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Oshlack / JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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extract_seq_from_fasta not getting installed #63

Closed Troyee13 closed 3 years ago

Troyee13 commented 3 years ago

Hello,

When I am manually trying to install

g++ -O3 -o bin/extract_seq_from_fasta ../src/extract_seq_from_fasta.c++

I am getting this error:

In file included from /usr/include/c++/4.8.2/unordered_set:35:0, from ../src/extract_seq_from_fasta.c++:19: /usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.

error This file requires compiler and library support for the \

^ ../src/extract_seq_from_fasta.c++: In function ‘int main(int, char**)’: ../src/extract_seq_from_fasta.c++:41:3: error: ‘unordered_set’ was not declared in this scope unordered_set ids_to_keep; ^ ../src/extract_seq_from_fasta.c++:41:23: error: expected primary-expression before ‘>’ token unordered_set ids_to_keep; ^ ../src/extract_seq_from_fasta.c++:41:25: error: ‘ids_to_keep’ was not declared in this scope unordered_set ids_to_keep; ^

My g++ version is g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

Please suggest how to resolve this.

Troyee13 commented 3 years ago

I tried running the installation on a different server with gccversion gcc (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609

Still getting the same error.

nadiadavidson commented 3 years ago

Hi,

Can you please try running the command: g++ -O3 -std=c++11 -o bin/extract_seq_from_fasta ../src/extract_seq_from_fasta.c++ and let me know if that compiles. Cheers, Nadia.

Troyee13 commented 3 years ago

Thanks for the reply. g++ -O3 -std=c++11 -o bin/extract_seq_from_fasta ../src/extract_seq_from_fasta.c++ This command actually worked for gcc 5.4.0 and I was able to run the demo data. I have also upgraded gcc from 4.8.5 to 7.3.0 and everything got installed without any warning. I have run my own data in direct mode. Everything is working out well till now. Thanks again.