abyss-konnector installation problem

[Felipe Aguilera]

Hi everyone,

Hope someone can help me to fix my installation problem with ABySS. I want to use transabyss 1.5.3 and am having problems to install ABySS 1.5.2. I got the following error during the installation process

make[2]: Entering directory `/usr/local/src/abyss-1.5.2/Bloom'

 /bin/mkdir -p '/usr/local/bin'

  /usr/bin/install -c abyss-bloom '/usr/local/bin'

make[2]: Nothing to be done for `install-data-am'.

make[2]: Leaving directory `/usr/local/src/abyss-1.5.2/Bloom'

make[1]: Leaving directory `/usr/local/src/abyss-1.5.2/Bloom'

Making install in Konnector

make[1]: Entering directory `/usr/local/src/abyss-1.5.2/Konnector'

/opt/rh/devtoolset-1.1/root/usr/bin/g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/usr/local/src/abyss-1.5.2     -isystem/usr/local/src/abyss-1.5.2/boost_1_55_0 -Wall -Wextra -Werror -fopenmp -g -O2 -MT konnector-konnector.o -MD -MP -MF .deps/konnector-konnector.Tpo -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc

In file included from /usr/local/include/boost/graph/breadth_first_search.hpp:21:0,

                 from ../Graph/BidirectionalBFS.h:8,

                 from konnector.h:7,

                 from konnector.cc:8:

/usr/local/include/boost/graph/graph_concepts.hpp: In instantiation of ‘boost::concepts::BidirectionalGraph<G>::~BidirectionalGraph() [with G = DBGBloom<BloomFilter>]’:

/usr/local/include/boost/graph/graph_concepts.hpp:114:1:   required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::BidirectionalGraphConcept<DBGBloom<BloomFilter> >]’

/usr/local/include/boost/concept_check.hpp:50:1:   required from ‘void boost::function_requires(Model*) [with Model = boost::concepts::BidirectionalGraphConcept<DBGBloom<BloomFilter> >]’

../Graph/BidirectionalBFS.h:90:2:   required from ‘void bidirectionalBFS(const BidirectionalGraph&, typename boost::graph_traits<BidirectionalGraph>::vertex_descriptor, typename boost::graph_traits<BidirectionalGraph>::vertex_descriptor, Buffer&, Buffer&, BidirectionalBFSVisitor<BidirectionalGraph>&, ColorMap&, ColorMap&) [with BidirectionalGraph = DBGBloom<BloomFilter>; Buffer = boost::queue<Kmer, std::deque<Kmer, std::allocator<Kmer> > >; ColorMap = DefaultColorMap<DBGBloom<BloomFilter> >; typename boost::graph_traits<BidirectionalGraph>::vertex_descriptor = Kmer]’

../Graph/BidirectionalBFS.h:155:2:   required from ‘void bidirectionalBFS(const BidirectionalGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, typename boost::graph_traits<Graph>::vertex_descriptor, BidirectionalBFSVisitor<BidirectionalGraph>&) [with BidirectionalGraph = DBGBloom<BloomFilter>; typename boost::graph_traits<Graph>::vertex_descriptor = Kmer]’

konnector.h:274:2:   required from ‘ConnectPairsResult connectPairs(unsigned int, const FastaRecord&, const FastaRecord&, const Graph&, const ConnectPairsParams&) [with Graph = DBGBloom<BloomFilter>]’

konnector.cc:304:48:   required from ‘void connectPair(const Graph&, const FastqRecord&, const FastqRecord&, const ConnectPairsParams&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&) [with Graph = DBGBloom<BloomFilter>; std::ofstream = std::basic_ofstream<char>]’

konnector.cc:424:4:   required from ‘void connectPairs(const Graph&, FastaStream&, const ConnectPairsParams&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&) [with Graph = DBGBloom<BloomFilter>; FastaStream = FastaConcat; std::ofstream = std::basic_ofstream<char>]’

konnector.cc:653:29:   required from here

/usr/local/include/boost/graph/graph_concepts.hpp:131:9: error: ‘degree’ was not declared in this scope

make[1]: *** [konnector-konnector.o] Error 1

make[1]: Leaving directory `/usr/local/src/abyss-1.5.2/Konnector'

make: *** [install-recursive] Error 1

I have GCC version 4.8.2 installed on my system

[felipe@fritzen felipe]$ gcc --version

gcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15)

Copyright (C) 2013 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I have googled for a solution but I couldn't find anything out there. Hope you can help me guys.

Thanks in advance,

Felipe

[Shaun Jackman]

Hi, Felipe. That error is reported on GitHub at https://github.com/bcgsc/abyss/issues/130

Please go there for more information.

Cheers,

Shaun