bowtie.git has added or updated architecture specific content in its
spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s):
https://src.fedoraproject.org/cgit/rpms/bowtie.git/commit/?id=1862384d6d0....
Change:
-%ifarch s390x
Thanks.
Full change:
============
commit 1862384d6d0359faae46be54101573b4518e326f
Author: Jun Aruga <jaruga(a)redhat.com>
Date: Tue Jul 28 22:06:28 2020 +0200
Update to upstream release 1.3.0
diff --git a/.gitignore b/.gitignore
index c3ee85b..2911c1c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,5 @@
/bowtie-1.0.1-src.zip
/bowtie-1.2.3-tests.tgz
/bowtie-src-x86_64.zip
+/bowtie-1.3.0-src.zip
+/bowtie-1.3.0-tests.tgz
diff --git a/bowtie-alphabet-error-narrowing.patch
b/bowtie-alphabet-error-narrowing.patch
deleted file mode 100644
index bc7417b..0000000
--- a/bowtie-alphabet-error-narrowing.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-diff --git a/alphabet.cpp b/alphabet.cpp
-index fe94493..6b7ff30 100644
---- a/alphabet.cpp
-+++ b/alphabet.cpp
-@@ -273,7 +273,7 @@ int dnacomp[5] = {
-
- const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";
-
--char mask2iupac[16] = {
-+signed char mask2iupac[16] = {
- -1,
- 'A', // 0001
- 'C', // 0010
-diff --git a/alphabet.h b/alphabet.h
-index fc03779..35a5699 100644
---- a/alphabet.h
-+++ b/alphabet.h
-@@ -227,7 +227,7 @@ extern uint8_t nuccol2nuc[5][5];
- extern uint8_t asc2dnamask[];
-
- /// Convert a 4-bit mask into an IUPAC code
--extern char mask2iupac[16];
-+extern signed char mask2iupac[16];
-
- /**
- * Return true iff c is an unambiguous Dna character.
---
-2.24.1
-
diff --git a/bowtie-enable-multi-arch.patch b/bowtie-enable-multi-arch.patch
deleted file mode 100644
index 8d58baa..0000000
--- a/bowtie-enable-multi-arch.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-diff --git a/Makefile b/Makefile
-index bbce0a2..9cac1fe 100644
---- a/Makefile
-+++ b/Makefile
-@@ -8,10 +8,10 @@ bindir = $(prefix)/bin
- SEQAN_DIR = ./SeqAn-1.1
- # treat SeqAn as a sysdir to suppress warnings
- SEQAN_INC = -isystem $(SEQAN_DIR)
--INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
--CPP = g++
--CXX = $(CPP)
--CC = gcc
-+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC)
-+CPP ?= g++
-+CXX ?= $(CPP)
-+CC ?= gcc
- LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
-@@ -162,6 +162,12 @@ VERSION = $(shell cat VERSION)
- BITS=32
- ifeq (x86_64,$(shell uname -m))
- BITS=64
-+else ifeq (aarch64,$(shell uname -m))
-+ BITS=64
-+else ifeq (s390x,$(shell uname -m))
-+ BITS=64
-+else ifeq (ppc64le,$(shell uname -m))
-+ BITS=64
- endif
- # msys will always be 32 bit so look at the cpu arch instead.
- ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
-@@ -180,8 +186,8 @@ ifeq (32,$(BITS))
- $(error bowtie2 compilation requires a 64-bit platform )
- endif
-
--DEBUG_FLAGS = -O0 -g3 -m64
--RELEASE_FLAGS = -O3 -m64
-+DEBUG_FLAGS = -O0 -g3
-+RELEASE_FLAGS = -O3
- NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-
---
-2.24.1
-
diff --git a/bowtie-fix-ppc64le-s390x-asm-pause-error.patch
b/bowtie-fix-ppc64le-s390x-asm-pause-error.patch
new file mode 100644
index 0000000..b25b6da
--- /dev/null
+++ b/bowtie-fix-ppc64le-s390x-asm-pause-error.patch
@@ -0,0 +1,36 @@
+From ea04fb256aa01ca1252613c5d5de3c9e2d6327ee Mon Sep 17 00:00:00 2001
+From: Rone Charles <rone_charles(a)fastmail.com>
+Date: Mon, 27 Jul 2020 19:19:34 -0400
+Subject: [PATCH] Potential fix for cpu_backoff related errors on ppc
+
+---
+ bt2_locks.h | 8 ++++++--
+ 1 file changed, 6 insertions(+), 2 deletions(-)
+
+diff --git a/bt2_locks.h b/bt2_locks.h
+index b956ea4..cddbd8b 100644
+--- a/bt2_locks.h
++++ b/bt2_locks.h
+@@ -12,13 +12,17 @@
+ class cpu_backoff {
+ public:
+ cpu_backoff(): count(1) {}
+- void pause() {
++ inline void pause() {
+ if (count <= LOOPS_BEFORE_YIELD) {
+ for (int32_t i = 0; i < count; i++) {
+ #ifdef __aarch64__
+ __asm__ __volatile__("yield" ::: "memory");
+-#else
++#elif __ppc__
++ __asm__ __volatile__("or 27,27,27" ::: "memory");
++#elif __x86_64__
+ __asm__ __volatile__("pause;");
++#else
++ // do nothing
+ #endif
+ }
+ count *= 2;
+--
+2.26.2
+
diff --git a/bowtie.spec b/bowtie.spec
index 8c73cfc..fc636fa 100644
--- a/bowtie.spec
+++ b/bowtie.spec
@@ -1,31 +1,23 @@
Name: bowtie
-Version: 1.2.3
-Release: 3%{?dist}
+Version: 1.3.0
+Release: 1%{?dist}
Summary: An ultrafast, memory-efficient short read aligner
# bowite: Artistic 2.0
# tinythread.{h,cpp}: zlib
-# SeqAn: GPLv3 and LGPLv3+
-# SeqAn license info is not enough?
-# https://github.com/BenLangmead/bowtie/issues/106
-License: Artistic 2.0 and zlib and GPLv3 and LGPLv3+
+License: Artistic 2.0 and zlib
URL: http://bowtie-bio.sourceforge.net/index.shtml
-# bowtie v1.2.3 archive file name is wrong.
-# https://github.com/BenLangmead/bowtie/issues/101
-Source0: http://downloads.sourceforge.net/%{name}-bio/%{name}-src-x86_64.zip
+Source0: http://downloads.sourceforge.net/%{name}-bio/%{name}-%{version}-src.zip
# git clone https://github.com/BenLangmead/bowtie.git
# cd bowtie
-# git checkout v1.2.3
-# tar czvf bowtie-1.2.3-tests.tgz scripts/test/
-Source1: bowtie-1.2.3-tests.tgz
-# Enable multiple CPU architecture builds.
-# https://github.com/BenLangmead/bowtie/pull/102
-Patch0: bowtie-enable-multi-arch.patch
+# git checkout v1.3.0
+# tar czvf bowtie-1.3.0-tests.tgz scripts/test/
+Source1: bowtie-%{version}-tests.tgz
+# Fix bt2_locks.h: Error: Unrecognized opcode: `pause' on ppc64le/s390x.
+# https://github.com/BenLangmead/bowtie/issues/114
+Patch0: bowtie-fix-ppc64le-s390x-asm-pause-error.patch
# Remove perl-Sys-Info module depenency, as it does not exist on Fedora.
Patch1: bowtie-test-remove-perl-Sys-Info-dep.patch
-# Fix error narrowing conversion for non x86_64 architectures.
-# https://github.com/BenLangmead/bowtie/pull/95
-Patch2: bowtie-alphabet-error-narrowing.patch
Requires: python3
BuildRequires: gcc-c++
BuildRequires: hostname
@@ -45,15 +37,6 @@ ExcludeArch: i686 armv7hl
# Bundled libraries
#
https://fedoraproject.org/wiki/Bundled_Libraries?rd=Packaging:Bundled_Lib...
-# SeqAn
-# http://www.seqan.de/
-# TODO: Use system seqan instead of bundled one.
-# https://src.fedoraproject.org/rpms/seqan
-# Update to seqan 1.4.2
-# https://github.com/BenLangmead/bowtie/pull/105
-# Note SeqAn will be removed at tne next release of version 1.2.3.
-# https://github.com/BenLangmead/bowtie/issues/106#issuecomment-593426727
-Provides: bundled(seqan) = 1.1
# TinyThread++
# https://tinythreadpp.bitsnbites.eu/
# https://gitorious.org/tinythread/tinythreadpp
@@ -68,24 +51,18 @@ B, et al. Ultrafast and memory-efficient alignment of short DNA
sequences to the human genome. Genome Biol 10:R25.
%prep
-%setup -q
+%setup -q -n %{name}-%{version}-src
-%patch0 -p1 -b .bowtie-enable-multi-arch.patch
-%patch2 -p1 -b .bowtie-alphabet-error-narrowing.patch
+%patch0 -p1
# Remove the directory to avoid building bowtie with bundled libraries.
rm -rf third_party/
# Fix shebang to use system python3.
for file in $(find . -name "*.py") bowtie bowtie-*; do
- sed -i '1s|/usr/bin/env python|%{__python3}|' "${file}"
+ sed -E -i '1s|/usr/bin/env python[3]?|%{__python3}|' "${file}"
done
-# Invalid double quote characters are used in the code.
-# https://github.com/BenLangmead/bowtie/issues/104
-sed -i 's/“/"/g' processor_support.h
-sed -i 's/”/"/g' processor_support.h
-
%build
# Set flags considering bowtie2's testing cases for each architecture.
@@ -93,7 +70,6 @@ sed -i 's/”/"/g' processor_support.h
# https://github.com/BenLangmead/bowtie/pull/102
%ifnarch x86_64
export POPCNT_CAPABILITY=0
-export NO_TBB=1
%endif
# Set debug flag "-g" to prevent the error
@@ -102,7 +78,7 @@ export NO_TBB=1
%install
-%make_install prefix="%{_usr}" DESTDIR="%{buildroot}"
+%make_install prefix="%{_prefix}"
mkdir -p %{buildroot}/%{_datadir}/bowtie
cp -a reads %{buildroot}/%{_datadir}/bowtie/
@@ -123,18 +99,12 @@ done
tar xzvf %{SOURCE1}
cat %{PATCH1} | patch -p1
-%ifarch s390x
-# The tests works with the number of thread: 1 on s390x.
-# https://github.com/BenLangmead/bowtie/pull/105
-sed -i 's/--threads $nthreads/--threads 1/' scripts/test/simple_tests.pl
-%endif
-
# See Makefile simple-test target.
scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
%files
-%license LICENSE SeqAn-1.1/{GPL,LGPL}.txt
+%license LICENSE
%doc MANUAL NEWS VERSION AUTHORS TUTORIAL doc/{manual.html,style.css}
%dir %{_datadir}/bowtie
%{_bindir}/bowtie
@@ -159,6 +129,9 @@ scripts/test/simple_tests.pl --bowtie=./bowtie
--bowtie-build=./bowtie-build
%changelog
+* Tue Jul 28 2020 Jun Aruga <jaruga(a)redhat.com> - 1.3.0-1
+- Update to upstream release 1.3.0
+
* Mon Jul 27 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.2.3-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
diff --git a/sources b/sources
index d91e553..a7a2dcf 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
-SHA512 (bowtie-1.2.3-tests.tgz) =
810120e7acc91cbc06dceba2387b921ada3644f63c3ffce4237fbb7edf317f8dba11d250e49dfb702ea3245dba27091f98bf3dec0b4c22b25e5b67fd2e78f5d3
-SHA512 (bowtie-src-x86_64.zip) =
3d902b8a060f1a6af41602c5169bea0b43a5d0f2f0c72286602dcd5f84c42f261d93acc05baa45a34a57fe9f2d223e3917b1aa29c7cb93d93f93b86a3f365174
+SHA512 (bowtie-1.3.0-src.zip) =
27c33221a395de6dbf086c63befd007ac6033ab0fca6ce6b79b6c13de6bd02d5585c0c38c442e50dca5cdf95cfca136310ace334bbf24ac90e8e7aece93001a7
+SHA512 (bowtie-1.3.0-tests.tgz) =
9e25cbba3da9085b8427a0e2df77c21864c7bfbf51aced784362873c801bee92a95456bbd5b1ea02bf4a4443edba748e830fe9b8fea95f0c61e37f6297f4383c