Your message dated Fri, 21 Jul 2023 12:42:53 +0200
with message-id <3dee454c-4f82-02cc-8e53-a3cf41f61...@debian.org>
and subject line Re: [Debian-med-packaging] Bug#1037585: augustus: ftbfs with
GCC-13
has caused the Debian Bug report #1037585,
regarding augustus: 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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--
1037585: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037585
Debian Bug Tracking System
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--- Begin Message ---
Package: src:augustus
Version: 3.5.0+dfsg-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/augustus_3.5.0+dfsg-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
[...]
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -c compileSpliceCands.c
compileSpliceCands.c: In function ‘getChromosome’:
compileSpliceCands.c:216:9: warning: ‘__builtin_strncat’ specified bound
depends on the length of the source argument [-Wstringop-overflow=]
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^
compileSpliceCands.c:216:9: note: length computed here
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c: In function ‘parseLine’:
compileSpliceCands.c:292:9: warning: ‘__builtin_strncpy’ specified bound 256
equals destination size [-Wstringop-truncation]
292 | strncpy(d->name,tokens[0],LINEBUFFER);
| ^
compileSpliceCands.c: In function ‘parseList’:
compileSpliceCands.c:333:69: warning: ‘left’ may be used uninitialized
[-Wmaybe-uninitialized]
333 | isCandidate =
((right->averageCoverage>=left->averageCoverage*threshold) ||
|
~~~~^~~~~~~~~~~~~~~~~
compileSpliceCands.c:314:14: note: ‘left’ was declared here
314 | Data left;
| ^~~~
compileSpliceCands.c: In function ‘main’:
compileSpliceCands.c:563:17: warning: ‘chromosomeLength’ may be used
uninitialized [-Wmaybe-uninitialized]
563 |
parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:416:18: note: ‘chromosomeLength’ was declared here
416 | long int chromosomeLength;
| ^~~~~~~~~~~~~~~~
cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -o compileSpliceCands
compileSpliceCands.o list.o
cp -f compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I./headers -I/usr/include/bamtools -c filterBam.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I./headers -I/usr/include/bamtools -c
functions/initOptions.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I./headers -I/usr/include/bamtools -c
functions/printElapsedTime.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I./headers -I/usr/include/bamtools -c
functions/MatePairs.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I./headers -I/usr/include/bamtools -c
functions/PairednessCoverage.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I./headers -I/usr/include/bamtools -c
BamToolsAccess.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib
-o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o
PairednessCoverage.o BamToolsAccess.o -lbamtools -lz
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare
-ansi -pedantic -std=c++0x -pthread -O2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I../include -c gene.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare
-ansi -pedantic -std=c++0x -pthread -O2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -I../include -c genome.cc
In file included from ../include/genome.hh:20,
from genome.cc:14:
../include/sqliteDB.hh:71:29: error: ‘uint64_t’ has not been declared
71 | void bindInt64(int idx, uint64_t x);
| ^~~~~~~~
../include/sqliteDB.hh:80:12: error: ‘uint64_t’ does not name a type
80 | inline uint64_t int64Column(int colNum){return
(uint64_t)sqlite3_column_int64(stmt,colNum);}
| ^~~~~~~~
../include/sqliteDB.hh:16:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’;
did you forget to ‘#include <cstdint>’?
15 | #include <sqlite3.h>
+++ |+#include <cstdint>
16 |
make[2]: *** [Makefile:48: genome.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
make[1]: *** [debian/rules:29: homGeneMapping] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Hi,
[...]
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.
Fixed in most recent upload. Will keep this open as requested though.
Since this is now RC, I would like to close this issue since the FTBFS
has been addressed for some time now.
Thanks
Sascha
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--- End Message ---
