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Old 08-13-2014, 03:21 PM   #1
Location: USA

Join Date: Aug 2014
Posts: 33
Default 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?
Pol8 is offline   Reply With Quote
Old 08-13-2014, 05:07 PM   #2
Senior Member
Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286

Just get the binaries instead of the source code
Wallysb01 is offline   Reply With Quote
Old 11-26-2014, 09:41 AM   #3
Junior Member
Location: SF Bay Area

Join Date: Nov 2014
Posts: 1
Default 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.
chuckcode is offline   Reply With Quote
Old 02-15-2016, 09:46 AM   #4
Location: Brazil_Bahia_Ilheus

Join Date: Dec 2015
Posts: 12

Thanks for the tip chuckcode.
It worked perfectly!
caiosuz is offline   Reply With Quote


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