trinity jellyfish error

Question

[cristina_sabiers]

Hi!

Im trying to run virusfinder, I got some problems before because I couldnt install trinity 2012 (must have that version to run virusfinder) in my ubuntu version 16.

Now I try with ubuntu version 15 64 bits.

And I get this error when "make" trinity, seems I have problem installing the plugin jellyfish, but I dont know if its a way to fix it...

Thanks!

In file included from ./jellyfish/square_binary_matrix.hpp:28:0,
             from jellyfish/square_binary_matrix.cc:18: 
 ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here
 Tptr<T> ptr;
       ^
 cc1plus: all warnings being treated as errors
Makefile:1165: recipe for target 'jellyfish/libjellyfish_la-square_binary_matrix.lo' failed 
make[2]: *** [jellyfish/libjellyfish_la-square_binary_matrix.lo] Error 1
make[2]: Leaving directory '/home/cris/Desktop/tri/trinity-plugins/jellyfish-1.1.5'
Makefile:650: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/home/cris/Desktop/tri/trinity-plugins/jellyfish-1.1.5'
Makefile:18: recipe for target 'all' failed
 make: *** [all] Error 2

[Michael]

Unfortunately, you didn't include the failing compiler command, always include the full command that is given by the make file, but I am guessing the problem is indicated by:

  cc1plus: all warnings being treated as errors

See http://stackoverflow.com/questions/11561261/how-to-compile-without-warnings-being-treated-as-errors

[cristina_sabiers]

thanks Michael

I was suposse to write this on my makefile?

KBUILD_CFLAGS += $(call cc-option,-Wno-error=unused-but-set-variable,)

I did but didnt worked for me....if I did right..I am not a programer, just have a tiny little idea

Anyhow I installed the trinity r2013 the next version..and worked!!!!!!!

Finally I can find my virus!!! ;;;___;;; Hapinesss

Thanks a lot!!!

[GenoMax]

Are you looking for a specific virus or "virii" in general? If former what is the use case for using trinity, why not a regular NGS aligner?

[cristina_sabiers]

no, nothing in special, just curiosity to see what finds Virus finder (Im bit stubborn when wants to make something to work :P ),

I just use trinity because virusfinder uses it :) before I allready alligned my unmmaped secuencies to virus genomes.

Im wondering if all of these tools really works, if I would have an exom secuency with a know virus I asume would be more easy to find out, but in my case I dont have.

Answer 1

[huang.wenxun]

I have the same question in linux.

cc1plus: all warnings being treated as errors make[2]: * [jellyfish/libjellyfish_la-square_binary_matrix.lo] Error 1 make[2]: Leaving directory /home/trinityrnaseq_r2012-06-08/trinity-plugins/jellyfish' make[1]: *** [all] Error 2 make[1]: Leaving directory/hom/trinityrnaseq_r2012-06-08/trinity-plugins/jellyfish' make: * [all] Error 2 [linux@ trinityrnaseq_r2012-06-08]$

[cristina_sabiers]

try trinity version r2013 (next version) maybe works like did with me