From d6e51b8f14f082f0d6065a93fd1f05fe8c92287a Mon Sep 17 00:00:00 2001 From: Jun Aruga Date: Nov 23 2019 00:33:54 +0000 Subject: Update to new Github-based upstream release 1.0.11. Remove mmseq-flags.patch file for now, as it was removed by "fedpkg import". --- diff --git a/.gitignore b/.gitignore index f1ce5b3..1761c03 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ /mmseq_0.9.18.zip /latest.zip /1.0.8a.zip +/1.0.11.zip diff --git a/mmseq-flags.patch b/mmseq-flags.patch deleted file mode 100644 index 6f0cf54..0000000 --- a/mmseq-flags.patch +++ /dev/null @@ -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 diff --git a/mmseq-iostream-c++11.patch b/mmseq-iostream-c++11.patch deleted file mode 100644 index 93fb4c0..0000000 --- a/mmseq-iostream-c++11.patch +++ /dev/null @@ -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(getline(ifs, transcriptID))); - } - - void HitsfileReader::readHeaderSchema1(vector *transcriptName, map *transcriptEffectiveLength, diff --git a/mmseq-sam-header.patch b/mmseq-sam-header.patch deleted file mode 100644 index a30dde0..0000000 --- a/mmseq-sam-header.patch +++ /dev/null @@ -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 - #include - #include - #include diff --git a/mmseq-static-data-members-initialization-c++11.patch b/mmseq-static-data-members-initialization-c++11.patch deleted file mode 100644 index cc98846..0000000 --- a/mmseq-static-data-members-initialization-c++11.patch +++ /dev/null @@ -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 Pnil; - bool fixalpha; - -- static const double g=2.0; -+ static constexpr double g=2.0; - gsl_rng ** rg; - int max_threads; - diff --git a/mmseq-zlib.patch b/mmseq-zlib.patch index 174d9f3..a9ec6ae 100644 --- a/mmseq-zlib.patch +++ b/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 diff --git a/mmseq.spec b/mmseq.spec index 01260c3..212e64d 100644 --- a/mmseq.spec +++ b/mmseq.spec @@ -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 @@ 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 -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 @@ install -p -m 0755 bin/ensembl_gtf_to_gff.pl %{buildroot}%{_bindir} %changelog +* Mon Nov 11 2019 Jun Aruga - 1.0.11-1 +- Update to new Github-based upstream release 1.0.11. + * Tue Aug 20 2019 Susi Lehtola - 1.0.8a-31 - Rebuilt for GSL 2.6. diff --git a/sources b/sources index e7249e0..b459aff 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -e4d73f76baba7bbd04b0e56d2620c57b 1.0.8a.zip +SHA512 (1.0.11.zip) = 064444603a6bf8af581187ace162fc03ea5699530b4cc53d35bb7ff1daadc9d651392f1e4bc6d0899c53e5a9e2a4f0c4fa8e8c8a641cd508d13e3f03679c80f5