Your message dated Sun, 23 Jul 2023 11:48:18 +0000
with message-id <e1qnxzs-008avh...@fasolo.debian.org>
and subject line Bug#1037879: fixed in unifrac-tools 1.3.2-2
has caused the Debian Bug report #1037879,
regarding unifrac-tools: 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.
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--
1037879: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037879
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:unifrac-tools
Version: 1.2-2
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/unifrac-tools_1.2-2_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
[...]
279 | int32_t BPTree::parent(uint32_t i) const {
| ^~~~~~
tree.cpp:279:24: error: ‘uint32_t’ was not declared in this scope
279 | int32_t BPTree::parent(uint32_t i) const {
| ^~~~~~~~
tree.cpp:279:24: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
tree.cpp:283:9: error: ‘int32_t su::BPTree::enclose’ is not a static data
member of ‘class su::BPTree’
283 | int32_t BPTree::enclose(uint32_t i) const {
| ^~~~~~
tree.cpp:283:25: error: ‘uint32_t’ was not declared in this scope
283 | int32_t BPTree::enclose(uint32_t i) const {
| ^~~~~~~~
tree.cpp:283:25: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
tree.cpp:290:9: error: ‘int32_t su::BPTree::bwd’ is not a static data member of
‘class su::BPTree’
290 | int32_t BPTree::bwd(uint32_t i, int d) const {
| ^~~~~~
tree.cpp:290:21: error: ‘uint32_t’ was not declared in this scope
290 | int32_t BPTree::bwd(uint32_t i, int d) const {
| ^~~~~~~~
tree.cpp:290:21: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
tree.cpp:290:33: error: expected primary-expression before ‘int’
290 | int32_t BPTree::bwd(uint32_t i, int d) const {
| ^~~
tree.cpp:290:38: error: expression list treated as compound expression in
initializer [-fpermissive]
290 | int32_t BPTree::bwd(uint32_t i, int d) const {
| ^
tree.cpp: In member function ‘void su::BPTree::newick_to_bp(std::string)’:
tree.cpp:350:5: error: ‘nparens’ was not declared in this scope; did you mean
‘parent’?
350 | nparens = structure.size();
| ^~~~~~~
| parent
tree.cpp: In member function ‘void su::BPTree::structure_to_openclose()’:
tree.cpp:365:22: error: invalid types ‘int[unsigned int]’ for array subscript
365 | openclose[i] = open_idx;
| ^
tree.cpp:366:22: error: invalid types ‘int[unsigned int]’ for array subscript
366 | openclose[open_idx] = i;
| ^
tree.cpp: In function ‘std::string& rtrim(std::string&)’:
tree.cpp:374:45: warning: ‘std::pointer_to_unary_function<_Arg, _Result>
std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is
deprecated: use 'std::function' instead [-Wdeprecated-declarations]
374 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(),
s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from tree.hpp:13:
/usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
tree.cpp: In member function ‘void su::BPTree::newick_to_metadata(std::string)’:
tree.cpp:412:24: error: ‘open’ was not declared in this scope; did you mean
‘popen’?
412 | open_idx = open(structure_idx);
| ^~~~
| popen
tree.cpp: At global scope:
tree.cpp:491:13: error: ‘uint32_t’ was not declared in this scope
491 | std::vector<uint32_t> BPTree::get_openclose() {
| ^~~~~~~~
tree.cpp:491:13: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you
forget to ‘#include <cstdint>’?
tree.cpp:491:21: error: template argument 1 is invalid
491 | std::vector<uint32_t> BPTree::get_openclose() {
| ^
tree.cpp:491:21: error: template argument 2 is invalid
make[3]: *** [Makefile:129: tree.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:9: api] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true"
PREFIX=/<<PKGBUILDDIR>>/debian/tmp/usr returned exit code 2
make[1]: *** [debian/rules:15: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: unifrac-tools
Source-Version: 1.3.2-2
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
unifrac-tools, 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 unifrac-tools
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, 23 Jul 2023 11:43:01 +0200
Source: unifrac-tools
Architecture: source
Version: 1.3.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1037879
Changes:
unifrac-tools (1.3.2-2) unstable; urgency=medium
.
* gcc-13.patch: new: fix build failures with gcc-13 (Closes: #1037879)
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