meme TEST FAILED

[Rocky Parida]

Hi All
I am trying to install meme_4.10.2 on my cluster account.
It is failing for just meme tests but passing for everything else.
I was looking for an attachment button but couldn't find to attach my make.log file.
Please let me know how I can do it so I can provide you with my log file attachment.

I have also tried meme_4.11.0 but it fails during make.

After troubleshooting for some time I think it may be the GCC compiler that is not compatible to this program script.

It is complaining about NAN (Not a Number) not declared but the script has #include <math.h> added on the top.

I edited all the scripts in the src folder of this program and added this line to declare NAN before assignment as follows:

#define NAN (0.0/0.0)

Now it is complaining about :

mast.c: In function 'main':

mast.c:2249: warning: implicit declaration of function 'WIFEXITED'

mast.c:2249: warning: implicit declaration of function 'WEXITSTATUS'

 

Then these errors happen:

mast-mast.o: In function `main':

mast.c:(.text+0x52b8): undefined reference to `WIFEXITED'

mast.c:(.text+0x52c5): undefined reference to `WEXITSTATUS'

mast.c:(.text+0x546d): undefined reference to `WIFEXITED'

mast.c:(.text+0x547a): undefined reference to `WEXITSTATUS'

collect2: ld returned 1 exit status

make[4]: *** [mast] Error 1

make[4]: Leaving directory `/Users/mparida/Software/meme_4.11.0/src'

make[3]: *** [all-recursive] Error 1

make[3]: Leaving directory `/Users/mparida/Software/meme_4.11.0/src'

make[2]: *** [all] Error 2

make[2]: Leaving directory `/Users/mparida/Software/meme_4.11.0/src'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/Users/mparida/Software/meme_4.11.0'

make: *** [all] Error 2

 

and the installation quits.

Is there anything I can do to fix it, something simple?

Rocky

[Rocky Parida]

Also I checked and I have this gcc version 4.1.2 20080704 (Red Hat 4.1.2-55) installed on my account on the cluster.
Python 2.7.3 on my account on the cluster.
perl, v5.8.8 built for x86_64-linux-thread-multi on my account on the cluster.

[CharlesEGrant]

Hi Rocky,

I was looking for an attachment button but couldn't find to attach my make.log file.
Please let me know how I can do it so I can provide you with my log file attachment.

Just above the left hand side of the formatting toolbar are three links. The first link is “Attach a file”. It has a paper clip icon to the left of it. Click on that link and you’ll be prompted for the location of the file you want to attach.

After troubleshooting for some time I think it may be the GCC compiler that is not compatible to this program script.

We use GCC as our standard compiler here too, so I doubt that it's a problem with GCC in general.

Also I checked and I have this gcc version 4.1.2 20080704 (Red Hat 4.1.2-55) installed on my account on the cluster.

This may be the problem. GCC 4.1.2 is several years old, but the real problem is that Red Hat 4.1.2 is almost 19 years old! Or do you mean Red Hat Enterprise Linux 4.1.2? According to Wikipedia, Red Hat 4.1.2 would be running a kernel in the 2.0 series. There have been many important changes to the kernel since then, including changes in the interfaces to some system and C runtime library calls. 

 

Then these errors happen:
mast-mast.o: In function `main':
mast.c:(.text+0x52b8): undefined reference to `WIFEXITED'
mast.c:(.text+0x52c5): undefined reference to `WEXITSTATUS'

WIFEXITED and WEXITSTATUS are preprocessor constants defined in <sys/wait.h> which is a system header file. If these constants aren't being found it may because the <sys/wait.h> interface has changed over the years. You might look at the man page for wait():

man 2 wait

and see if it mentions WIFEXITED and WEXITSTATUS. If it doesn't, then the problem is the old version of the OS and C run time. If those constants are listed in the man page, then I'd double check that you didn't introduce an error when you added the NAN macro.

It may take quite a bit of work to get a relatively current version of the MEME Suite running on a version of the OS this old. Depending on the features you need it might actually be easier to use one of the older versions of MEME.

[Jorge Boucas]

Hi Rocky,

you can add 

#include <sys/wait.h>

to 

line 73 of 

src/mast.c

Best,

Jorge