Randfold installation problem

[dsperley]

Hi

I'm trying to install randfold2.0 as part of mirdeep. I've installed squid1.9g, and edited the randfold makefile to include the path of the squid1.9g directory. When I run make, I get the following warnings and errors:


Hydrogen-2:randfold-2.0 danielleperley$ make
gcc -O3 -I. -I/Users/danielleperley/squid-1.9g/ -L/Users/danielleperley/squid-1.9g/. -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid
randfold.c:64:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (c = *++argv[0])
~~^~~~~~~~~~~~
randfold.c:64:13: note: place parentheses around the assignment to silence this warning
while (c = *++argv[0])
^
( )
randfold.c:64:13: note: use '==' to turn this assignment into an equality comparison
while (c = *++argv[0])
^
==
randfold.c:89:2: warning: implicitly declaring library function 'strcpy' with type 'char *(char *, const char *)'
strcpy(seqfile,*argv);
^
randfold.c:89:2: note: please include the header <string.h> or explicitly provide a declaration for 'strcpy'
randfold.c:103:38: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)'
structure = malloc(sizeof(char) * (strlen(seq)+1));
^
randfold.c:103:38: note: please include the header <string.h> or explicitly provide a declaration for 'strlen'
randfold.c:147:3: warning: expression result unused [-Wunused-value]
free_arrays;
^~~~~~~~~~~
4 warnings generated.
Undefined symbols for architecture x86_64:
"_HairpinE", referenced from:
_fill_arrays in fold.o
_backtrack in fold.o
_stack_energy in fold.o
"_LoopEnergy", referenced from:
_fill_arrays in fold.o
_backtrack in fold.o
_stack_energy in fold.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [randfold] Error 1

Do I need to link another library? Any ideas/suggestions?

[ehutchins]

I'm having the same issues. I fixed 3/4 warnings by:

1) adding #include<string.h> to the header in the randfold.c file. This defines the strcpy and strncpy library functions (see a related stackoverflow thread here).

2) editing line 64 of randfold.c to have '==' as requested: while (c == *++argv[0])

With these fixes, I can run it on my Ubuntu Linux machine without issue, but I am still getting a similar error message on my OS 10.9.5 (Xcode 5.1.1) machine. I browsed some C developer forums and see that the fix could be multiple issues, and I haven't figured it out yet. I'm not a C developer myself so it's a bit beyond me, but I'll let you know if I find a full solution.




Error after incorporating the above fix:
$ make
gcc -c energy_par.c
gcc -c params.c
gcc -c fold.c
gcc -c fold_vars.c
gcc -c utils.c
gcc -O3 -I. -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid
randfold.c:148:3: warning: expression result unused [-Wunused-value]
free_arrays;
^~~~~~~~~~~
1 warning generated.
Undefined symbols for architecture x86_64:
"_HairpinE", referenced from:
_fill_arrays in fold.o
_backtrack in fold.o
_stack_energy in fold.o
"_LoopEnergy", referenced from:
_fill_arrays in fold.o
_backtrack in fold.o
_stack_energy in fold.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [randfold] Error 1