The package rpms/bwa.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/bwa.git/commit/?id=35343396072320....
Change:
+ExclusiveArch: x86_64
Thanks.
Full change:
============
commit 49d6fb76fbdea02923e38a579ebffef774d3fbe7
Author: Jun Aruga <jaruga(a)redhat.com>
Date: Wed Mar 25 20:01:42 2020 +0100
Move bwakit files to data directory to avoid conflicts.
diff --git a/bwa.spec b/bwa.spec
index 6979a46..55626e9 100644
--- a/bwa.spec
+++ b/bwa.spec
@@ -34,13 +34,13 @@ make %{?_smp_mflags} CFLAGS="%{optflags}"
%install
rm -rf %{buildroot}
mkdir -p %{buildroot}/%{_bindir}
+mkdir -p %{buildroot}/%{_datadir}/%{name}/bwakit
mkdir -p %{buildroot}/%{_mandir}/man1
install -m 0755 bwa %{buildroot}/%{_bindir}
install -m 0755 qualfa2fq.pl %{buildroot}/%{_bindir}
install -m 0755 xa2multi.pl %{buildroot}/%{_bindir}
-
-install -m 0755 bwakit/* %{buildroot}/%{_bindir}
+install -m 0755 bwakit/* %{buildroot}/%{_datadir}/%{name}/bwakit
install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
@@ -49,14 +49,18 @@ install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
%files
-%doc COPYING NEWS.md README.md README-alt.md
+%doc COPYING NEWS.md README.md README-alt.md
+%{_bindir}/bwa
+%{_bindir}/qualfa2fq.pl
+%{_bindir}/xa2multi.pl
+%{_datadir}/%{name}/*
%{_mandir}/man1/%{name}.1*
-%{_bindir}/*
%changelog
-* Sun Mar 22 2020 Jun Aruga <jaruga(a)redhat.com> - 0.7.17-1
+* Thu Apr 16 2020 Jun Aruga <jaruga(a)redhat.com> - 0.7.17-1
- Update to upstream release 0.7.17
+- Move bwakit files to data directory to avoid conflicts.
* Tue Jan 28 2020 Fedora Release Engineering <releng(a)fedoraproject.org> -
0.7.15-10
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
commit 35343396072320ad18c6425083f3e2a959c7d135
Author: Jun Aruga <jaruga(a)redhat.com>
Date: Sun Mar 22 21:37:03 2020 +0100
Update to upstream release 0.7.17
diff --git a/.gitignore b/.gitignore
index a35d82f..81e5c7e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ bwa-0.5.8a.tar.bz2
/bwa-0.7.12.tar.bz2
/bwa-0.7.13.tar.bz2
/bwa-0.7.15.tar.bz2
+/bwa-0.7.17.tar.bz2
diff --git a/bwa-fix-build-gcc10.patch b/bwa-fix-build-gcc10.patch
new file mode 100644
index 0000000..32c9f9b
--- /dev/null
+++ b/bwa-fix-build-gcc10.patch
@@ -0,0 +1,28 @@
+From 039e5733af162692ad670d5c6fb4a9d8fa5e3d02 Mon Sep 17 00:00:00 2001
+From: David Seifert <soap(a)gentoo.org>
+Date: Wed, 26 Feb 2020 13:24:17 +0100
+Subject: [PATCH] Fix building against GCC 10
+
+* GCC 10 defaults to `-fno-common`, which makes C behave
+ more like C++ in that you can only ever have one definition
+ of an object per executable.
+---
+ rle.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/rle.h b/rle.h
+index 0d59484..4f8946d 100644
+--- a/rle.h
++++ b/rle.h
+@@ -30,7 +30,7 @@ extern "C" {
+ *** 43+3 codec ***
+ ******************/
+
+-const uint8_t rle_auxtab[8];
++extern const uint8_t rle_auxtab[8];
+
+ #define RLE_MIN_SPACE 18
+ #define rle_nptr(block) ((uint16_t*)(block))
+--
+2.25.1
+
diff --git a/bwa-nosse2-i386.patch b/bwa-nosse2-i386.patch
deleted file mode 100644
index b9b9ea5..0000000
--- a/bwa-nosse2-i386.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- bwa-0.6.1/Makefile 2011-11-28 14:55:02.000000000 +0000
-+++ bwa-0.6.1.new/Makefile 2012-05-13 20:52:46.889400339 +0100
-@@ -2,7 +2,7 @@
- CXX= g++
- CFLAGS= -g -Wall -O2
- CXXFLAGS= $(CFLAGS)
--DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
-+DFLAGS= -DHAVE_PTHREAD -D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
- OBJS= QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
- is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o \
- bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
diff --git a/bwa.spec b/bwa.spec
index b5dfcc5..6979a46 100644
--- a/bwa.spec
+++ b/bwa.spec
@@ -1,13 +1,16 @@
Name: bwa
-Version: 0.7.15
-Release: 10%{?dist}
+Version: 0.7.17
+Release: 1%{?dist}
Summary: Burrows-Wheeler Alignment tool
License: GPLv3
URL:
http://bio-bwa.sourceforge.net/
Source0:
http://downloads.sourceforge.net/bio-%{name}/%{name}-%{version}.tar.bz2
+# Fix building against GCC 10.
+#
https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284
+Patch0: bwa-fix-build-gcc10.patch
# 0.7.x versions only build on x86_64
-ExclusiveArch: x86_64
+ExclusiveArch: x86_64
BuildRequires: gcc
BuildRequires: perl-generators
@@ -21,6 +24,7 @@ for read shorter than 150bp and the other for longer reads.
%prep
%setup -q
+%patch0 -p1
%build
@@ -40,6 +44,10 @@ install -m 0755 bwakit/* %{buildroot}/%{_bindir}
install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
+%check
+./bwa 2>&1 | grep '^Version: %{version}'
+
+
%files
%doc COPYING NEWS.md README.md README-alt.md
%{_mandir}/man1/%{name}.1*
@@ -47,6 +55,9 @@ install -m 0644 bwa.1 %{buildroot}/%{_mandir}/man1/bwa.1
%changelog
+* Sun Mar 22 2020 Jun Aruga <jaruga(a)redhat.com> - 0.7.17-1
+- Update to upstream release 0.7.17
+
* Tue Jan 28 2020 Fedora Release Engineering <releng(a)fedoraproject.org> -
0.7.15-10
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
diff --git a/sources b/sources
index a161cbf..ce3983e 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-fcf470a46a1dbe2f96a1c5b87c530554 bwa-0.7.15.tar.bz2
+SHA512 (bwa-0.7.17.tar.bz2) =
67cccfef1c7aa1b5aad6b59a49390e8d96f64320c414bfffacf232aeb08c15861e98be826c1b42b6222d6ff086eeb055b1318ea2e9eebfd87b2365d06fc89802