Your message dated Wed, 19 Jul 2023 22:35:36 +0000
with message-id <e1qmflg-009imr...@fasolo.debian.org>
and subject line Bug#1037772: fixed in mash 2.3+dfsg-4
has caused the Debian Bug report #1037772,
regarding mash: 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
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--
1037772: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037772
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:mash
Version: 2.3+dfsg-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/mash_2.3+dfsg-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
[...]
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for zlib.h... yes
checking for capnp... yes
checking for capnp/common.h... yes
checking for gsl/gsl_cdf.h... yes
configure: creating ./config.status
config.status: creating Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j8
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src/mash/capnp;export
PATH=/usr/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games;capnp
compile -I /usr/include -oc++ MinHash.capnp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/Command.o
src/mash/Command.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandBounds.o
src/mash/CommandBounds.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandContain.o
src/mash/CommandContain.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandDistance.o
src/mash/CommandDistance.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandTaxScreen.o
src/mash/CommandTaxScreen.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandScreen.o
src/mash/CommandScreen.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandTriangle.o
src/mash/CommandTriangle.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -std=c++14 -Isrc -I/usr/include
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -o src/mash/CommandFind.o
src/mash/CommandFind.cpp
src/mash/Command.cpp: In member function ‘void
mash::Command::Option::setArgument(std::string)’:
src/mash/Command.cpp:70:42: error: ‘uint64_t’ was not declared in this scope
70 | else if ( type == Integer && uint64_t(argumentAsNumber) !=
argumentAsNumber )
| ^~~~~~~~
src/mash/Command.cpp:14:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’;
did you forget to ‘#include <cstdint>’?
13 | #include "version.h"
+++ |+#include <cstdint>
14 |
src/mash/Command.cpp:102:9: error: ‘uint64_t’ was not declared in this scope
102 | uint64_t factor = 1;
| ^~~~~~~~
src/mash/Command.cpp:102:9: note: ‘uint64_t’ is defined in header ‘<cstdint>’;
did you forget to ‘#include <cstdint>’?
src/mash/Command.cpp:110:33: error: ‘factor’ was not declared in this scope;
did you mean ‘vector’?
110 | factor = 1000;
| ^~~~~~
| vector
src/mash/Command.cpp:143:49: error: expected ‘)’ before ‘argumentAsNumber’
143 | if ( argumentAsNumber <= 0 || (uint64_t)argumentAsNumber !=
argumentAsNumber )
| ~ ^~~~~~~~~~~~~~~~
| )
src/mash/Command.cpp:154:29: error: ‘factor’ was not declared in this scope;
did you mean ‘vector’?
154 | argumentAsNumber *= factor;
| ^~~~~~
| vector
make[1]: *** [Makefile:41: src/mash/Command.o] Error 1
make[1]: *** Waiting for unfinished jobs....
In file included from src/mash/CommandTaxScreen.cpp:11:
src/mash/taxdb.hpp: In member function ‘void mash::TaxDB::writeReport(FILE*,
const std::unordered_map<long unsigned int, mash::TaxCounts>&, long unsigned
int, long unsigned int, mash::TaxID, int)’:
src/mash/taxdb.hpp:218:59: warning: format ‘%llu’ expects argument of type
‘long long unsigned int’, but argument 9 has type ‘mash::TaxID’ {aka ‘long
unsigned int’} [-Wformat=]
218 | fprintf(FP, "%.4f\t%i\t%i\t%i\t%i\t%s\t%llu\t%s%s\n",
| ~~~^
| |
| long long
unsigned int
| %lu
......
224 | taxon->rank.c_str(), taxID,
std::string(2*depth, ' ').c_str(), taxon->name.c_str());
| ~~~~~
| |
| mash::TaxID {aka
long unsigned int}
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:14: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: mash
Source-Version: 2.3+dfsg-4
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
mash, 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 mash 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: Thu, 20 Jul 2023 00:17:07 +0200
Source: mash
Architecture: source
Version: 2.3+dfsg-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: 1037772
Changes:
mash (2.3+dfsg-4) unstable; urgency=medium
.
* Team upload.
* gcc-13.patch: new: fix ftbfs with gcc-13. (Closes: #1037772)
* d/control: declare compliance to standards version 4.6.2.
Checksums-Sha1:
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Checksums-Sha256:
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mash_2.3+dfsg-4.dsc
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mash_2.3+dfsg-4.debian.tar.xz
Files:
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