[Debian-med-packaging] Bug#1037772: mash: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:28:22 BST 2023
Package: src:mash
Version: 2.3+dfsg-3
Severity: normal
Tags: sid trixie
User: debian-gcc at 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
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