Question: trinity jellyfish error
0
gravatar for cristina_sabiers
12 months ago by
Spain
cristina_sabiers40 wrote:

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
jellyfish • 527 views
ADD COMMENTlink modified 12 months ago by huang.wenxun0 • written 12 months ago by cristina_sabiers40

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

ADD REPLYlink written 12 months ago by Michael Dondrup43k

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!!!

ADD REPLYlink written 12 months ago by cristina_sabiers40

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?

ADD REPLYlink written 12 months ago by genomax39k

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.

ADD REPLYlink written 12 months ago by cristina_sabiers40
0
gravatar for huang.wenxun
12 months ago by
China
huang.wenxun0 wrote:

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]$

ADD COMMENTlink modified 12 months ago • written 12 months ago by huang.wenxun0

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

ADD REPLYlink written 12 months ago by cristina_sabiers40
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