Abyss Installation Error - KCONNECTOR

Question

[waqasnayab]

Dear ABYSS USERS,

I got following error during ABYSS installation:

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

I am already on root. What should I do now?

Regards,
Waqasuddin Khan

[Michael]

The relevant portion of error is before what you posted, please provide at 10 significant lines from the output plus the output of uname -a, gcc -v, the version of the software you downloaded. I guess you are running make? you don't need to be root to run make, only make install needs root to install into standard location.

[waqasnayab]

The outputs are as follows:

uname -a:

Linux penguin 2.6.18-194.el5 #1 SMP Fri Apr 2 14:58:14 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux

gcc -v:

Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)

ABYSS version: 1.5.2

The output of make (not full but just some lasy lines before error appears):

konnector.h:283:   instantiated from 'ConnectPairsResult connectPairs(unsigned int, const FastaRecord&, const FastaRecord&, const Graph&, const ConnectPairsParams&) [with Graph = DBGBloom<BloomFilter>]'
konnector.cc:304:   instantiated from 'void connectPair(const Graph&, const FastqRecord&, const FastqRecord&, const ConnectPairsParams&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&) [with Graph = DBGBloom<BloomFilter>]'
konnector.cc:424:   instantiated from 'void connectPairs(const Graph&, FastaStream&, const ConnectPairsParams&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&) [with Graph = DBGBloom<BloomFilter>, FastaStream = FastaConcat]'
konnector.cc:653:   instantiated from here
../Graph/HashGraph.h:61: warning: converting to 'size_t' from 'double'
../Graph/ConstrainedBidiBFSVisitor.h: In member function 'BFSVisitorResult ConstrainedBidiBFSVisitor<G>::checkMemLimit() [with G = DBGBloom<BloomFilter>]':
../Graph/ConstrainedBidiBFSVisitor.h:333:   instantiated from 'BFSVisitorResult ConstrainedBidiBFSVisitor<G>::recordEdgeTraversal(const typename boost::graph_traits<Graph>::edge_descriptor&, const G&, Direction) [with G = DBGBloom<BloomFilter>]'
../Graph/ConstrainedBidiBFSVisitor.h:180:   instantiated from 'BFSVisitorResult ConstrainedBidiBFSVisitor<G>::tree_edge(const typename boost::graph_traits<Graph>::edge_descriptor&, const G&, Direction) [with G = DBGBloom<BloomFilter>]'
konnector.cc:737:   instantiated from here
../Graph/ConstrainedBidiBFSVisitor.h:315: warning: converting to 'size_t' from 'double'
make[2]: *** [konnector-konnector.o] Error 1
make[2]: Leaving directory `/home/lifescope/Desktop/abyss-1.5.2/Konnector'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lifescope/Desktop/abyss-1.5.2'
make: *** [all] Error 2

Kindly guide me, any idea?

Regards,
Waqasuddin Khan

[Michael]

Not that I have ever built this software from source, but... I don't really see the error source right here, I think if you just try make konnector-konnector.o and post the full output of this target one could see it. konnector-konnector.o should be the name of the target that fails.

[Shaun Jackman]

ABySS 1.5.2 does not compile with GCC 4.1, unfortunately. The next release of ABySS will compile with GCC 4.1. Try installing a newer compiler if possible. Try

sudo yum install gcc44 gcc44-c++
./configure CC=gcc44 CXX=g++44
make

Answer 1

[Shaun Jackman]

ABySS 1.5.2 does not compile with GCC 4.1, unfortunately. The next release of ABySS will compile with GCC 4.1. Try installing a newer compiler if possible. Try

sudo yum install gcc44 gcc44-c++
./configure CC=gcc44 CXX=g++44
make

[waqasnayab]

Yeah, after installing gcc4.8, problem has been resolved.

Thanks to all,

[Shaun Jackman]

Great. I'm glad that you got GCC 4.8 working. It might also be possible to compile using GCC 4.1 by disabling warnings-as-errors. The default value of AM_CXXFLAGS is AM_CXXFLAGS = -Wall -Wextra -Werror

./configure
make AM_CXXFLAGS=-Wall

[waqasnayab]

Thanks, I will keep in mind for future use