Your message dated Wed, 24 Sep 2025 20:40:43 +0000
with message-id <[email protected]>
and subject line Bug#1097779: fixed in readseq 1-16
has caused the Debian Bug report #1097779,
regarding readseq: 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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--
1097779: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097779
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:readseq
Version: 1-15
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/readseq_1-15_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
[...]
1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen,
checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:1972:37: warning: format ‘%X’ expects argument of type ‘unsigned
int’, but argument 5 has type ‘long unsigned int’ [-Wformat=]
1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen,
checksum);
| ~^
~~~~~~~~
| | |
| unsigned int
long unsigned int
| %lX
ureadseq.c:1979:25: warning: format ‘%d’ expects argument of type ‘int’, but
argument 3 has type ‘long int’ [-Wformat=]
1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname);
| ~~^ ~~~~~~
| | |
| int long int
| %4ld
ureadseq.c:2002:27: warning: format ‘%d’ expects argument of type ‘int’, but
argument 4 has type ‘long int’ [-Wformat=]
2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen,
checksum);
| ~^ ~~~~~~
| | |
| int long int
| %ld
ureadseq.c:2002:37: warning: format ‘%X’ expects argument of type ‘unsigned
int’, but argument 5 has type ‘long unsigned int’ [-Wformat=]
2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen,
checksum);
| ~^
~~~~~~~~
| | |
| unsigned int
long unsigned int
| %lX
ureadseq.c:2043:42: warning: format ‘%d’ expects argument of type ‘int’, but
argument 3 has type ‘long int’ [-Wformat=]
2043 | if (numline==1) fprintf(outf,"%-9d ",i+1);
| ~~~^ ~~~
| | |
| int long int
| %-9ld
ureadasn.c: In function ‘listASNSeqs’:
ureadasn.c:189:24: warning: passing argument 1 of ‘AsnIoOpen’ discards ‘const’
qualifier from pointer target type [-Wdiscarded-qualifiers]
189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto
errxit;
| ^~~~~~~~
In file included from /usr/include/ncbi/ncbi.h:57,
from ureadasn.c:13:
/usr/include/ncbi/asn.h:384:54: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but
argument is of type ‘const char *’
384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr
mode));
/usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’
192 | #define PROTO(x) x /* Prototypes are acceptable */
| ^
ureadasn.c: In function ‘readASNSeq’:
ureadasn.c:261:24: warning: passing argument 1 of ‘AsnIoOpen’ discards ‘const’
qualifier from pointer target type [-Wdiscarded-qualifiers]
261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto
errxit;
| ^~~~~~~~
/usr/include/ncbi/asn.h:384:54: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but
argument is of type ‘const char *’
384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr
mode));
/usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’
192 | #define PROTO(x) x /* Prototypes are acceptable */
| ^
ureadasn.c:262:31: warning: ‘fgets’ writing 255 bytes into a region of size 200
overflows the destination [-Wstringop-overflow=]
262 | for (i=0; i<skiplines; i++) fgets( stemp, 255, aip->fp); /* this may
mess up asn routines... */
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadasn.c:241:15: note: destination object ‘stemp’ of size 200
241 | char *seq, stemp[200];
| ^~~~~
In file included from ureadasn.c:8:
/usr/include/stdio.h:654:14: note: in a call to function ‘fgets’ declared with
attribute ‘access (write_only, 1, 2)’
654 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict
__stream)
| ^~~~~
make[1]: *** [Makefile:51: build] Error 1
make[1]: Leaving directory '/build/reproducible-path/readseq-1'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned
exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: readseq
Source-Version: 1-16
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
readseq, 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.
Étienne Mollier <[email protected]> (supplier of updated readseq 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: SHA512
Format: 1.8
Date: Wed, 24 Sep 2025 21:50:54 +0200
Source: readseq
Architecture: source
Version: 1-16
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097779
Changes:
readseq (1-16) unstable; urgency=medium
.
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097779)
* d/control: declare compliance to standards version 4.7.2.
* d/control: remove redundant Rules-Requires-Root.
* d/watch: migrate to untrackable v5 watch file.
* d/control: add myself to uploaders.
* d/get-orig-source: delete: unneeded.
* buffer_overflow.patch: normalize Last-Update.
* d/rules: convert Stdfiles to Unicode.
* hardening.patch: also propagate CPPFLAGS.
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