compile problem: comparison between pointer and zero character constant [-Wpointer-compare]

[taoqxtaozi]

Hi,

When I compile the C files, I get such warnings:

/root/miniconda3/bin/x86_64-conda-linux-gnu-cc -std=c99 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /root/miniconda3/include -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /root/miniconda3/include -I inc -I ../lib/  -c impl/*.c
impl/bioioC.c: In function 'parseInt':
impl/bioioC.c:268:23: warning: comparison between pointer and zero character constant [-Wpointer-compare]
  268 |         while(*string != '\0' && !isspace(**string)) {
      |                       ^~
impl/bioioC.c:268:15: note: did you mean to dereference the pointer?
  268 |         while(*string != '\0' && !isspace(**string)) {
      |               ^
impl/bioioC.c: In function 'parseFloat':
impl/bioioC.c:289:23: warning: comparison between pointer and zero character constant [-Wpointer-compare]
  289 |         while(*string != '\0' && !isspace(**string)) {
      |                       ^~
impl/bioioC.c:289:15: note: did you mean to dereference the pointer?
  289 |         while(*string != '\0' && !isspace(**string)) {
      |               ^
impl/bioioC.c: In function 'parseString':
impl/bioioC.c:310:23: warning: comparison between pointer and zero character constant [-Wpointer-compare]
  310 |         while(*string != '\0' && !isspace(**string)) {
      |                       ^~
impl/bioioC.c:310:15: note: did you mean to dereference the pointer?
  310 |         while(*string != '\0' && !isspace(**string)) {
      |               ^
impl/sonLibList.c: In function 'st_list_sortP':
impl/sonLibList.c:258:13: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic]
  258 |     return ((int (*)(const void *, const void *))fn)(*((char **)a), *((char **)b));
      |             ^
impl/sonLibList.c: In function 'stList_sort':
impl/sonLibList.c:262:76: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic]
  262 |     sort_r(list->list, stList_length(list), sizeof(void *), st_list_sortP, (void *)cmpFn);
      |                                                                            ^
impl/sonLibList.c: In function 'st_list_sort2P':
impl/sonLibList.c:267:56: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic]
  267 |     int (*cmpFn)(const void *, const void *, void *) = (int (*)(const void *, const void *, void *))(((void **)extra)[0]);
      |                                                        ^
impl/sonLibList.c: In function 'stList_sort2':
impl/sonLibList.c:273:24: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic]
  273 |     void *extra[2] = { (void *)cmpFn, (void *)extraArg };

and finally when I try commands in ./bin, I get Segmentation fault. I think it's the pointer problem, but I see many platforms and get no solutions.

Thanks!

[glennhickey]

This version of sonlib is better-maintained https://github.com/ComparativeGenomicsToolkit/sonLib

[taoqxtaozi]

This version of sonlib is better-maintained https://github.com/ComparativeGenomicsToolkit/sonLib

Hi, Thanks for your quick reply! I follow the instruction on https://github.com/ComparativeGenomicsToolkit/cactus/blob/genome_research_alignment_paper/doc/INSTALL.txt And I notice that the next step is "(2) Download and install jobTree. See https://github.com/benedictpaten/jobTree ", and in your jobtree website, it says reqiurement is Python 2.5 or later, but less than 3.0, but the sonLib you point to me is based on python3, also in https://github.com/ComparativeGenomicsToolkit, I don't find jobTree folder, so does that work? I want to install and run the cactus that is not progressive one.

Thanks a lot!

[glennhickey]

I want to install and run the cactus that is not progressive one.

Why?

[taoqxtaozi]

I want to install and run the cactus that is not progressive one.

Why?

Because I want to only align four taxa without the guide tree.

[glennhickey]

Your best bet is to use cactus. Either don't give it a guide tree, or specify a star tree.

[taoqxtaozi]

Your best bet is to use cactus. Either don't give it a guide tree, or specify a star tree.

ok, thanks!