error: first parameter of 'main' (argument count) must be of type 'int'

[lamanda0227]

Hi, I was trying to compile the pairwise hierarchical model following the instruction. But when I was running the make command, it is always generating the error ./util.h:10:10: fatal error: 'cblas.h file not found”.
I tried to include a cflag indicating where the cblas.h file is in the CLAPACK 3.2.1 folder, but it is generating even more errors.

phm.c:209:106: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                fprintf(stderr, "NaN is found at (%d, %d) element! (replaced by 0.0)\n", i, j);
                                                                  ~~                                     ^
                                                                  %ld
phm.c:209:109: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                fprintf(stderr, "NaN is found at (%d, %d) element! (replaced by 0.0)\n", i, j);
                                                                      ~~                                    ^
                                                                      %ld
phm.c:272:79: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
        if(lkhd<(-1e20)){fprintf(stderr, "Inf produced at line %d (%lf %lf %lf) \n", i+1,  y[i*H+0], y[i*H+1], y[i*H+2]); return 0.0;}
                                                               ~~                    ^~~
                                                               %ld
phm.c:273:87: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
        if(isnan(lkhd)>0){fprintf(stderr, "NaN produced at line %d (%lf %lf %lf) \n", i+1,  y[i*H+0], y[i*H+1], y[i*H+2]); return 0.0;}
                                                                ~~                    ^~~
                                                                %ld
phm.c:315:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
phm.c:476:69: warning: format specifies type 'int *' but the argument has type 'long *' [-Wformat]
            sscanf(s+mtot, "%c%ld%n", &(type[0][i]), &(nexp[0][i]), &m);
                                 ~~                                 ^~
phm.c:536:1: warning: return type of 'main' is not 'int' [-Wmain-return-type]
long main(long argc, char** argv){
^
phm.c:536:1: note: change return type to 'int'
long main(long argc, char** argv){
^~~~
int
phm.c:536:6: error: first parameter of 'main' (argument count) must be of type 'int'
long main(long argc, char** argv){
     ^
7 warnings and 1 error generated.
make: *** [phm.o] Error 1

I’m wondering what should I do or am I doing anything wrong?

Thanks very much!

Amanda

[natsuhiko]

Hi Amanda,

I uploaded the latest C codes. Could you download and compile again?

Sorry for the inconvenience.

Best,
Natsuhiko

[lamanda0227]

Hi Natsuhiko,

I have downloaded the code and tried to compile.
But it is generating this error:

Undefined symbols for architecture x86_64:
  "__gfortran_st_write", referenced from:
      _xerbla_ in liblapack.a(xerbla.o)
  "__gfortran_st_write_done", referenced from:
      _xerbla_ in liblapack.a(xerbla.o)
  "__gfortran_stop_string", referenced from:
      _xerbla_ in liblapack.a(xerbla.o)
  "__gfortran_string_len_trim", referenced from:
      _xerbla_ in liblapack.a(xerbla.o)
  "__gfortran_transfer_character_write", referenced from:
      _xerbla_ in liblapack.a(xerbla.o)
  "__gfortran_transfer_integer_write", referenced from:
      _xerbla_ in liblapack.a(xerbla.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: *** [phm] Error 1

I wonder if it is because I did not install the libraries properly? (since I haven't really used C before, so did not install any libraries bedsides the ones required for phm)

For the CFLAGS, I was using:

CFLAGS="-I/usr/local/include -I/PATH/TO/htslib-1.9 -I/PATH/TO/CLAPACK-3.2.1/INCLUDE -I//PATH/TO/CLAPACK-3.2.1/BLAS/WRAP -I/PATH/TO/gsl-2.6/include/gsl

where /BLAS/WRAP contains the cblas.h and /gsl-2.6/include/gsl include all the gsl_*.h

For the LDFLAGS, I was using

"-L/usr/local/lib -L/PATH/TO/htslib-1.9 -L/PATH/TO/CLAPACK-3.2.1 -L/PATH/TO/gsl-2.6/lib"

for /PATH/TO/CLAPACK-3.2.1/, I copied the libf2c.a and /PATH/TO/gsl-2.6/lib is where the gsl libs (libgsl.a libgslcblas.a) are at.

Thank you so much for your time, really appreciate your help!

Best,
Amanda

[natsuhiko]

Hi Amanda,

You cannot copy the archived files (*.a files) once you installed. In order to install them in a desired location, you need to set the prefix option when you compile CLAPACK and GSL. Please check e.g., https://askubuntu.com/questions/891835/what-does-prefix-do-exactly-when-used-in-configure, to install CLAPACK and GSL in an appropriate locations.

Best regards,
Natsuhiko

[lamanda0227]

I'll check it out. Thank you very much!