Error during compilation of RSEM

Question

[Lucas Peres]

Hello everyone,

I'm trying to install RSEM (https://github.com/deweylab/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

[WouterDeCoster]

Have you tried installing using conda? https://anaconda.org/bioconda/rsem

[h.mon]

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.