Your message dated Sat, 12 Aug 2023 19:33:53 +0000
with message-id <e1quumz-00etwj...@fasolo.debian.org>
and subject line Bug#1037655: fixed in filtlong 0.2.1-4
has caused the Debian Bug report #1037655,
regarding filtlong: ftbfs with GCC-13
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1037655: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037655
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:filtlong
Version: 0.2.1-3
Severity: normal
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/filtlong_0.2.1-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html
[...]
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:107:13: error: ‘reverse_kmer’ was not declared in this scope
107 | reverse_kmer = starting_kmer_to_bits_reverse(sequence);
| ^~~~~~~~~~~~
src/kmers.cpp:107:28: error: ‘starting_kmer_to_bits_reverse’ was not declared
in this scope
107 | reverse_kmer = starting_kmer_to_bits_reverse(sequence);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:109:21: error: ‘void*’ is not a pointer-to-object type
109 | (this->*add_kmer)(forward_kmer);
| ^~~~~~~~
src/kmers.cpp:110:21: error: ‘void*’ is not a pointer-to-object type
110 | (this->*add_kmer)(reverse_kmer);
| ^~~~~~~~
src/kmers.cpp:114:33: error: ‘base_to_bits_forward’ was not declared in this
scope
114 | forward_kmer |= base_to_bits_forward(sequence[i]);
| ^~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:117:33: error: ‘base_to_bits_reverse’ was not declared in this
scope
117 | reverse_kmer |= base_to_bits_reverse(sequence[i]);
| ^~~~~~~~~~~~~~~~~~~~
src/kmers.cpp:119:25: error: ‘void*’ is not a pointer-to-object type
119 | (this->*add_kmer)(forward_kmer);
| ^~~~~~~~
src/kmers.cpp:120:25: error: ‘void*’ is not a pointer-to-object type
120 | (this->*add_kmer)(reverse_kmer);
| ^~~~~~~~
src/kmers.cpp: At global scope:
src/kmers.cpp:137:6: error: variable or field ‘add_kmer_require_one_copy’
declared void
137 | void Kmers::add_kmer_require_one_copy(uint32_t kmer) {
| ^~~~~
src/kmers.cpp:137:39: error: ‘uint32_t’ was not declared in this scope
137 | void Kmers::add_kmer_require_one_copy(uint32_t kmer) {
| ^~~~~~~~
src/kmers.cpp:137:39: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did
you forget to ‘#include <cstdint>’?
src/kmers.cpp:142:6: error: variable or field
‘add_kmer_require_multiple_copies’ declared void
142 | void Kmers::add_kmer_require_multiple_copies(uint32_t kmer) {
| ^~~~~
src/kmers.cpp:142:46: error: ‘uint32_t’ was not declared in this scope
142 | void Kmers::add_kmer_require_multiple_copies(uint32_t kmer) {
| ^~~~~~~~
src/kmers.cpp:142:46: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did
you forget to ‘#include <cstdint>’?
src/kmers.cpp:170:6: error: ‘bool Kmers::is_kmer_present’ is not a static data
member of ‘class Kmers’
170 | bool Kmers::is_kmer_present(uint32_t kmer) {
| ^~~~~
src/kmers.cpp:170:29: error: ‘uint32_t’ was not declared in this scope
170 | bool Kmers::is_kmer_present(uint32_t kmer) {
| ^~~~~~~~
src/kmers.cpp:170:29: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did
you forget to ‘#include <cstdint>’?
src/kmers.cpp:176:1: error: ‘uint32_t’ does not name a type
176 | uint32_t Kmers::base_to_bits_forward(char base) {
| ^~~~~~~~
src/kmers.cpp:176:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
src/kmers.cpp:199:1: error: ‘uint32_t’ does not name a type
199 | uint32_t Kmers::base_to_bits_reverse(char base) {
| ^~~~~~~~
src/kmers.cpp:199:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
src/kmers.cpp:222:1: error: ‘uint32_t’ does not name a type
222 | uint32_t Kmers::starting_kmer_to_bits_forward(char * sequence) {
| ^~~~~~~~
src/kmers.cpp:222:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
src/kmers.cpp:232:1: error: ‘uint32_t’ does not name a type
232 | uint32_t Kmers::starting_kmer_to_bits_reverse(char * sequence) {
| ^~~~~~~~
src/kmers.cpp:232:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
make[2]: *** [Makefile:49: src/kmers.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned
exit code 2
make[1]: *** [debian/rules:10: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: filtlong
Source-Version: 0.2.1-4
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
filtlong, 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 1037...@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 filtlong 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: Sat, 12 Aug 2023 20:45:37 +0200
Source: filtlong
Architecture: source
Version: 0.2.1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1037655
Changes:
filtlong (0.2.1-4) unstable; urgency=medium
.
* Team upload.
* gcc-13.patch: new: fix ftbfs with gcc-13. (Closes: #1037655)
* hardening.patch: declare forwarding not-needed.
* hardening.patch: also propagate preprocessor flags.
* d/control: declare compliance to standards version 4.6.2
Checksums-Sha1:
ef34ad61e540bd7d8a6ef77b0dfc684309b61e84 2183 filtlong_0.2.1-4.dsc
2b707ac8f1bb5eaeef7316a748cd2f1e76cacfed 6876 filtlong_0.2.1-4.debian.tar.xz
Checksums-Sha256:
349b94bb44e52c2f44f82f7b8e1c71bee62710bae1d28159dd91f64aef9ea8f0 2183
filtlong_0.2.1-4.dsc
e9f0ae075e5b720c275c9f5100078b383572812ab7701c4a9145f3a83cbef9bb 6876
filtlong_0.2.1-4.debian.tar.xz
Files:
0f08f209949a7ef5846952b2e72a71fe 2183 science optional filtlong_0.2.1-4.dsc
b5ab0f227cd06a3a6e34109579786ba7 6876 science optional
filtlong_0.2.1-4.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=qMxy
-----END PGP SIGNATURE-----
--- End Message ---
