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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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Building LACHESIS with Amazon Red Hat instance #2

Closed cwbeitel closed 10 years ago

cwbeitel commented 10 years ago

When compiling, saw the error below. Fixed by adding #include to ChromLinkMatrix.cc. Afterwards was able to run ./Lachesis INIs/test_case.ini without segfault error seen on Ubuntu. These are the additions I made to the base instance:

sudo yum upgrade sudo yum install gcc-c++ sudo yum install boost-devel.x86_64 sudo yum install zlib-devel

a - MarkovModel.o a - MarkovChain.o a - HMM.o make[2]: Leaving directory /home/ec2-user/LACHESIS-master/include/markov' make[1]: Leaving directory/home/ec2-user/LACHESIS-master/include' g++ -c Lachesis.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/home/ec2-user/samtools-0.1.19 g++ -c Reporter.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/home/ec2-user/samtools-0.1.19 g++ -c ChromLinkMatrix.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/home/ec2-user/samtools-0.1.19 In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/hash_set:60, from /usr/include/boost/graph/adjacency_list.hpp:25, from ChromLinkMatrix.cc:22: /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. ChromLinkMatrix.cc: In member function ‘ContigOrdering ChromLinkMatrix::MakeFullOrder(int, bool) const’: ChromLinkMatrix.cc:970: error: ‘setprecision’ was not declared in this scope make: *\ [ChromLinkMatrix.o] Error 1

JingaJenga commented 10 years ago

I'm sorry - what were the changes you made to the base instance? If it's just a matter of adding one or more #includes, feel free to add them to the repository.

-- Josh

cwbeitel commented 10 years ago

Ah looks like I didn't specify which include to add, sorry. It worked after adding #include to ChromLinkMatrix.cc. Also when I'm talking about "changing the base instance" I mean the base red hat VM instance on Amazon and those commands I put at the top are what you need, here they are again:

sudo yum upgrade sudo yum install gcc-c++ sudo yum install boost-devel.x86_64 sudo yum install zlib-devel

cwbeitel commented 10 years ago

Oh interesting, Github stripped something out of my comment. I was trying to write "#include ".

JingaJenga commented 10 years ago

Haha, that makes a whole lot more sense now! I'll add that.

-- Josh