on SOAP program

Pol8 · 08-13-2014, 03:21 PM

Hi everyone,

I just typed 'make' to install SOAP, but I got this error.

main.c

.text.startup+0xff): undefined reference to `call_pregraph_sparse'
collect2: error: ld returned 1 exit status
make: *** [SOAPdenovo-63mer] Error 1

Any help?
Thanks!

Wallysb01 · 08-13-2014, 05:07 PM

Just get the binaries instead of the source code

chuckcode · 11-26-2014, 09:41 AM

On my ubuntu system pregraph_sparse.cpp was failing to compile because the includes for getopt and usleep were missing. I added them to the SOAPdenovo2-src-r240/sparsePregraph/inc/stdinc.h file so they would get included other places if needed as well and then compilation finished fine for me.

Specifically in file SOAPdenovo2-src-r240/sparsePregraph/inc/stdinc.h I have:
...
#include <pthread.h>
#include <getopt.h> /* added to find getopt functions */
#include <unistd.h> /* added to find usleep, may be different on your system */
using namespace std;

Probably too late to help original post but maybe help other folks in the future as google points to this post.

caiosuz · 02-15-2016, 09:46 AM

Thanks for the tip chuckcode.
It worked perfectly!

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08-13-2014, 03:21 PM	#1
Pol8 Member Location: USA Join Date: Aug 2014 Posts: 33	on SOAP program Hi everyone, I just typed 'make' to install SOAP, but I got this error. main.c.text.startup+0xff): undefined reference to `call_pregraph_sparse' collect2: error: ld returned 1 exit status make: *** [SOAPdenovo-63mer] Error 1 Any help? Thanks!

11-26-2014, 09:41 AM	#3
chuckcode Junior Member Location: SF Bay Area Join Date: Nov 2014 Posts: 1	add includes On my ubuntu system pregraph_sparse.cpp was failing to compile because the includes for getopt and usleep were missing. I added them to the SOAPdenovo2-src-r240/sparsePregraph/inc/stdinc.h file so they would get included other places if needed as well and then compilation finished fine for me. Specifically in file SOAPdenovo2-src-r240/sparsePregraph/inc/stdinc.h I have: ... #include <pthread.h> #include <getopt.h> /* added to find getopt functions / #include <unistd.h> / added to find usleep, may be different on your system */ using namespace std; Probably too late to help original post but maybe help other folks in the future as google points to this post.

08-13-2014, 05:07 PM	#2
Wallysb01 Senior Member Location: San Francisco, CA Join Date: Feb 2011 Posts: 286	Just get the binaries instead of the source code

02-15-2016, 09:46 AM	#4
caiosuz Member Location: Brazil_Bahia_Ilheus Join Date: Dec 2015 Posts: 12	Thanks for the tip chuckcode. It worked perfectly!