Your message dated Mon, 24 Mar 2025 09:50:57 +0000
with message-id <[email protected]>
and subject line Bug#1096345: fixed in augustus 3.5.0+dfsg-5
has caused the Debian Bug report #1096345,
regarding augustus: ftbfs with GCC-15
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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--
1096345: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096345
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:augustus
Version: 3.5.0+dfsg-4
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/augustus_3.5.0+dfsg-4_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html
[...]
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 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c -o
list.o list.c
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o
compileSpliceCands compileSpliceCands.o list.o
cp -f compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory
'/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory
'/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory
'/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g
-O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -I./headers -I/usr/include/bamtools -c
filterBam.cc
In file included from ./headers/filterBam.h:10,
from filterBam.cc:28:
./headers/bamaccess.hh:76:13: error: ‘uint32_t’ does not name a type
76 | virtual uint32_t countEqualSignsInQuerySequence() const = 0;
| ^~~~~~~~
./headers/bamaccess.hh:10:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’;
this is probably fixable by adding ‘#include <cstdint>’
9 | #include <memory>
+++ |+#include <cstdint>
10 |
./headers/bamaccess.hh:84:13: error: ‘uint32_t’ does not name a type
84 | virtual uint32_t countCigarOperations(const char& type) const = 0;
| ^~~~~~~~
./headers/bamaccess.hh:84:13: note: ‘uint32_t’ is defined in header
‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
In file included from filterBam.cc:34:
./headers/bamtoolsaccess.hh:81:21: error: ‘uint32_t
BamToolsAlignmentRecord::countEqualSignsInQuerySequence() const’ marked
‘override’, but does not override
81 | inline uint32_t countEqualSignsInQuerySequence() const override
final;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./headers/bamtoolsaccess.hh:81:21: error: ‘uint32_t
BamToolsAlignmentRecord::countEqualSignsInQuerySequence() const’ marked
‘final’, but is not virtual
./headers/bamtoolsaccess.hh:89:21: error: ‘uint32_t
BamToolsAlignmentRecord::countCigarOperations(const char&) const’ marked
‘override’, but does not override
89 | inline uint32_t countCigarOperations(const char& type) const
override final;
| ^~~~~~~~~~~~~~~~~~~~
./headers/bamtoolsaccess.hh:89:21: error: ‘uint32_t
BamToolsAlignmentRecord::countCigarOperations(const char&) const’ marked
‘final’, but is not virtual
filterBam.cc: In function ‘int main(int, char**)’:
filterBam.cc:304:49: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named
‘countEqualSignsInQuerySequence’
304 | percId = (float) 100 *
(al->countEqualSignsInQuerySequence() - al->countCigarOperations('D')) /
qLength;
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filterBam.cc:304:88: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
304 | percId = (float) 100 *
(al->countEqualSignsInQuerySequence() - al->countCigarOperations('D')) /
qLength;
|
^~~~~~~~~~~~~~~~~~~~
filterBam.cc:306:65: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named
‘countEqualSignsInQuerySequence’
306 | else if (checkForEqualSigns && (numEquals =
al->countEqualSignsInQuerySequence()) != 0) {
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filterBam.cc:309:61: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
309 | percId = (float) 100 * (numEquals -
al->countCigarOperations('D')) / qLength;
|
^~~~~~~~~~~~~~~~~~~~
filterBam.cc:315:74: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
315 | percId = (float) 100 * (qLength - editDistance -
al->countCigarOperations('S')) / qLength;
|
^~~~~~~~~~~~~~~~~~~~
filterBam.cc:338:40: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
338 | countIOperations = al->countCigarOperations('I');
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:339:47: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
339 | coverage = (float) 100 * (al->countCigarOperations('M')
+ countIOperations) / qLength; // sumMandIOperations() - Equiv to $qEnd-$qStart
in PSL
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:352:34: error: ‘using std::__shared_ptr_access<BamAlignmentRecord,
__gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’
{aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
352 | baseInsert = al->countCigarOperations('D') +
countIOperations;
| ^~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:68: filterBam.o] Error 1
make[3]: Leaving directory
'/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
make[2]: *** [Makefile:7: all] Error 2
make[2]: Leaving directory
'/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam'
make[1]: *** [debian/rules:26: filterBam] Error 2
make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: augustus
Source-Version: 3.5.0+dfsg-5
Done: Sascha Steinbiss <[email protected]>
We believe that the bug you reported is fixed in the latest version of
augustus, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sascha Steinbiss <[email protected]> (supplier of updated augustus 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 24 Mar 2025 00:47:37 +0100
Source: augustus
Architecture: source
Version: 3.5.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Sascha Steinbiss <[email protected]>
Closes: 1096345
Changes:
augustus (3.5.0+dfsg-5) unstable; urgency=medium
.
* Add patch to enable building with GCC 15.
Closes: #1096345
* Bump Standards-Version.
* Bump copyright date for debian/ directory.
* Use libncurses-dev instead of libncurses5-dev.
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