Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

.gitignore

@@ -4,3 +4,4 @@
 /mmseq_0.9.18.zip
 /latest.zip
 /1.0.8a.zip
+/1.0.11.zip

mmseq-flags.patch

@@ -1,11 +0,0 @@
-diff -ur mmseq-1.0.8a/src/Makefile mmseq-1.0.8a-new/src/Makefile
---- mmseq-1.0.8a/src/Makefile	2014-01-09 22:45:54.000000000 +0000
-+++ mmseq-1.0.8a-new/src/Makefile	2015-03-01 22:35:22.349761703 +0000
-@@ -75,6 +75,7 @@
- 	$(CXX) ${OPT} -c sokal.cc
- 
- fasta.o : fasta.c fasta.h
-+	$(CC) $(CXXFLAGS)  -c fasta.c
- 
- uh.o : uh.cpp uh.hh
- 	$(CXX) ${OMP} ${OPT} -c uh.cpp 

mmseq-iostream-c++11.patch

@@ -1,12 +0,0 @@
-diff -ur mmseq-1.0.8a/src/hitsio.cpp mmseq-1.0.8a.new/src/hitsio.cpp
---- mmseq-1.0.8a/src/hitsio.cpp	2014-01-09 22:45:54.000000000 +0000
-+++ mmseq-1.0.8a.new/src/hitsio.cpp	2016-02-12 09:46:01.800529284 +0000
-@@ -343,7 +343,7 @@
- 
- bool HitsfileReader::readReadMapRecordTranscriptIDSchema0(string &transcriptID) {
- 	if ((ifs.eof()) || (ifs.peek() == '>')) { return false; }
--	return(getline(ifs, transcriptID));
-+	return(static_cast<bool>(getline(ifs, transcriptID)));
- }
- 
- void HitsfileReader::readHeaderSchema1(vector<string> *transcriptName, map<string, double> *transcriptEffectiveLength,

mmseq-sam-header.patch

@@ -1,11 +0,0 @@
---- mmseq_0.9.14/src/bam2hits.cpp	2011-09-22 16:24:55.000000000 +0100
-+++ mmseq_0.9.14.new/src/bam2hits.cpp	2011-10-07 15:22:12.387102321 +0100
-@@ -15,7 +15,7 @@
- **    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
- */
- 
--#include "sam.h"
-+#include <samtools/sam.h>
- #include <iostream>
- #include <fstream>
- #include <string>

mmseq-static-data-members-initialization-c++11.patch

@@ -1,12 +0,0 @@
-diff -ur mmseq-1.0.8a/src/bms.hpp mmseq-1.0.8a.new/src/bms.hpp
---- mmseq-1.0.8a/src/bms.hpp	2014-01-09 22:45:54.000000000 +0000
-+++ mmseq-1.0.8a.new/src/bms.hpp	2016-02-12 10:00:33.330772798 +0000
-@@ -135,7 +135,7 @@
-   vector<bool> Pnil;
-   bool fixalpha;
- 
--  static const double g=2.0;
-+  static constexpr double g=2.0;
-   gsl_rng ** rg;
-   int max_threads;
- 

mmseq-zlib.patch

@@ -1,11 +1,11 @@
---- mmseq_0.9.18/src/Makefile	2011-12-16 14:44:46.000000000 +0000
-+++ mmseq_0.9.18.new/src/Makefile	2012-01-11 15:03:03.091319510 +0000
-@@ -11,7 +11,7 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -13,7 +13,7 @@
 
  CC = gcc
  CXX = g++
--LIBS = -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -lz -llapack -lblas -lgfortran
-+LIBS = -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -llapack -lblas -lgfortran -Wl,--as-needed -lz
+-LIBS = -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lz -llapack -lblas 
++LIBS = -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -llapack -lblas -Wl,--as-needed -lz
  OMP = -fopenmp
  OPT = -O3
  OPTSAFE = -O2

mmseq.spec

@@ -1,25 +1,29 @@
 Name:		mmseq
-Version:	1.0.8a
-Release:	27%{?dist}
+Version:	1.0.11
+Release:	16%{?dist}
 Summary:	Haplotype and isoform specific expression estimation for RNA-seq
 
-Group:		Applications/Engineering
+%if 0%{?fedora} >= 33
+%bcond_without flexiblas
+%endif
+
 License:	GPLv2+
 URL:		https://github.com/eturro/%{name}
 Source0:	https://github.com/eturro/%{name}/archive/%{version}.zip
-Patch0:		mmseq-sam-header.patch
 #Patch1:		mmseq-flags.patch
 Patch2:		mmseq-zlib.patch
-Patch3:		mmseq-iostream-c++11.patch
-Patch4:		mmseq-static-data-members-initialization-c++11.patch
 
 BuildRequires:  gcc-c++
+BuildRequires:	make
 BuildRequires:	boost-devel
 BuildRequires:	perl-generators
-BuildRequires:	samtools-devel
+BuildRequires:	htslib-devel
 BuildRequires:	gsl-devel
 BuildRequires:	zlib-devel
 BuildRequires:	armadillo-devel
+%if %{with flexiblas}
+BuildRequires:	flexiblas-devel
+%endif
 
 Requires:	ruby
 Requires:	samtools
@@ -31,29 +35,26 @@ estimation using multi-mapping RNA-seq reads.  Example scripts are included.
 
 %prep
 %setup -q -n %{name}-%{version}
-#Look for samtools headers in the correct location for Fedora
-%patch0 -p1 -b .mmseq-sam-header.patch
 #Use Fedora compilation headers
 #%%patch1 -p1 -b .mmseq-flags.patch
 #Fix zlib linking
 %patch2 -p1 -b .mmseq-zlib.patch
 
-# Apply c++11 patches for gcc >= 6
-%if 0%{?fedora} >= 24
-#Fix for C++11 iostream changes
-%patch3 -p1 -b .mmseq-iostream-c++11.patch
-#Fix for C++11 static data member initialization changes
-%patch4 -p1 -b .mmseq-static-data-members-initialization-c++11.patch
-%endif
+# Remove bundled binaries
+# Only 2 bin/*-linux files are included in Source0 archive.
+rm -f bin/*-linux
 
-#Remove bundled binaries
-rm bin/*-linux
-rm bin/*-mac
+%if %{with flexiblas}
+sed -e 's/-lblas/-lflexiblas/g' -e 's/-llapack/-lflexiblas/g' -i src/Makefile
+%endif
 
 %build
 cd src
 make %{?_smp_mflags} CXXFLAGS="%{optflags}"
 
+%check
+# Check src/VERSION is correctly set.
+test "$(bin/mmseq --version 2>&1 || true)" = "%{name}-%{version}"
 
 %install
 rm -rf %{buildroot}
@@ -93,6 +94,66 @@ install -p -m 0755 bin/ensembl_gtf_to_gff.pl %{buildroot}%{_bindir}
 
 
 %changelog
+* Thu Jul 20 2023 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-16
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Mon Feb 20 2023 Jonathan Wakely <jwakely@redhat.com> - 1.0.11-15
+- Rebuilt for Boost 1.81
+
+* Thu Jan 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-14
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
+
+* Tue Aug 23 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 1.0.11-13
+- Rebuild for gsl-2.7.1
+
+* Thu Jul 21 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-12
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
+* Wed May 04 2022 Thomas Rodgers <trodgers@redhat.com> - 1.0.11-11
+- Rebuilt for Boost 1.78
+
+* Thu Jan 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-10
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Sat Aug 07 2021 Jonathan Wakely <jwakely@redhat.com> - 1.0.11-9
+- Rebuilt for Boost 1.76
+
+* Thu Jul 22 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-8
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-7
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Fri Jan 22 2021 Jonathan Wakely <jwakely@redhat.com> - 1.0.11-6
+- Rebuilt for Boost 1.75
+
+* Thu Aug 27 2020 Iñaki Úcar <iucar@fedoraproject.org> - 1.0.11-5
+- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager
+
+* Tue Jul 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Thu May 28 2020 Jonathan Wakely <jwakely@redhat.com> - 1.0.11-3
+- Rebuilt for Boost 1.73
+
+* Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.11-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Mon Nov 11 2019 Jun Aruga <jaruga@redhat.com> - 1.0.11-1
+- Update to new Github-based upstream release 1.0.11.
+
+* Tue Aug 20 2019 Susi Lehtola <jussilehtola@fedoraproject.org> - 1.0.8a-31
+- Rebuilt for GSL 2.6.
+
+* Thu Jul 25 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.8a-30
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
+
+* Fri Feb 01 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.8a-29
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
+
+* Fri Jan 25 2019 Jonathan Wakely <jwakely@redhat.com> - 1.0.8a-28
+- Rebuilt for Boost 1.69
+
 * Fri Aug 17 2018 José Abílio Matos <jamatos@fc.up.pt> - 1.0.8a-27
 - rebuild for armadillo soname bump
 

sources

@@ -1 +1 @@
-e4d73f76baba7bbd04b0e56d2620c57b  1.0.8a.zip
+SHA512 (1.0.11.zip) = 064444603a6bf8af581187ace162fc03ea5699530b4cc53d35bb7ff1daadc9d651392f1e4bc6d0899c53e5a9e2a4f0c4fa8e8c8a641cd508d13e3f03679c80f5