RSEM installation Errors

Question

[XBria]

Hello,

I'm trying to install RSEM on Ubuntu 17. Following errors do not let compilation process go:

g++ -Wall -O2 -c -I. parseIt.cpp
In file included from parseIt.cpp:22:0:
SingleHit.h: In member function ‘bool SingleHit::read(std::istream&)’:
SingleHit.h:46:22: error: cannot convert ‘std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}’ to ‘bool’ in return
  return (in>>sid>>pos);
                      ^
In file included from parseIt.cpp:23:0:
PairedEndHit.h: In member function ‘bool PairedEndHit::read(std::istream&)’:
PairedEndHit.h:29:34: error: cannot convert ‘std::basic_istream<char>::__istream_type {aka std::basic_istream<char>}’ to ‘bool’ in return
     return (in>>sid>>pos>>insertL);
                                  ^
Makefile:58: recipe for target 'parseIt.o' failed
make: *** [parseIt.o] Error 1

Do you have any suggestion to make them work?

Thanks !

[GenoMax]

See if the answer at the top of this thread helps.

[XBria]

Can you please clarify where exactly set CC=gcc-6 and CXX=g++-6 ? by the way, compiler is already gcc-6

[GenoMax]

Can you check to see if there a Makefile? You could potentially edit that. What command are you using for this compilation? If you have an older version of GCC compiler available you could try that as an alternative.

[XBria]

if you mean in the RSEM folder, yes there exists. But where in that file should I add those two ?

... sudo apt-get install gcc-6 ...

Reading package lists... Done Building dependency tree
Reading state information... Done gcc-6 is already the newest version (6.3.0-12ubuntu2). The following package was automatically installed and is no longer required: libhts1 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 134 not upgraded.

[moustafa_abohawya]

I have the same error? Is there anyway you managed to fix this?

Answer 1

[ATpoint]

You can always install via conda if compilation fails: https://anaconda.org/bioconda/rsem

This does not solve the compilation problem itself but saves you time to focus on what is important: Your analysis.