yjx1217 commented 6 years ago

Hello,

I encountered the following error when compiling smartdenovo. Could you help to diagnose what might have caused this problem? Thanks! .... wtzmo.c:91:1: note: in expansion of macro ‘define_list’ define_list(pbreadv, pbread_t); ^~~ wtzmo.c: In function ‘push_long_read_wtzmo’: wtzmo.c:210:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(ptr, name, name_len); ^~ wtzmo.c:210:2: note: include ‘’ or provide a declaration of ‘memcpy’ wtzmo.c: In function ‘thread_midx_func’: wtzmo.c:247:1: warning: incompatible implicit declaration of built-in function ‘memset’ memset(&U, 0, sizeof(hzmh_t)); ^~ wtzmo.c:247:1: note: include ‘’ or provide a declaration of ‘memset’ wtzmo.c: In function ‘thread_mzmo_func’: wtzmo.c:789:1: warning: incompatible implicit declaration of built-in function ‘memset’ memset(&SEED[0], 0, sizeof(wt_seed_t)); ^~ wtzmo.c:789:1: note: include ‘’ or provide a declaration of ‘memset’ wtzmo.c:1058:15: warning: implicit declaration of function ‘strdup’ [-Wimplicit-function-declaration] HIT.cigar = strdup(cigar_str->string); ^~ wtzmo.c:1058:15: warning: incompatible implicit declaration of built-in function ‘strdup’ In file included from wtzmo.c:25:0: wtzmo.c: In function ‘main’: file_reader.h:97:30: warning: implicit declaration of function ‘ref_VStrv’; did you mean ‘ref_diagv’? [-Wimplicit-function-declaration]

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:28: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:28: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:53: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:79: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1766:43: note: in expansion of macro ‘get_col_str’ if((pb1 = kv_get_cuhash(wt->rdname2id, get_col_str(fr, 0))) == 0xFFFFFFFFU) continue; ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1767:43: note: in expansion of macro ‘get_col_str’ if((pb2 = kv_get_cuhash(wt->rdname2id, get_col_str(fr, 1))) == 0xFFFFFFFFU) continue; ^~~ Makefile:33: recipe for target 'wtzmo' failed make: *** [wtzmo] Error 1

Best, Jia-Xing

ruanjue commented 6 years ago

Hi, Jia-Xing

I guess you can fix it from https://github.com/ruanjue/wtdbg/issues/4

Otherwise, please tell me again.

Best, Jue

yjx1217 commented 6 years ago

Hi Jue, I worked around that problem by switching to an alternative server for my task. But now since I need to work with my main server, I need to reopen this issue to look for a formal solution. I have checked the the thread that you mentioned and did similar check. But since what I got is a bit different from what the other user described in that thread, so I might need you further help for this.

Here is what I got after typing gcc -v and cpp -v:

gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper OFFLOAD_TARGET_NAMES=hsa:nvptx-none Target: x86_64-suse-linux Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,ada,go --enable-offload-targets=hsa,nvptx-none=/usr/nvptx-none, --without-cuda-driver --enable-checking=release --disable-werror --with-gxx-include-dir=/usr/include/c++/7 --enable-ssp --disable-libssp --disable-libvtv --disable-libcc1 --enable-plugin --with-bugurl=http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --with-default-libstdcxx-abi=gcc4-compatible --enable-version-specific-runtime-libs --with-gcc-major-version-only --enable-linker-build-id --enable-linux-futex --enable-gnu-indirect-function --program-suffix=-7 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux Thread model: posix gcc version 7.3.0 (SUSE Linux)

cpp -v Using built-in specs. COLLECT_GCC=cpp COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper OFFLOAD_TARGET_NAMES=hsa:nvptx-none Target: x86_64-suse-linux Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,ada,go --enable-offload-targets=hsa,nvptx-none=/usr/nvptx-none, --without-cuda-driver --enable-checking=release --disable-werror --with-gxx-include-dir=/usr/include/c++/7 --enable-ssp --disable-libssp --disable-libvtv --disable-libcc1 --enable-plugin --with-bugurl=http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --with-default-libstdcxx-abi=gcc4-compatible --enable-version-specific-runtime-libs --with-gcc-major-version-only --enable-linker-build-id --enable-linux-futex --enable-gnu-indirect-function --program-suffix=-7 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux Thread model: posix gcc version 7.3.0 (SUSE Linux)

Thanks!

Best, Jia-Xing

ruanjue commented 6 years ago

Let us first check the issue in https://github.com/ruanjue/wtdbg/issues/4 . 1, echo $CPATH 2, cpp -v, you post partial text in last message

Also, please make sure the compilation error was the same with the first message you had reported.

Best, Jue

yjx1217 commented 6 years ago

Hi Jue,

Thanks for the quick reply. See the following for details:

jxyue2@professorx:~> echo $CPATH

jxyue2@professorx:~> cpp -v Using built-in specs. COLLECT_GCC=cpp COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper OFFLOAD_TARGET_NAMES=hsa:nvptx-none Target: x86_64-suse-linux Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,ada,go --enable-offload-targets=hsa,nvptx-none=/usr/nvptx-none, --without-cuda-driver --enable-checking=release --disable-werror --with-gxx-include-dir=/usr/include/c++/7 --enable-ssp --disable-libssp --disable-libvtv --disable-libcc1 --enable-plugin --with-bugurl= http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --with-default-libstdcxx-abi=gcc4-compatible --enable-version-specific-runtime-libs --with-gcc-major-version-only --enable-linker-build-id --enable-linux-futex --enable-gnu-indirect-function --program-suffix=-7 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux Thread model: posix gcc version 7.3.0 (SUSE Linux)

And here is the full compilation record:

jxyue2@professorx> make gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o pairaln file_reader.c ksw.c pairaln.c -lm -lpthread In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.c: In function ‘popen_m_filereader’: file_reader.c:32:47: warning: incompatible implicit declaration of built-in function ‘strlen’ fc->filename = (char)malloc(sizeof(char) (strlen(filenames[i])+1)); ^~ file_reader.c:32:47: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:33:3: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:33:3: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c: In function ‘fopen_m_filereader’: file_reader.c:66:13: warning: incompatible implicit declaration of built-in function ‘strlen’ } else if(strlen(filenames[i]) > 3 && strcmp(filenames[i] + strlen(filenames[i]) - 3, ".gz") == 0){ ^~ file_reader.c:66:13: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:70:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, cmd); ^~ file_reader.c:70:4: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c:76:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:76:4: note: include ‘’ or provide a declaration of ‘strcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.c: In function ‘fopen_filereader2’: file_reader.c:114:20: warning: incompatible implicit declaration of built-in function ‘strlen’ filename = alloca(strlen(prefix) + strlen(postfix) + 1); ^ file_reader.c:114:20: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:116:2: warning: incompatible implicit declaration of built-in function ‘strcat’ strcat(filename, prefix); ^~ file_reader.c:116:2: note: include ‘’ or provide a declaration of ‘strcat’ file_reader.c: In function ‘string_filereader’: file_reader.c:131:14: warning: incompatible implicit declaration of built-in function ‘strlen’ fr->size = strlen(string); ^~ file_reader.c:131:14: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c: In function ‘fread_line2’: file_reader.c:190:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(fr->buffer, fr->buffer + fr->ptr, fr->size - fr->ptr); ^~~ file_reader.c:190:5: note: include ‘’ or provide a declaration of ‘memmove’ file_reader.c: In function ‘init_delimiters’: file_reader.c:246:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(delimiters, 0, sizeof(int) 128); ^~ file_reader.c:246:2: note: include ‘’ or provide a declaration of ‘memset’ file_reader.c:247:8: warning: incompatible implicit declaration of built-in function ‘strlen’ len = strlen(expr); ^~ file_reader.c:247:8: note: include ‘’ or provide a declaration of ‘strlen’ In file included from dna.h:27:0, from pairaln.c:20: bitvec.h: In function ‘zeros_bitvec’: bitvec.h:192:48: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void zeros_bitvec(BitVec bitv){ memset(bitv->bits, 0, bitv->n_cap / 8); } ^~ bitvec.h:192:48: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘ones_bitvec’: bitvec.h:194:47: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void ones_bitvec(BitVec bitv){ memset(bitv->bits, 0xFFU, bitv->n_cap / 8); } ^~ bitvec.h:194:47: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘encap_bitvec’: bitvec.h:214:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(((void)bitv->bits) + cap / 8, 0, (bitv->n_cap - cap) / 8 + 8); ^~ bitvec.h:214:2: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘recap_bitvec’: bitvec.h:223:3: warning: incompatible implicit declaration of built-in function ‘memset’ memset(((void)bitv->bits) + bitv->n_cap / 8, 0, (new_cap - bitv->n_cap) / 8 + 8); ^~ bitvec.h:223:3: note: include ‘’ or provide a declaration of ‘memset’ In file included from pairaln.c:20:0: dna.h: In function ‘init_basebank’: dna.h:334:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits, 0, 8 (bnk->cap / 32)); ^~ dna.h:334:2: note: include ‘’ or provide a declaration of ‘memset’ dna.h: In function ‘encap_basebank’: dna.h:355:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits + (old / 32), 0, (bnk->cap - old) / 4); ^~ dna.h:355:2: note: include ‘’ or provide a declaration of ‘memset’ dna.h: In function ‘clear_basebank’: dna.h:359:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits, 0, ((bnk->size + 31) / 32) 8); ^~ dna.h:359:2: note: include ‘’ or provide a declaration of ‘memset’ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from pairaln.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from pairaln.c:22:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from pairaln.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from pairaln.c:22:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from pairaln.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from pairaln.c:22:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtpre file_reader.c wtpre.c -lm -lpthread In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.c: In function ‘popen_m_filereader’: file_reader.c:32:47: warning: incompatible implicit declaration of built-in function ‘strlen’ fc->filename = (char)malloc(sizeof(char) (strlen(filenames[i])+1)); ^~ file_reader.c:32:47: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:33:3: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:33:3: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c: In function ‘fopen_m_filereader’: file_reader.c:66:13: warning: incompatible implicit declaration of built-in function ‘strlen’ } else if(strlen(filenames[i]) > 3 && strcmp(filenames[i] + strlen(filenames[i]) - 3, ".gz") == 0){ ^~ file_reader.c:66:13: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:70:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, cmd); ^~ file_reader.c:70:4: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c:76:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:76:4: note: include ‘’ or provide a declaration of ‘strcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.c: In function ‘fopen_filereader2’: file_reader.c:114:20: warning: incompatible implicit declaration of built-in function ‘strlen’ filename = alloca(strlen(prefix) + strlen(postfix) + 1); ^ file_reader.c:114:20: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:116:2: warning: incompatible implicit declaration of built-in function ‘strcat’ strcat(filename, prefix); ^~ file_reader.c:116:2: note: include ‘’ or provide a declaration of ‘strcat’ file_reader.c: In function ‘string_filereader’: file_reader.c:131:14: warning: incompatible implicit declaration of built-in function ‘strlen’ fr->size = strlen(string); ^~ file_reader.c:131:14: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c: In function ‘fread_line2’: file_reader.c:190:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(fr->buffer, fr->buffer + fr->ptr, fr->size - fr->ptr); ^~~ file_reader.c:190:5: note: include ‘’ or provide a declaration of ‘memmove’ file_reader.c: In function ‘init_delimiters’: file_reader.c:246:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(delimiters, 0, sizeof(int) 128); ^~ file_reader.c:246:2: note: include ‘’ or provide a declaration of ‘memset’ file_reader.c:247:8: warning: incompatible implicit declaration of built-in function ‘strlen’ len = strlen(expr); ^~ file_reader.c:247:8: note: include ‘’ or provide a declaration of ‘strlen’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from wtpre.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtpre.c:20:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from wtpre.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtpre.c:20:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from wtpre.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtpre.c:20:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ wtpre.c: In function ‘main’: wtpre.c:116:32: warning: implicit declaration of function ‘strncmp’ [-Wimplicit-function-declaration] if(lst_tag->size == size && strncmp(lst_tag->string, seq->tag.string, size) == 0){ ^~~ gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtcyc file_reader.c ksw.c wtcyc.c -lm -lpthread In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.c: In function ‘popen_m_filereader’: file_reader.c:32:47: warning: incompatible implicit declaration of built-in function ‘strlen’ fc->filename = (char)malloc(sizeof(char) (strlen(filenames[i])+1)); ^~ file_reader.c:32:47: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:33:3: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:33:3: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c: In function ‘fopen_m_filereader’: file_reader.c:66:13: warning: incompatible implicit declaration of built-in function ‘strlen’ } else if(strlen(filenames[i]) > 3 && strcmp(filenames[i] + strlen(filenames[i]) - 3, ".gz") == 0){ ^~ file_reader.c:66:13: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:70:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, cmd); ^~ file_reader.c:70:4: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c:76:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:76:4: note: include ‘’ or provide a declaration of ‘strcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.c: In function ‘fopen_filereader2’: file_reader.c:114:20: warning: incompatible implicit declaration of built-in function ‘strlen’ filename = alloca(strlen(prefix) + strlen(postfix) + 1); ^ file_reader.c:114:20: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:116:2: warning: incompatible implicit declaration of built-in function ‘strcat’ strcat(filename, prefix); ^~ file_reader.c:116:2: note: include ‘’ or provide a declaration of ‘strcat’ file_reader.c: In function ‘string_filereader’: file_reader.c:131:14: warning: incompatible implicit declaration of built-in function ‘strlen’ fr->size = strlen(string); ^~ file_reader.c:131:14: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c: In function ‘fread_line2’: file_reader.c:190:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(fr->buffer, fr->buffer + fr->ptr, fr->size - fr->ptr); ^~~ file_reader.c:190:5: note: include ‘’ or provide a declaration of ‘memmove’ file_reader.c: In function ‘init_delimiters’: file_reader.c:246:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(delimiters, 0, sizeof(int) 128); ^~ file_reader.c:246:2: note: include ‘’ or provide a declaration of ‘memset’ file_reader.c:247:8: warning: incompatible implicit declaration of built-in function ‘strlen’ len = strlen(expr); ^~ file_reader.c:247:8: note: include ‘’ or provide a declaration of ‘strlen’ In file included from dna.h:27:0, from kswx.h:24, from wtcyc.c:20: bitvec.h: In function ‘zeros_bitvec’: bitvec.h:192:48: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void zeros_bitvec(BitVec bitv){ memset(bitv->bits, 0, bitv->n_cap / 8); } ^~ bitvec.h:192:48: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘ones_bitvec’: bitvec.h:194:47: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void ones_bitvec(BitVec bitv){ memset(bitv->bits, 0xFFU, bitv->n_cap / 8); } ^~ bitvec.h:194:47: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘encap_bitvec’: bitvec.h:214:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(((void)bitv->bits) + cap / 8, 0, (bitv->n_cap - cap) / 8 + 8); ^~ bitvec.h:214:2: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘recap_bitvec’: bitvec.h:223:3: warning: incompatible implicit declaration of built-in function ‘memset’ memset(((void)bitv->bits) + bitv->n_cap / 8, 0, (new_cap - bitv->n_cap) / 8 + 8); ^~ bitvec.h:223:3: note: include ‘’ or provide a declaration of ‘memset’ In file included from kswx.h:24:0, from wtcyc.c:20: dna.h: In function ‘init_basebank’: dna.h:334:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits, 0, 8 (bnk->cap / 32)); ^~ dna.h:334:2: note: include ‘’ or provide a declaration of ‘memset’ dna.h: In function ‘encap_basebank’: dna.h:355:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits + (old / 32), 0, (bnk->cap - old) / 4); ^~ dna.h:355:2: note: include ‘’ or provide a declaration of ‘memset’ dna.h: In function ‘clear_basebank’: dna.h:359:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits, 0, ((bnk->size + 31) / 32) 8); ^~ dna.h:359:2: note: include ‘’ or provide a declaration of ‘memset’ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from kswx.h:24, from wtcyc.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtcyc.c:23:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from kswx.h:24, from wtcyc.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtcyc.c:23:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from kswx.h:24, from wtcyc.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtcyc.c:23:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtmer file_reader.c wtmer.c -lm -lpthread In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.c: In function ‘popen_m_filereader’: file_reader.c:32:47: warning: incompatible implicit declaration of built-in function ‘strlen’ fc->filename = (char)malloc(sizeof(char) (strlen(filenames[i])+1)); ^~ file_reader.c:32:47: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:33:3: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:33:3: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c: In function ‘fopen_m_filereader’: file_reader.c:66:13: warning: incompatible implicit declaration of built-in function ‘strlen’ } else if(strlen(filenames[i]) > 3 && strcmp(filenames[i] + strlen(filenames[i]) - 3, ".gz") == 0){ ^~ file_reader.c:66:13: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:70:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, cmd); ^~ file_reader.c:70:4: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c:76:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:76:4: note: include ‘’ or provide a declaration of ‘strcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.c: In function ‘fopen_filereader2’: file_reader.c:114:20: warning: incompatible implicit declaration of built-in function ‘strlen’ filename = alloca(strlen(prefix) + strlen(postfix) + 1); ^ file_reader.c:114:20: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:116:2: warning: incompatible implicit declaration of built-in function ‘strcat’ strcat(filename, prefix); ^~ file_reader.c:116:2: note: include ‘’ or provide a declaration of ‘strcat’ file_reader.c: In function ‘string_filereader’: file_reader.c:131:14: warning: incompatible implicit declaration of built-in function ‘strlen’ fr->size = strlen(string); ^~ file_reader.c:131:14: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c: In function ‘fread_line2’: file_reader.c:190:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(fr->buffer, fr->buffer + fr->ptr, fr->size - fr->ptr); ^~~ file_reader.c:190:5: note: include ‘’ or provide a declaration of ‘memmove’ file_reader.c: In function ‘init_delimiters’: file_reader.c:246:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(delimiters, 0, sizeof(int) 128); ^~ file_reader.c:246:2: note: include ‘’ or provide a declaration of ‘memset’ file_reader.c:247:8: warning: incompatible implicit declaration of built-in function ‘strlen’ len = strlen(expr); ^~ file_reader.c:247:8: note: include ‘’ or provide a declaration of ‘strlen’ In file included from dna.h:27:0, from wtmer.c:20: bitvec.h: In function ‘zeros_bitvec’: bitvec.h:192:48: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void zeros_bitvec(BitVec bitv){ memset(bitv->bits, 0, bitv->n_cap / 8); } ^~ bitvec.h:192:48: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘ones_bitvec’: bitvec.h:194:47: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void ones_bitvec(BitVec bitv){ memset(bitv->bits, 0xFFU, bitv->n_cap / 8); } ^~ bitvec.h:194:47: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘encap_bitvec’: bitvec.h:214:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(((void)bitv->bits) + cap / 8, 0, (bitv->n_cap - cap) / 8 + 8); ^~ bitvec.h:214:2: note: include ‘’ or provide a declaration of ‘memset’ bitvec.h: In function ‘recap_bitvec’: bitvec.h:223:3: warning: incompatible implicit declaration of built-in function ‘memset’ memset(((void)bitv->bits) + bitv->n_cap / 8, 0, (new_cap - bitv->n_cap) / 8 + 8); ^~ bitvec.h:223:3: note: include ‘’ or provide a declaration of ‘memset’ In file included from wtmer.c:20:0: dna.h: In function ‘init_basebank’: dna.h:334:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits, 0, 8 (bnk->cap / 32)); ^~ dna.h:334:2: note: include ‘’ or provide a declaration of ‘memset’ dna.h: In function ‘encap_basebank’: dna.h:355:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits + (old / 32), 0, (bnk->cap - old) / 4); ^~ dna.h:355:2: note: include ‘’ or provide a declaration of ‘memset’ dna.h: In function ‘clear_basebank’: dna.h:359:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(bnk->bits, 0, ((bnk->size + 31) / 32) 8); ^~ dna.h:359:2: note: include ‘’ or provide a declaration of ‘memset’ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from wtmer.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtmer.c:22:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from wtmer.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtmer.c:22:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from dna.h:24, from wtmer.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from wtmer.c:22:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtzmo file_reader.c ksw.c wtzmo.c -lm -lpthread In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_read’: file_reader.h:194:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:194:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:195:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:195:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.h:198:5: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] if(strcmp(full_name, "-") == 0){ ^~ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_write’: file_reader.h:219:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:219:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:220:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:220:3: note: include ‘’ or provide a declaration of ‘memcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.h: In function ‘open_file_for_append’: file_reader.h:246:29: warning: incompatible implicit declaration of built-in function ‘strlen’ full_name = (char)alloca(strlen(name) + strlen(suffix) + 1); ^ file_reader.h:246:29: note: include ‘’ or provide a declaration of ‘strlen’ In file included from file_reader.c:20:0: file_reader.h:247:3: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(full_name, name, strlen(name)); ^~ file_reader.h:247:3: note: include ‘’ or provide a declaration of ‘memcpy’ file_reader.c: In function ‘popen_m_filereader’: file_reader.c:32:47: warning: incompatible implicit declaration of built-in function ‘strlen’ fc->filename = (char)malloc(sizeof(char) (strlen(filenames[i])+1)); ^~ file_reader.c:32:47: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:33:3: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:33:3: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c: In function ‘fopen_m_filereader’: file_reader.c:66:13: warning: incompatible implicit declaration of built-in function ‘strlen’ } else if(strlen(filenames[i]) > 3 && strcmp(filenames[i] + strlen(filenames[i]) - 3, ".gz") == 0){ ^~ file_reader.c:66:13: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:70:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, cmd); ^~ file_reader.c:70:4: note: include ‘’ or provide a declaration of ‘strcpy’ file_reader.c:76:4: warning: incompatible implicit declaration of built-in function ‘strcpy’ strcpy(fc->filename, filenames[i]); ^~ file_reader.c:76:4: note: include ‘’ or provide a declaration of ‘strcpy’ In file included from /usr/include/stdlib.h:492:0, from file_reader.h:23, from file_reader.c:20: file_reader.c: In function ‘fopen_filereader2’: file_reader.c:114:20: warning: incompatible implicit declaration of built-in function ‘strlen’ filename = alloca(strlen(prefix) + strlen(postfix) + 1); ^ file_reader.c:114:20: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c:116:2: warning: incompatible implicit declaration of built-in function ‘strcat’ strcat(filename, prefix); ^~ file_reader.c:116:2: note: include ‘’ or provide a declaration of ‘strcat’ file_reader.c: In function ‘string_filereader’: file_reader.c:131:14: warning: incompatible implicit declaration of built-in function ‘strlen’ fr->size = strlen(string); ^~ file_reader.c:131:14: note: include ‘’ or provide a declaration of ‘strlen’ file_reader.c: In function ‘fread_line2’: file_reader.c:190:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(fr->buffer, fr->buffer + fr->ptr, fr->size - fr->ptr); ^~~ file_reader.c:190:5: note: include ‘’ or provide a declaration of ‘memmove’ file_reader.c: In function ‘init_delimiters’: file_reader.c:246:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(delimiters, 0, sizeof(int) 128); ^~ file_reader.c:246:2: note: include ‘’ or provide a declaration of ‘memset’ file_reader.c:247:8: warning: incompatible implicit declaration of built-in function ‘strlen’ len = strlen(expr); ^~ file_reader.c:247:8: note: include ‘’ or provide a declaration of ‘strlen’ In file included from list.h:24:0, from wtzmo.c:20: ./string.h:56:20: error: expected ‘)’ before ‘VString’ define_list(VStrv, VString); ^~~ In file included from list.h:24:0, from wtzmo.c:20: ./string.h:251:71: error: unknown type name ‘VStrv’; did you mean ‘VString’? static inline string_size_t split_string(String str, char separator, VStrv vstrs){ ^~~~~

VString ./string.h:276:73: error: unknown type name ‘VStrv’; did you mean ‘VString’? static inline string_size_t split_vstring(VString str, char separator, VStrv vstrs, string_size_t cut){

^~~~~

VString In file included from wtzmo.c:20:0: list.h: In function ‘encap_list’: list.h:69:16: warning: implicit declaration of function ‘memset’ [-Wimplicit-function-declaration] if(mem_zeros) memset(ptr + cur_cap, 0, e_size (cap - cur_cap)); ^~ list.h:69:16: warning: incompatible implicit declaration of built-in function ‘memset’ list.h:69:16: note: include ‘’ or provide a declaration of ‘memset’ list.h: In function ‘zerosu8list’: list.h:191:56: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void zeros##list_type(list_type list){ memset(list->buffer, 0, list->cap sizeof(e_type)); } \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8t); ^~~~~~ list.h:191:56: note: include ‘’ or provide a declaration of ‘memset’ static inline void zeros##list_type(list_type list){ memset(list->buffer, 0, list->cap sizeof(e_type)); } \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘encap_and_zeros_u8list’: list.h:221:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(list->buffer + old, 0, (list->cap - old) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:221:2: note: include ‘’ or provide a declaration of ‘memset’ memset(list->buffer + old, 0, (list->cap - old) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘insert_u8list’: list.h:291:3: warning: implicit declaration of function ‘memmove’ [-Wimplicit-function-declaration] memmove(list->buffer + idx + 1, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:291:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + idx + 1, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:291:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + idx + 1, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘insert_array_u8list’: list.h:302:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + idx + size, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:302:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + idx + size, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:304:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(list->buffer + idx, es, size sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:304:2: note: include ‘’ or provide a declaration of ‘memcpy’ memcpy(list->buffer + idx, es, size sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘remove_u8list’: list.h:311:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + idx, list->buffer + idx + 1, (list->size - idx - 1) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:311:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + idx, list->buffer + idx + 1, (list->size - idx - 1) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘remove_array_u8list’: list.h:319:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + off, list->buffer + off + len, (list->size - off

len) * sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:319:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + off, list->buffer + off + len, (list->size - off
len) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘append_u8list’: list.h:370:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(list1->buffer + list1->size, list2->buffer, sizeof(e_type) list2->size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:370:2: note: include ‘’ or provide a declaration of ‘memcpy’ memcpy(list1->buffer + list1->size, list2->buffer, sizeof(e_type) list2->size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘append_array_u8list’: list.h:377:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(list1->buffer + list1->size, ary, sizeof(e_type) size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:377:2: note: include ‘’ or provide a declaration of ‘memcpy’ memcpy(list1->buffer + list1->size, ary, sizeof(e_type) size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘delete_u8list’: list.h:440:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + i - 1, list->buffer + i, (list->size - i) sizeof(e_type)); \ ^ list.h:487:1: note: in expansion of macro ‘define_list_ext’ define_list_ext(name, e_type, size_t, native_number_cmp); ^~~~~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h:440:5: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + i - 1, list->buffer + i, (list->size - i) sizeof(e_type)); \ ^ list.h:487:1: note: in expansion of macro ‘define_list_ext’ define_list_ext(name, e_type, size_t, native_number_cmp); ^~~~~~~ list.h:489:1: note: in expansion of macro ‘define_native_list’ define_native_list(u8list, uint8_t); ^~~~~~ list.h: In function ‘zerosu1v’: list.h:191:56: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void zeros##list_type(list_type list){ memset(list->buffer, 0, list->cap sizeof(e_type)); } \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8t); ^~~~~~ list.h:191:56: note: include ‘’ or provide a declaration of ‘memset’ static inline void zeros##list_type(list_type list){ memset(list->buffer, 0, list->cap sizeof(e_type)); } \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘encap_and_zeros_u1v’: list.h:221:2: warning: incompatible implicit declaration of built-in function ‘memset’ memset(list->buffer + old, 0, (list->cap - old) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:221:2: note: include ‘’ or provide a declaration of ‘memset’ memset(list->buffer + old, 0, (list->cap - old) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘insert_u1v’: list.h:291:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + idx + 1, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:291:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + idx + 1, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘insert_array_u1v’: list.h:302:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + idx + size, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:302:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + idx + size, list->buffer + idx, (list->size - idx) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:304:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(list->buffer + idx, es, size sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:304:2: note: include ‘’ or provide a declaration of ‘memcpy’ memcpy(list->buffer + idx, es, size sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘remove_u1v’: list.h:311:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + idx, list->buffer + idx + 1, (list->size - idx - 1) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:311:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + idx, list->buffer + idx + 1, (list->size - idx - 1) * sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘remove_array_u1v’: list.h:319:3: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + off, list->buffer + off + len, (list->size - off
len) * sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:319:3: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + off, list->buffer + off + len, (list->size - off
len) sizeof(e_type)); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘append_u1v’: list.h:370:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(list1->buffer + list1->size, list2->buffer, sizeof(e_type) list2->size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:370:2: note: include ‘’ or provide a declaration of ‘memcpy’ memcpy(list1->buffer + list1->size, list2->buffer, sizeof(e_type) list2->size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘append_array_u1v’: list.h:377:2: warning: incompatible implicit declaration of built-in function ‘memcpy’ memcpy(list1->buffer + list1->size, ary, sizeof(e_type) size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:377:2: note: include ‘’ or provide a declaration of ‘memcpy’ memcpy(list1->buffer + list1->size, ary, sizeof(e_type) size); \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘delete_u1v’: list.h:440:5: warning: incompatible implicit declaration of built-in function ‘memmove’ memmove(list->buffer + i - 1, list->buffer + i, (list->size - i) sizeof(e_type)); \ ^ list.h:487:1: note: in expansion of macro ‘define_list_ext’ define_list_ext(name, e_type, size_t, native_number_cmp); ^~~~~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h:440:5: note: include ‘’ or provide a declaration of ‘memmove’ memmove(list->buffer + i - 1, list->buffer + i, (list->size - i) sizeof(e_type)); \ ^ list.h:487:1: note: in expansion of macro ‘define_list_ext’ define_list_ext(name, e_type, size_t, native_number_cmp); ^~~~~~~ list.h:490:1: note: in expansion of macro ‘define_native_list’ define_native_list(u1v, uint8_t); ^~~~~~ list.h: In function ‘zerosu16list’: list.h:191:56: warning: incompatible implicit declaration of built-in function ‘memset’ static inline void zeros##list_type(list_type list){ memset(list->buffer, 0, list->cap * sizeof(e_type)); } \ ^ list.h:486:1: note: in expansion of macro ‘define_list_core’ define_list_core(name, e_type, size_t, 0xFFFFFU); \ ^~~~ list.h

yjx1217 commented 6 years ago

hmm, I noticed that my email got truncated somehow. So here I re-paste the very last few lines for the compilation error:

wtzmo.c:1058:15: warning: incompatible implicit declaration of built-in function ‘strdup’ In file included from wtzmo.c:25:0: wtzmo.c: In function ‘main’: file_reader.h:97:30: warning: implicit declaration of function ‘ref_VStrv’; did you mean ‘ref_diagv’? [-Wimplicit-function-declaration]

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:28: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:28: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:53: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1738:79: note: in expansion of macro ‘get_col_str’ set_read_clip_wtzmo(wt, get_col_str(fr, 0), atoi(get_col_str(fr, 1)), atoi(get_col_str(fr, 2))); ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1766:43: note: in expansion of macro ‘get_col_str’ if((pb1 = kv_get_cuhash(wt->rdname2id, get_col_str(fr, 0))) == 0xFFFFFFFFU) continue; ^~~ file_reader.h:97:56: error: invalid type argument of ‘->’ (have ‘int’)

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

wtzmo.c:1767:43: note: in expansion of macro ‘get_col_str’ if((pb2 = kv_get_cuhash(wt->rdname2id, get_col_str(fr, 1))) == 0xFFFFFFFFU) continue; ^~~ Makefile:33: recipe for target 'wtzmo' failed make: *** [wtzmo] Error 1

ruanjue commented 6 years ago

Thanks. It was caused by gcc locating string.h in '.' instead of system include path. 1, Please give the result of echo $CPATH. 2, Have A look at https://github.com/ruanjue/wtdbg/issues/4, cpp -v gave more information than you got.

In my computer: cpp -v

> cpp -v
Using built-in specs.
COLLECT_GCC=cpp
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --prefix=/public/software/gcc-5.2.0 --enable-threads=posix --disable-checking --disable-multilib --enable-languages=c,c++ --with-gmp=/public/software/gcc-5.2.0/gmp-4.2.3 --with-mpfr=/public/software/gcc-5.2.0/mpfr-2.4.2 --with-mpc=/public/software/gcc-5.2.0/mpc-0.8.1
Thread model: posix
gcc version 5.2.0 (GCC)
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
 /public/software/gcc-5.2.0/libexec/gcc/x86_64-unknown-linux-gnu/5.2.0/cc1 -E -quiet -v - -mtune=generic -march=x86-64
ignoring nonexistent directory "/public/software/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/../../../../x86_64-unknown-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 /public/software/compiler/intel/composer_xe_2013_sp1.0.080/mkl/include
 /public/software/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/include
 /usr/local/include
 /public/software/gcc-5.2.0/include
 /public/software/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/include-fixed
 /usr/include
End of search list.

Best, Jue

yjx1217 commented 6 years ago

Hi Jue,

My $CPATH is empty. "echo $CPATH" returns nothing.

Also, "cpp -v" only returns the following on my system, nothing about the include paths... :

jxyue@professorx:~> cpp -v Using built-in specs. COLLECT_GCC=cpp COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper OFFLOAD_TARGET_NAMES=hsa:nvptx-none Target: x86_64-suse-linux Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,ada,go --enable-offload-targets=hsa,nvptx-none=/usr/nvptx-none, --without-cuda-driver --enable-checking=release --disable-werror --with-gxx-include-dir=/usr/include/c++/7 --enable-ssp --disable-libssp --disable-libvtv --disable-libcc1 --enable-plugin --with-bugurl= http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --with-default-libstdcxx-abi=gcc4-compatible --enable-version-specific-runtime-libs --with-gcc-major-version-only --enable-linker-build-id --enable-linux-futex --enable-gnu-indirect-function --program-suffix=-7 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux Thread model: posix gcc version 7.3.0 (SUSE Linux)

Best, Jia-Xing

On Wed, Jun 13, 2018 at 7:41 AM, Jue Ruan notifications@github.com wrote:

Thanks. It was caused by gcc locating string.h in '.' instead of system include path. 1, Please give the result of echo $CPATH. 2, Have A look at ruanjue/wtdbg#4 https://github.com/ruanjue/wtdbg/issues/4, cpp -v gave more information than you got.

In my computer: cpp -v

cpp -v Using built-in specs. COLLECT_GCC=cpp Target: x86_64-unknown-linux-gnu Configured with: ./configure --prefix=/public/software/gcc-5.2.0 --enable-threads=posix --disable-checking --disable-multilib --enable-languages=c,c++ --with-gmp=/public/software/gcc-5.2.0/gmp-4.2.3 --with-mpfr=/public/software/gcc-5.2.0/mpfr-2.4.2 --with-mpc=/public/software/gcc-5.2.0/mpc-0.8.1 Thread model: posix gcc version 5.2.0 (GCC) COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' /public/software/gcc-5.2.0/libexec/gcc/x86_64-unknown-linux-gnu/5.2.0/cc1 -E -quiet -v - -mtune=generic -march=x86-64 ignoring nonexistent directory "/public/software/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/../../../../x86_64-unknown-linux-gnu/include"

include "..." search starts here:

include <...> search starts here:

/public/software/compiler/intel/composer_xe_2013_sp1.0.080/mkl/include /public/software/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/include /usr/local/include /public/software/gcc-5.2.0/include /public/software/gcc-5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/include-fixed /usr/include End of search list.

Best, Jue

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-- Jia-Xing Yue

Population Genomics and Complex Traits Group Tour Pasteur 8eme etage Faculté de Médecine Institute for Research on Cancer and Aging, Nice (IRCAN) CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA) 28 Avenue de Valombrose https://maps.google.com/?q=28+Avenue+de+Valombrose&entry=gmail&source=g 06107 NICE Cedex 2 France

Twitter: @iAmphioxus https://twitter.com/iAmphioxus Personal website: http://www.iamphioxus.org/ Lab website: https://litilab.wordpress.com/ Yeast Population Reference Panel: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/

ruanjue commented 6 years ago

Ok, let us try cpp -v /dev/null -o /dev/null.

yjx1217 commented 6 years ago

I got the following results:

jxyue@professorx:~> cpp -v /dev/null -o /dev/null Using built-in specs. COLLECT_GCC=cpp COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper OFFLOAD_TARGET_NAMES=hsa:nvptx-none Target: x86_64-suse-linux Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,ada,go --enable-offload-targets=hsa,nvptx-none=/usr/nvptx-none, --without-cuda-driver --enable-checking=release --disable-werror --with-gxx-include-dir=/usr/include/c++/7 --enable-ssp --disable-libssp --disable-libvtv --disable-libcc1 --enable-plugin --with-bugurl= http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --with-default-libstdcxx-abi=gcc4-compatible --enable-version-specific-runtime-libs --with-gcc-major-version-only --enable-linker-build-id --enable-linux-futex --enable-gnu-indirect-function --program-suffix=-7 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux Thread model: posix gcc version 7.3.0 (SUSE Linux) COMPILER_PATH=/usr/lib64/gcc/x86_64-suse-linux/7/:/usr/lib64/gcc/x86_64-suse-linux/7/:/usr/lib64/gcc/x86_64-suse-linux/:/usr/lib64/gcc/x86_64-suse-linux/7/:/usr/lib64/gcc/x86_64-suse-linux/:/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ LIBRARY_PATH=/usr/lib64/gcc/x86_64-suse-linux/7/:/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/lib/:/usr/lib64/gcc/x86_64-suse-linux/7/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-o' '/dev/null' '-mtune=generic' '-march=x86-64' /usr/lib64/gcc/x86_64-suse-linux/7/collect2 -plugin /usr/lib64/gcc/x86_64-suse-linux/7/liblto_plugin.so -plugin-opt=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper -plugin-opt=-fresolution=/tmp/ccDBelpF.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --build-id --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o /dev/null /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crt1.o /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/7/crtbegin.o -L/usr/lib64/gcc/x86_64-suse-linux/7 -L/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/7/../../.. /dev/null -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib64/gcc/x86_64-suse-linux/7/crtend.o /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crtn.o /dev/null: file not recognized: File truncated collect2: error: ld returned 1 exit status

Best, Jia-Xing

On Wed, Jun 13, 2018 at 7:56 AM, Jue Ruan notifications@github.com wrote:

Ok, let us try cpp -v /dev/null -o /dev/null.

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-- Jia-Xing Yue

Population Genomics and Complex Traits Group Tour Pasteur 8eme etage Faculté de Médecine Institute for Research on Cancer and Aging, Nice (IRCAN) CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA) 28 Avenue de Valombrose https://maps.google.com/?q=28+Avenue+de+Valombrose&entry=gmail&source=g 06107 NICE Cedex 2 France

Twitter: @iAmphioxus https://twitter.com/iAmphioxus Personal website: http://www.iamphioxus.org/ Lab website: https://litilab.wordpress.com/ Yeast Population Reference Panel: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/

ruanjue commented 6 years ago

I haven't upgrate gcc to 7.3. Let us try: 1, echo | gcc -E -Wp,-v - 2, echo $C_INCLUDE_PATH 3, echo $CPLUS_INCLUDE_PATH

yjx1217 commented 6 years ago

1, echo | gcc -E -Wp,-v -

jxyue@professorx:~> echo | gcc -E -Wp,-v -

include "..." search starts here:

include <...> search starts here:

. /scratch/bin/samtools/include/ /usr/lib64/gcc/x86_64-suse-linux/7/include /usr/local/include /usr/lib64/gcc/x86_64-suse-linux/7/include-fixed /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/include /usr/include End of search list.

1 ""

31 ""

1 "/usr/include/stdc-predef.h" 1 3 4

32 "" 2

1 ""

2, echo $C_INCLUDE_PATH

jxyue@professorx:~> echo $C_INCLUDE_PATH :/scratch/bin/samtools/include/

3, echo $CPLUS_INCLUDE_PATH jxyue@professorx:~> echo $CPLUS_INCLUDE_PATH

(# this one returns empty results)

Best, Jia-Xing

On Wed, Jun 13, 2018 at 8:07 AM, Jue Ruan notifications@github.com wrote:

I haven't upgrate gcc to 7.3. Let us try: 1, echo | gcc -E -Wp,-v - 2, echo $C_INCLUDE_PATH 3, echo $CPLUS_INCLUDE_PATH

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-- Jia-Xing Yue

Population Genomics and Complex Traits Group Tour Pasteur 8eme etage Faculté de Médecine Institute for Research on Cancer and Aging, Nice (IRCAN) CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA) 28 Avenue de Valombrose https://maps.google.com/?q=28+Avenue+de+Valombrose&entry=gmail&source=g 06107 NICE Cedex 2 France

Twitter: @iAmphioxus https://twitter.com/iAmphioxus Personal website: http://www.iamphioxus.org/ Lab website: https://litilab.wordpress.com/ Yeast Population Reference Panel: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/

ruanjue commented 6 years ago

Yeah! Found it. The dot .

#include "..." search starts here:
#include <...> search starts here:
 .
 /scratch/bin/samtools/include/

Now, modify the C_INCLUDE_PATH, export C_INCLUDE_PATH=/scratch/bin/samtools/include/, and compile program again.

Regards, Jue

yjx1217 commented 6 years ago

Hi Jue,

Many thanks for locating the issue! I set C_INCLUDE_PATH="" and redo the compilation. Now everything works!

Best, Jia-Xing

On Wed, Jun 13, 2018 at 8:22 AM, Jue Ruan notifications@github.com wrote:

Yeah! Found it. The dot .

include "..." search starts here:

include <...> search starts here:

. /scratch/bin/samtools/include/

Now, modify the C_INCLUDE_PATH, export C_INCLUDE_PATH=/scratch/bin/ samtools/include/, and compile program again.

Regards, Jue

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-- Jia-Xing Yue

Population Genomics and Complex Traits Group Tour Pasteur 8eme etage Faculté de Médecine Institute for Research on Cancer and Aging, Nice (IRCAN) CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA) 28 Avenue de Valombrose https://maps.google.com/?q=28+Avenue+de+Valombrose&entry=gmail&source=g 06107 NICE Cedex 2 France

Twitter: @iAmphioxus https://twitter.com/iAmphioxus Personal website: http://www.iamphioxus.org/ Lab website: https://litilab.wordpress.com/ Yeast Population Reference Panel: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/

ruanjue commented 6 years ago

Cheers

ruanjue / smartdenovo

Compilation error #17

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

define get_col_str(fr, col) ref_VStrv((fr)->tabs, col)->string

include "..." search starts here:

include <...> search starts here:

include "..." search starts here:

include <...> search starts here:

1 ""

1 ""

1 ""

31 ""

1 "/usr/include/stdc-predef.h" 1 3 4

32 "" 2

1 ""

include "..." search starts here:

include <...> search starts here: