How can I run this C code

include<tissue.h> not found

I tried to run it using visual studio 2005.
although the files are all there, it generates many errors . first error states that it cannot find tissue.h !

>> include<tissue.h> not found

Are you sure that's the exact error message ?

I copied the error message bellow

tlr-lt.c:7:20: tissue.h: No such file or directory

Are the header file(s) for libtissue installed in the include path ? Either the system's or compiler's include directory, the project directory, or another directory that was specified in the compilation command ?

I put them in the project directory , and then build the project. But I got the error along with others of the same nature

Can you show the contents of your project directory ?

>> you probably need to change from <tissue.h> to "tissue.h"

<> should also look in the current directory.

I've got to get some sleep now, so I'll leave it to you, jhshukla :)

thank you it did solve the problem of tissue.h :)

but know I have another error

#include <asm/unistd.h>
13:24: asm/unistd.h: No such file or directory

isn't asm/unistd.h a built in like math.h?

>> isn't asm/unistd.h a built in like math.h?

The <unistd.h> file is quite standard on Unix like platforms, but <asm/unistd.h> less so, especially since you're apparently doing this in CYGWIN.

Sorry ozo - forgot to refresh.

OK thank you all

here is what I'm going to do I'll remove asm/ part and see what I'll get

>> <> should also look in the current directory.

Btw, I just realized I've been "spoiled" by my current setup - what I said earlier is not true in the general case heh.

hello again,
 
 unistd.h error is gone now :)

and of course I got another

in tlr, I got this error:

tlr-lt.c: In function `random_lock':
tlr-lt.c:178: error: `nsyscalls' undeclared (first use in this function)

although it was declared in syscall (attached)

/******************************************************************************/
/* tlr                                                                        */
/* (c) 2006 jamie twycross, jpt AT cs.nott.ac.uk                              */
/* released under gnu gpl v2                                                  */
/******************************************************************************/
 
#include "tissue.h"
#include "syscall.h"
 
#include <stdlib.h>
#include <unistd.h>
#include <err.h>
#include <sys/time.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <math.h>
.
.
.
/* create antigen receptor */
/* 4 characters - syscall number as 4-digit hex */
Antigen *random_lock(void)
{
	Antigen *lock = NULL;
	static char line[64];
	static int sc;
	register unsigned int i;
 
	while(!lock) {
		/* set lock to random syscall number */
		sc = (int) (((double) nsyscalls * rand()) / (RAND_MAX + 1.0));
		snprintf(line, sizeof(line), "%.4x", sc);
		lock = set_antigen(lock, line);
		/* check to see not known antigen */
		for(i = 0; i < num_known_antigen; i++)
			if(antigen_match(lock, known_antigen[i])) {
				lock = NULL;
				break;
			}
	}
 
	return lock;}
                                              

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thank you a lot, you are saving me here :)

I have this error
tlr-lt.c: In function `main':
tlr-lt.c:665: warning: passing arg 2 of `init_tissue' makes pointer from integer without a cast
tlr-lt.c:665: error: too few arguments to function `init_tissue'

I know that I should pass socket name as a parameter to
init_tissue((int16_t) ts_port, max_antigen, max_cytokines, \
                  max_cells);

so it will become some thing like
init_tissue((int16_t) ts_port, sockname,  max_antigen, max_cytokines, \
                  max_cells)

the thing is that I didn't find it in the  parameter file (the initialization file, that is read by tlr)

/******************************************************************************/
/* tlr                                                                        */
/* (c) 2006 jamie twycross, jpt AT cs.nott.ac.uk                              */
/* released under gnu gpl v2                                                  */
/******************************************************************************/
 
//changed 
#include "tissue.h"
#include "syscall.h"
 
#include <stdlib.h>
#include <unistd.h>
#include <err.h>
#include <sys/time.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <math.h>
 
/* model parameters */
unsigned int max_antigen;
unsigned int antigen_multiplier;
unsigned int max_cytokines;
unsigned int max_cells;
unsigned int cell_update_rate;
unsigned int num_cells_1;
unsigned int cell_lifespan_1;
unsigned int num_antigen_1;
unsigned int num_antigen_receptors_1;
unsigned int num_antigen_producers_1;
unsigned int antigen_producer_action_time;
unsigned int num_cytokine_receptors_1;
unsigned int num_cells_2;
unsigned int cell_lifespan_2;
unsigned int num_cell_receptors_2;
unsigned int num_vr_receptors_2;
unsigned int num_progeny_2;
unsigned int cell_lifespan_3;
unsigned int cell_lifespan_4;
unsigned int cell_lifespan_5;
unsigned int ts_port = TS_DEFAULT_PORT;
unsigned int log_tissue = 0;
unsigned int probe_rate = 0;
 
char parameter_file[1024] = "";
char known_antigen_file[1024] = "";
char known_signals_file[1024] = "";
 
unsigned int num_known_antigen, num_known_signals;
Antigen **known_antigen;
Signal **known_signals;
 
// change
  extern const unsigned int nsyscalls;//added
  
unsigned int uniqueid = 1;
.
.
.
int main(int argc, char **argv)
{
	Tissue *tissue;
	register unsigned int i, j, k, ind;
	Antigen *lock;
 
	parse_command_line(argc, argv);
 
	/* create a tissue compartment */
	tissue = init_tissue((int16_t) ts_port, max_antigen, max_cytokines, \
			max_cells);
.
.
.}
-----------------------------------------------------------------------
/******************************************************************************/
/* (c) 2006 jamie twycross, jpt AT cs.nott.ac.uk                              */
/* released under gnu gpl v2                                                  */
/* tissue api                                                                 */
/******************************************************************************/
 
#include "tissue.h"
 
#include <stdio.h>
#include <stdlib.h>
#include <signal.h>
#include <unistd.h>
#include <time.h>
#include <arpa/inet.h>
/*my change <netinet/sctp.h>*/
#include <netinet/tcp.h>
#include <netdb.h>
#include <strings.h>
#include <string.h>
#include <errno.h>
#include <err.h>
.
.
.
/* initialise the tissue */
Tissue *init_tissue(const uint16_t server_port,
		const char *sockname,
		const unsigned int num_antigen,
		const unsigned int num_cytokines,
		const unsigned int num_cells)
{
	Tissue *tissue;
	static int done;
	unsigned int i;
	struct sigaction siga;
	struct nbio *l;
 
	srand(time(NULL));
	srand48(time(NULL));
	
	if ( done == 0 ) {
		eventloop_poll_ctor();
		eventloop_epoll_ctor();
		done = 1;
	}
 
	/* setup logfile */
	open_logfile();
	logtime_tissue("starting tissue server");
 
	/* allocate memory */
	if(!(tissue = calloc(1, sizeof(Tissue))))
		logfatal_tissue("couldn't allocate memory for tissue");
 
	if ( !nbio_init(&tissue->nbio, NULL) )
		logfatal_tissue("couldn't initialize nonblocking I/O");
 
	tissue->num_antigen = num_antigen;
	if(tissue->num_antigen)
		if(!(tissue->antigen = calloc(tissue->num_antigen, sizeof(Antigen *))))
			logfatal_tissue("couldn't allocate memory for antigen");
	tissue->num_cytokines = num_cytokines;
	if(tissue->num_cytokines) {
		if(!(tissue->cytokine = calloc(tissue->num_cytokines, \
				sizeof(Cytokine *))))
			logfatal_tissue("couldn't allocate memory for cytokines");
		if(!(tissue->cytokine_type = calloc(tissue->num_cytokines, \
				sizeof(int))))
			logfatal_tissue("couldn't allocate memory for cytokine types");
		for(i = 0; i < tissue->num_cytokines; i++) {
			tissue->cytokine[i] = init_cytokine();
			tissue->cytokine[i]->id = i;
			tissue->cytokine_type[i] = DEF_CYTOKINE_TYPE;
		}
	}
	tissue->num_cells = num_cells;
	if(tissue->num_cells)
		if(!(tissue->cell = calloc(tissue->num_cells, sizeof(Cell *))))
			logfatal_tissue("couldn't allocate memory for cells");
 
	/* capture INT to exit cleanly */
	tcopy = tissue;
	siga.sa_handler = sigint_handler;
	sigemptyset(&siga.sa_mask);
	siga.sa_flags = SA_RESTART;
	if(sigaction(SIGINT, &siga, NULL) == -1)
		logfatal_tissue("couldn't setup sigint handler");
 
	/* set defaults */
	tissue->log = 0;  /* no logging of server */
	tissue->cytokine_decay_rate = DEF_DECAY_RATE;  /* cytokine decay rate */
	tissue->antigen_multiplier = 1;  /* how many copies of incoming antigen */
/*my change IPPORTO_stpc*/
	l = listener_inet(IPPROTO_TCP, INADDR_ANY,
				(server_port) ? server_port : TS_DEFAULT_PORT,
				accept_cb, tissue);
	if ( l == NULL )
		logfatal_tissue("couldn't create remote server socket");
	tissue->remote_svr = l;
	listener_add(&tissue->nbio, l);
 
	if ( sockname ) {
		l = listener_unix(sockname, accept_cb, tissue);
		if ( l == NULL )
			logfatal_tissue("couldn't create local server socket");
 
		tissue->local_svr = l;
		listener_add(&tissue->nbio, l);
	}
 
	INIT_LIST_HEAD(&tissue->clients);
	INIT_LIST_HEAD(&tissue->timers);
	return tissue;
}
.
.
.
                                              

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to tlr I added

char *sockname="";

and the error was gone of course :) but I'm not sure if it will function correctly
 

I used the latest versions as the author recommended

I'm testing it right now but I got these warning , I'll look into them. and then ask you of course :)

>> I'm testing it right now but I got these warning , I'll look into them. and then ask you of course :)

Good :)

hello,

Infinity08, you were right there was some missing functions in libtissue that I found in previous versions :)

now I run the project and I got the following message :

------------------------------------------------------------------------------------------------------------------------------
Running "C:\cygwin\bin\make.exe  -f Makefile CONF=Debug clean" in C:\Documents and Settings\R AM\My Documents\NetBeansProjects\Application_1

rm -f *.o *~ tlr-lt tissue.log

Clean successful. Exit value 0.

Running "C:\cygwin\bin\make.exe  -f Makefile CONF=Debug" in C:\Documents and Settings\R AM\My Documents\NetBeansProjects\Application_1

gcc -Wall -O2 -g  -lpthread -ltissue -lm -o tlr-lt tlr-lt.c
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -ltissue
collect2: ld returned 1 exit status
make: *** [tlr-lt] Error 1

Build failed. Exit value 2.
------------------------------------------------------------------------------------------------------------------------------
 

>> Infinity08, you were right there was some missing functions in libtissue that I found in previous versions :)

So, I assume you're now using the right version of the library ?


>> cannot find -ltissue

is libtissue.a where it's supposed to be ?

I hope I'm using the correct version now

>> is libtissue.a where it's supposed to be ?

I'm not sure I understand your question
do you mean the program is expecting to find a file in some folder called libtissue.a? because I don't have such a folder

The tissue library (probably named libtissue.a) - where did you put it ?

I add it in the same folder as project folder

>> I add it in the same folder as project folder

What's its name ?

the folder name: Application_1

>> the folder name: Application_1

No, the compiled library itself. It's one file (likely named libtissue.a), which is the result of compiling the library.

I didn't use the library as a library. I took the files and add it directly to the project folder

so there is no complied library

>> so there is no complied library

Right, so then you also don't have to link against it :)

sorry, but I don't understand! does that mean that there is no error?

then what does the message mean? why did it stop running?

 

OK, I think I'm starting to understand :)

I have to change the makefile, right?

I did some changing (by guessing of course), but got an "undefined reference" errors

I know that I'm asking too much, but I really need to run this program :(

I really appreciate your help

CFLAGS=-Wall -O2 -g
CINCS=
CLIBS=-lpthread -ltissue -lm
CINCS_STATIC=-I${HOME}/opt/libtissue
CLIBS_STATIC=-lm -L${HOME}/opt/libtissue
 
all: tlr-lt 
 
tlr-lt:
	gcc $(CFLAGS) $(CINCS) $(CLIBS) -o tlr-lt tlr-lt.c
 
tlr-lt-static:
	gcc $(CFLAGS) $(CINCS_STATIC) $(CLIBS_STATIC) -o tlr-lt tlr-lt.c
 
install: uninstall
	install tlr-lt $(HOME)/bin
 
uninstall:
	rm -f $(HOME)/bin/tlr-lt
 
clean:
	rm -f *.o *~ tlr-lt tissue.log
                                              

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>> CLIBS=-lpthread -ltissue -lm

This is the line that specifies the libraries the code should be linked to. Just take out the tissue library, and rebuild it.

that is what I did before but I got an undefined reference errors

e.g.
/cygdrive/c/Documents and Settings/R AM/My Documents/NetBeansProjects/Application_1/tlr-lt.c:81: undefined reference to `_writelog_tissue'

>> undefined reference to `_writelog_tissue'

Since you're not building the library as a library, you'll have to compile it as separate object files, and then link all of those into your application ...

(note that it would have been easier to just build the library - it saves you a lot of this trouble)

OK, I'll add it as a library as you  advise.

hello again,

here is what I've been doing:
I create a project named tissue and successfully complied it
I created another project named tlr-lt and add tissue as its library

but when I build tlr-lt I got the same error
------------------------------------------------------------------------------------------------------------------------------
Running "C:\cygwin\bin\make.exe  -f Makefile CONF=Debug" in C:\Documents and Settings\R AM\My Documents\NetBeansProjects\tlr-lt

gcc -Wall -O2 -g  -lpthread -ltissue -lm -o tlr-lt tlr-lt.c
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -ltissue
collect2: ld returned 1 exit status
make: *** [tlr-lt] Error 1

Build failed. Exit value 2.
------------------------------------------------------------------------------------------------------------------------------

so I tried removing ltissue from
 CLIBS=-lpthread -ltissue -lm

and I got a previous error
-----------------------------------------------------------------------------------------------------------------------------
Running "C:\cygwin\bin\make.exe  -f Makefile CONF=Debug" in C:\Documents and Settings\R AM\My Documents\NetBeansProjects\tlr-lt

gcc -Wall -O2 -g  -lpthread -lm -o tlr-lt tlr-lt.c
/cygdrive/c/DOCUME~1/RAM~1/LOCALS~1/Temp/cclYyGob.o: In function `probe_tissue':
/cygdrive/c/Documents and Settings/R AM/My Documents/NetBeansProjects/tlr-lt/tlr-lt.c:81: undefined reference to `_writelog_tissue'
.
.
.
------------------------------------------------------------------------------------------------------------------------------

:(

What's the name of the compiled tissue library, and where is it located ?

libtissue.a  is located in

C:\Documents and Settings\R AM\My Documents\NetBeansProjects\tissue\dist\Debug\Cygwin-Windows

>> libtissue.a  is located in

And is that directory in your library search path ? Try placing libtissue.a in the project folder instead and see what happens.

yes it is in project library path

I'll try what you suggested (placing libtissue.a in the project folder instead), and give you the feed back

thank you :)

What do you mean by "project" btw ? Aren't you just using the makefiles ?

I mean by project: source and header files

to run the code I build the project, that is what I mean

ok. I thought you were using some kind of IDE ;) Let me know what the progress is on http:#24618229

I am o-o

i'm using NetBeans IDE with cygwin compiler. is it what causing run problems? should I get back to visual studio ?

I tried placing libtissue.a in project folder but no change ( cannot find -ltissue )

>>try running the compilation command from the command line. ie. navigate to the directory that contains both tlr-lt.c and libtissue.a, and then execute :

        gcc -Wall -O2 -g  -lpthread -ltissue -lm -o tlr-lt tlr-lt.c

got this message

'gcc' is not recognized as an internal or external command, operable program or batch file.

That means your PATH variable isn't set correctly. Just add the path where gcc is installed. Something like :

        C:\path\to\gcc ...

Alternatively, you can always make sure that the PATH variable contains the directory that holds the gcc executable.

I did add it to the PATH variable but nothing changes

I'll give up here. first, because I have to complete a report about this before wed. and second I have consumed your time.

thank you

thank you so much. I really appreciate your help :)