Compilation error
Closed this issue · 14 comments
yjx1217 commented
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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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
yjx1217 commented
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
Let us first check the issue in ruanjue/wtdbg#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
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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ or provide a declaration of
‘memset’
list.h: In function ‘zeros_u8list’:
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, uint8_t);
^~~~~~~~~~~~~~~~~~
list.h:191:56: note: include ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘zeros_u1v’:
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, uint8_t);
^~~~~~~~~~~~~~~~~~
list.h:191:56: note: include ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘<string.h>’ 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 ‘zeros_u16list’:
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
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
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, 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
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 ***@***.***> 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
<ruanjue/wtdbg#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
Ok, let us try cpp -v /dev/null -o /dev/null.
yjx1217 commented
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 ***@***.***> wrote:
Ok, let us try cpp -v /dev/null -o /dev/null.
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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
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
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 "<stdin>"
# 1 "<built-in>"
# 1 "<command-line>"
# 31 "<command-line>"
# 1 "/usr/include/stdc-predef.h" 1 3 4
# 32 "<command-line>" 2
# 1 "<stdin>"
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 ***@***.***> 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
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
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 ***@***.***> 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
Cheers