Question: Error during compilation of RSEM
gravatar for Lucas Peres
12 months ago by
Lucas Peres50
Brazil, Belém
Lucas Peres50 wrote:

Hello everyone,

I'm trying to install RSEM ( for further differential expression analysis of RNA-Seq data and during the compilation (the first step when we type make), the following error always pops up, probably regarding some dependency. I have already installed R and Bowtie2, besides Perl and g++, which come natively with Debian 6.

I have looked for some people who may have had the same issue, but I didn't succeed. Hope you can help me.

Thanks in advance!

g++ -std=gnu++98 -Wall -I. -I. -Isamtools-1.3/htslib-1.3  -O3 -c -o extractRef.o extractRef.cpp
In file included from /usr/local/include/assert.h:5:0,
                 from /usr/include/c++/6/cassert:44,
                 from utils.h:10,
                 from extractRef.cpp:13:
/usr/local/include/except.h:15:32: error: conflicting declaration ‘typedef struct Except_Frame_T* Except_Frame_T’
 typedef struct Except_Frame_T Except_Frame_T;
/usr/local/include/except.h:15:16: note: previous declaration as ‘struct Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
/usr/local/include/except.h:17:18: error: field ‘prev’ has incomplete type ‘Except_Frame_T’
   Except_Frame_T prev;
/usr/local/include/except.h:16:8: note: definition of ‘struct Except_Frame_T’ is not complete until the closing brace
 struct Except_Frame_T {
Makefile:70: recipe for target 'extractRef.o' failed
make: ** [extractRef.o] Error 1

rna-seq software error • 624 views
ADD COMMENTlink written 12 months ago by Lucas Peres50

Several pointers: broken headers, maybe added by GSNAP, maybe renaming them will solve. Try to find out how they were installed, and uninstall them properly, to avoid further issues.

ADD REPLYlink written 12 months ago by h.mon23k

Have you tried installing using conda?

ADD REPLYlink written 12 months ago by WouterDeCoster36k
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