هل يوجد متخصص قادر على حل مشكلتي في البرمجه

المصدر: هل يوجد متخصص قادر على حل مشكلتي في البرمجه
في منتدى : قسم الكومبيوتر العام ( حل مشاكل - تبادل خبرات )

السلام عليكم

اواجه مشكلة في تشغيل اكواد معينة لتحليل تسلسل الحمض النووي لاستخراض الطفرات بين عينتين الطبيعية
والمطفرة
قمت بتشغيل الاكواد في برنامج cygwin64 في نظام ويندوز

ونتج عن ذلك مايلي:
$ ./scripts/simple.sh
rm -f gmon.out *.o a.out bwa *~ *.a
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
In file included from kseq.h:31,
from bwa.c:24:
bwa.c: In function ‘trim_readno’:
bwa.c:29:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
29 | if (s->l > 2 && s->s[s->l-2] == '/' && isdigit(s->s[s->l-1]))
| ~~~~^~~~~~~~
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:878:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
878 | bgint_t oldInverseSa0RelativeRank = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:952:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
952 | unsigned int bitsInWordMinusBitPerChar;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
In file included from kopen.c:4:
kopen.c: In function ‘kftp_get_response’:
kopen.c:161:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
161 | if (n >= 4 && isdigit(aux->response[0]) && isdigit(aux->response[1]) && isdigit(aux->response[2])
| ~~~~~~~~~~~~~^~~
kopen.c:161:68: warning: array subscript has type ‘char’ [-Wchar-subscripts]
161 | if (n >= 4 && isdigit(aux->response[0]) && isdigit(aux->response[1]) && isdigit(aux->response[2])
| ~~~~~~~~~~~~~^~~
kopen.c:161:97: warning: array subscript has type ‘char’ [-Wchar-subscripts]
161 | if (n >= 4 && isdigit(aux->response[0]) && isdigit(aux->response[1]) && isdigit(aux->response[2])
| ~~~~~~~~~~~~~^~~
kopen.c: In function ‘cmd2argv’:
kopen.c:238:19: warning: array subscript has type ‘char’ [-Wchar-subscripts]
238 | if (!isspace(cmd)) break;
| ~~~^~~
kopen.c:241:19: warning: array subscript has type ‘char’ [-Wchar-subscripts]
241 | if (!isspace(cmd[beg])) break;
| ~~~^~~~~
kopen.c:244:18: warning: array subscript has type ‘char’ [-Wchar-subscripts]
244 | if (isspace(cmd) && !isspace(cmd[i-1]))
| ~~~^~~
kopen.c:244:38: warning: array subscript has type ‘char’ [-Wchar-subscripts]
244 | if (isspace(cmd) && !isspace(cmd[i-1]))
| ~~~^~~~~
kopen.c:250:18: warning: array subscript has type ‘char’ [-Wchar-subscripts]
250 | if (isspace(str)) str = 0;
| ~~~^~~
kopen.c: In function ‘kopen’:
kopen.c:285:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
285 | if (!isspace(*p)) break;
| ^~
kopen.c:291:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
291 | if (ispunct(*q) && *q != '.' && *q != '_' && *q != '-' && *q != ':')
| ^~
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
In file included from fastmap.c:7:
fastmap.c: In function ‘main_mem’:
fastmap.c:170:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
170 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:170:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
170 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
fastmap.c:180:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
180 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:180:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
180 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
fastmap.c:185:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
185 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:185:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
185 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
fastmap.c:190:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
190 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:190:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
190 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
fastmap.c:215:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
215 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:215:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
215 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
fastmap.c:220:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
220 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:220:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
220 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
fastmap.c:222:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
222 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ^~
fastmap.c:222:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
222 | if (*p != 0 && ispunct(*p) && isdigit(p[1]))
| ~^~~
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o

gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*

المبرمج اختبره في نظام سينتوس
وهذا المصدر https://github.com/wacguy/Simple

تم تجربته في نظام MacOS ظهرت نفس المشكله

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