Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 append to cflags

Makefile | 20 10 + 10 - 0 !
1 file changed, 10 insertions(+), 10 deletions(-)

 support ldflags in upstream build system
 This patch was made using the following command:
   sed -i 's/\(gcc.*\)/\1 \$(LDFLAGS)/' Makefile

Makefile | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 use destdir during installation

Makefile | 20 10 + 10 - 0 !
1 file changed, 10 insertions(+), 10 deletions(-)

 do not hard code gcc
Bug: https://github.com/thegenemyers/DALIGNER/pull/54
Bug-Debian: https://bugs.debian.org/968434

Makefile | 20 10 + 10 - 0 !
1 file changed, 10 insertions(+), 10 deletions(-)

 apply cppflags too.
 Among other things, it enables fortifying sources.

ONElib.c | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 fix missing include.

ONE2LA.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix build failure with gcc 14.
 Since gcc 14, incompatible pointer type casting is now an error.  In
 the case of daligner, the build results in the following errors:
 .
  ONE2LA.c:135:13: error: assignment to int64 * {aka long long int *} from incompatible pointer type I64 * {aka long int *} [-Wincompatible-pointer-types]
    135 |       list  = oneIntList(file1);
        |             ^
  ONE2LA.c:202:20: error: assignment to int64 * {aka long long int *} from incompatible pointer type I64 * {aka long int *} [-Wincompatible-pointer-types]
    202 |               list = oneIntList(file1);
        |                    ^
  ONE2LA.c:210:20: error: assignment to int64 * {aka long long int *} from incompatible pointer type I64 * {aka long int *} [-Wincompatible-pointer-types]
    210 |               list = oneIntList(file1);
        |                    ^
  ONE2LA.c:220:20: error: assignment to int64 * {aka long long int *} from incompatible pointer type I64 * {aka long int *} [-Wincompatible-pointer-types]
    220 |               list = oneIntList(file1);
        |                    ^
  ONE2LA.c:227:20: error: assignment to int64 * {aka long long int *} from incompatible pointer type I64 * {aka long int *} [-Wincompatible-pointer-types]
    227 |               list = oneIntList(file1);
        |                    ^
 .
 Typing the list the same way as the return type of the oneIntList
 function is one possible way of resolving the issue.