diff --git a/mmseq-iostream-c++11.patch b/mmseq-iostream-c++11.patch new file mode 100644 index 0000000..93fb4c0 --- /dev/null +++ b/mmseq-iostream-c++11.patch @@ -0,0 +1,12 @@ +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.spec b/mmseq.spec index dd5cf64..874bb0c 100644 --- a/mmseq.spec +++ b/mmseq.spec @@ -1,6 +1,6 @@ Name: mmseq Version: 1.0.8a -Release: 9%{?dist} +Release: 10%{?dist} Summary: Haplotype and isoform specific expression estimation for RNA-seq Group: Applications/Engineering @@ -10,6 +10,7 @@ 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 BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: boost-devel @@ -34,6 +35,8 @@ estimation using multi-mapping RNA-seq reads. Example scripts are included. #%%patch1 -p1 -b .mmseq-flags.patch #Fix zlib linking %patch2 -p1 -b .mmseq-zlib.patch +#Fix for C++11 iostream changes +%patch3 -p1 -b .mmseq-iostream-c++11.patch #Remove bundled binaries rm bin/*-linux @@ -86,6 +89,9 @@ rm -rf %{buildroot} %changelog +* Fri Feb 12 2016 Adam Huffman - 1.0.8a-10 +- patch to add compatibility with C++11 iostream + * Wed Feb 10 2016 Adam Huffman - 1.0.8a-9 - rebuilt to pick up new armadillo