Your message dated Sun, 09 Mar 2025 10:04:37 +0000
with message-id <e1trdwp-00bnqg...@fasolo.debian.org>
and subject line Bug#1099828: fixed in diamond-aligner 2.1.11-2
has caused the Debian Bug report #1099828,
regarding diamond-aligner :FTBFS:build failed ( error: ‘memcpy’ was not
declared in this scope)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1099828: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1099828
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: diamond-aligner
Version: 2.1.11-1
Severity: serious
Tags: FTBFS, patch
User: debian-ri...@lists.debian.org
Usertags: riscv64
X-Debbugs-Cc: debian-ri...@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
fix_diamond-aligner_missing_cstring.patch
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: diamond-aligner
Source-Version: 2.1.11-2
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
diamond-aligner, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1099...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated diamond-aligner
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 09 Mar 2025 10:47:09 +0100
Source: diamond-aligner
Architecture: source
Version: 2.1.11-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1099828
Changes:
diamond-aligner (2.1.11-2) unstable; urgency=medium
.
[ Gui-Yue ]
* fix memcpy not defined on riscv64. (Closes: #1099828)
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28fbdffd1badf92cf3563400408b957635b84d7ae8af33894180341cfa0c5a6f 138004
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Files:
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