#3 Update to new Github-based upstream release 1.0.11.
Merged 14 days ago by jaruga. Opened a month ago by jaruga.
rpms/ jaruga/mmseq feature/update-to-1.0.11  into  master

file modified
+1

@@ -4,3 +4,4 @@ 

  /mmseq_0.9.18.zip

  /latest.zip

  /1.0.8a.zip

+ /1.0.11.zip

file removed
-11

@@ -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 

@@ -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,

file removed
-11

@@ -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>

@@ -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;

-  

file modified
+5 -5

@@ -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

file modified
+12 -19

@@ -1,21 +1,18 @@ 

  Name:		mmseq

- Version:	1.0.8a

- Release:	31%{?dist}

+ Version:	1.0.11

+ Release:	1%{?dist}

  Summary:	Haplotype and isoform specific expression estimation for RNA-seq

  

  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:	boost-devel

  BuildRequires:	perl-generators

- BuildRequires:	samtools-devel

+ BuildRequires:	htslib-devel

  BuildRequires:	gsl-devel

  BuildRequires:	zlib-devel

  BuildRequires:	armadillo-devel

@@ -30,29 +27,22 @@ 

  

  %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

- rm bin/*-linux

- rm bin/*-mac

+ # Remove bundled binaries

+ # Only 2 bin/*-linux files are included in Source0 archive.

+ rm -f bin/*-linux

  

  %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}

@@ -92,6 +82,9 @@ 

  

  

  %changelog

+ * 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.

  

file modified
+1 -1

@@ -1,1 +1,1 @@ 

- e4d73f76baba7bbd04b0e56d2620c57b  1.0.8a.zip

+ SHA512 (1.0.11.zip) = 064444603a6bf8af581187ace162fc03ea5699530b4cc53d35bb7ff1daadc9d651392f1e4bc6d0899c53e5a9e2a4f0c4fa8e8c8a641cd508d13e3f03679c80f5

To test this PR on your local, you need to download following Source0 file.

$ wget https://github.com/eturro/mmseq/archive/1.0.11.zip

You need to do cherry-pick, then fedpkg srpm and fedpkg import *.src.rpm (sources and .gitignore are updated) and squash the additional commit by yourself. Maybe you know the way.

I did following tests.

See https://src.fedoraproject.org/rpms/mmseq/pull-request/2 for rpmlint check.

rebased onto d6e51b8

14 days ago

Pull-Request has been merged by jaruga

14 days ago