smartdenovo make error

[liguiyang410]

when make in fold smartdenovo, errors were showed as follows:
/tmp/ccTfg5aF.o: In function merge_bubbles_strgraph': wtlay.c:(.text+0x984d): undefined reference to cut_biedge_strgraph2'
wtlay.c:(.text+0x9861): undefined reference to cut_biedge_strgraph2' wtlay.c:(.text+0x992d): undefined reference to cut_biedge_strgraph2'
wtlay.c:(.text+0x994a): undefined reference to `cut_biedge_strgraph2'
collect2: error: ld returned 1 exit status
Makefile:48: recipe for target 'wtlay' failed
make: *** [wtlay] Error 1

[ruanjue]

Please tell me your gcc version. Try to modify

smartdenovo/Makefile

Line 48 in 5cc1356

$(CC) $(CFLAGS) -o wtlay file_reader.c wtlay.c $(GLIBS)

into $(CC) $(CFLAGS) -o wtlay file_reader.c wtlay.c wtlay.h $(GLIBS), then make wtlay again.

[liguiyang410]

GCC 4.8 . I modified the line 48, but still the same errors.

[ruanjue]

Let me think that your compiler is not C but C++. Then try to remove

smartdenovo/wtlay.h

Lines 95 to 97 in 5cc1356

	#ifdef _CPLUSPLUS
	extern "C" {
	#endif

smartdenovo/wtlay.h

Lines 832 to 834 in 5cc1356

	#ifdef _CPLUSPLUS
	}
	#endif

and compile wtlay again.

[ruanjue]

If there is still error, also try to remove the modifier inline in

smartdenovo/wtlay.h

Lines 491 to 518 in 5cc1356

	inline int cut_edge_strgraph(StringGraph *g, uint32_t node_id, int dir, uint32_t eidx){
	sg_edge_t *e;
	e = edge_strgraph(g, node_id, dir, eidx);
	if(e->closed) return 0;
	e->closed = 1;
	return 1;
	}
	inline sg_edge_t* edge_partner_strgraph(StringGraph *g, uint32_t node_id, int dir, uint32_t eidx){
	sg_edge_t *e1, *e2;
	e1 = edge_strgraph(g, node_id, dir, eidx);
	e2 = edge_strgraph(g, e1->node_id, !e1->dir, e1->rev_idx);
	return e2;
	}
	inline int cut_biedge_strgraph_core(StringGraph *g, uint32_t node_id, int dir, uint32_t eidx, int closed){
	edge_strgraph(g, node_id, dir, eidx)->closed = closed;
	edge_partner_strgraph(g, node_id, dir, eidx)->closed = closed;
	return 1;
	}
	inline int cut_biedge_strgraph(StringGraph *g, uint32_t node_id, int dir, uint32_t eidx){
	return cut_biedge_strgraph_core(g, node_id, dir, eidx, 1);
	}
	inline int cut_biedge_strgraph2(StringGraph *g, uint32_t node_id, int dir, uint32_t eidx){
	return cut_biedge_strgraph_core(g, node_id, dir, eidx, 2);
	}

[emaleckova]

I also had trouble installing SMARTdenovo, similar to those described here as well as in issue #22. Since it took me several tries to install successfully, I would like to share what helped in my case:

1. Changes in the Makefile as mentioned here
2. Removing lines 95 to 97 and 832 to 834 in wtlay.h as mentioned here
3. Add static before all five occurrences of inline (lines 491 to 518) in wtlay.h

For completeness, I work on Ubuntu 19.04 and run gcc 8.3.0.

[ruanjue]

Thanks!

[miltongr21]

@emaleckova

This solved the problem for me!
Thanks bro!

[cfz1998]

I also had trouble installing SMARTdenovo, similar to those described here as well as in issue #22. Since it took me several tries to install successfully, I would like to share what helped in my case:

1. Changes in the Makefile as mentioned here
2. Removing lines 95 to 97 and 832 to 834 in wtlay.h as mentioned here
3. Add static before all five occurrences of inline (lines 491 to 518) in wtlay.h

For completeness, I work on Ubuntu 19.04 and run gcc 8.3.0.

Thanks！