[Debian-med-packaging] Bug#1099828: diamond-aligner :FTBFS:build failed ( error: ‘memcpy’ was not declared in this scope)

[Yue Gui]

Source: diamond-aligner
Version:  2.1.11-1
Severity: serious
Tags: FTBFS, patch
User: debian-riscv at lists.debian.org
Usertags: riscv64
X-Debbugs-Cc: debian-riscv at lists.debian.org

Dear diamond-aligner maintainer,
The package diamond-aligner build failed on riscv64.The crucial buildd log
below:
```

/build/reproducible-path/diamond-aligner-2.1.11/src/search/finger_print.h:
In constructor ‘Byte_finger_print_48::Byte_finger_print_48(const
Letter*)’:
/build/reproducible-path/diamond-aligner-2.1.11/src/search/finger_print.h:138:17:
error: ‘memcpy’ was not declared in this scope
  138 |                 memcpy(r, q - 16, 48);
      |                 ^~~~~~
/build/reproducible-path/diamond-aligner-2.1.11/src/search/finger_print.h:26:1:
note: ‘memcpy’ is defined in header ‘<cstring>’; this is probably
fixable by adding ‘#include <cstring>’
   25 | #include "basic/value.h"
  +++ |+#include <cstring>
   26 |
At global scope:
cc1plus: note: unrecognized command-line option
‘-Wno-unknown-warning-option’ may have been intended to silence
earlier diagnostics
make[3]: *** [CMakeFiles/arch_generic.dir/build.make:96:
CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from /usr/include/c++/14/list:62,
                 from
/build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/swipe_wrapper.cpp:22:
In function ‘typename
__gnu_cxx::__enable_if<std::__is_scalar<_Tp>::__value, void>::__type
std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with
_ForwardIterator = int*; _Tp = int]’,
    inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with
_FIte = int*; _Tp = int]’ at
/usr/include/c++/14/bits/stl_algobase.h:998:21,
    inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator,
const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at
/usr/include/c++/14/bits/stl_algobase.h:1029:20,
    inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix<Sv>::Matrix(int,
int) [with Sv = int]’ at
/build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/full_matrix.h:66:12:
/usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void*
__builtin_memset(void*, int, long unsigned int)’ specified bound
18446744073709551612 exceeds maximum object size 9223372036854775807
[-Wstringop-overflow=]
  952 |         *__first = __tmp;
      |         ~~~~~~~~~^~~~~~~
At global scope:
cc1plus: note: unrecognized command-line option
‘-Wno-unknown-warning-option’ may have been intended to silence
earlier diagnostics
make[3]: Leaving directory
'/build/reproducible-path/diamond-aligner-2.1.11/obj-riscv64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:93: CMakeFiles/arch_generic.dir/all] Error 2
make[2]: Leaving directory
'/build/reproducible-path/diamond-aligner-2.1.11/obj-riscv64-linux-gnu'
make[1]: *** [Makefile:149: all] Error 2
make[1]: Leaving directory
'/build/reproducible-path/diamond-aligner-2.1.11/obj-riscv64-linux-gnu'
dh_auto_build: error: cd obj-riscv64-linux-gnu && make -j4
"INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:16: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned
exit status 2

```
The full buildd log is here:
https://buildd.debian.org/status/fetch.php?pkg=diamond-aligner&arch=riscv64&ver=2.1.11-1&stamp=1741409747&raw=0
My solution to this issue:
  This issue occurs because the memcpy function is defined in the <cstring>
header file, but the code does not include this header. Therefore, it can
be resolved by adding #include <cstring>.I have tested this locally,and it
works well.The debpatch is in the attachment.Please let me know whether
this solution can be accepted.
Gui-Yue
Best Regards
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