Your message dated Thu, 22 Aug 2024 21:56:47 +0000
with message-id <[email protected]>
and subject line Bug#1075419: fixed in python-pairix 0.3.8-1
has caused the Debian Bug report #1075419,
regarding python-pairix: ftbfs with GCC-14
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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--
1075419: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075419
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:python-pairix
Version: 0.3.7-7
Severity: important
Tags: sid trixie
User: [email protected]
Usertags: ftbfs-gcc-14
[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-14/g++-14, but succeeds to build with gcc-13/g++-13. 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/2024/07/01/python-pairix_0.3.7-7_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html
[...]
1246 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
| ^~~~~~~~~~
src/index.c:1263:59: error: passing argument 2 of ‘ti_querys_2d_multi’ from
incompatible pointer type [-Wincompatible-pointer-types]
1263 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions,
n_sub_list);
| ^~~~~~~
| |
| char **
src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type
‘char **’
131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char
**regs, int nRegs);
|
~~~~~~~~~~~~~^~~~
src/index.c: In function ‘ti_query_2d_tid’:
src/index.c:1417:31: error: returning ‘ti_iter_t’ {aka ‘struct __ti_iter_t *’}
from a function with return type ‘int’ makes integer from pointer without a
cast [-Wint-conversion]
1417 | if (name == 0) return ti_iter_first();
| ^~~~~~~~~~~~~~~
src/index.c: In function ‘create_merged_iter’:
src/index.c:1469:10: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
1469 | if( miter->iu = calloc(n,sizeof(iter_unit*))) {
| ^~~~~
src/index.c: In function ‘merged_ti_read’:
src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from
pointer target type [-Wdiscarded-qualifiers]
1537 | miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter,
miu[i]->len, seqonly);
| ^
src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from
pointer target type [-Wdiscarded-qualifiers]
1543 | miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter,
miu[0]->len, seqonly); // get next entry for the flushed iter
| ^
src/index.c: In function ‘sequential_ti_read’:
src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from
pointer target type [-Wdiscarded-qualifiers]
1573 | char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len,
0);
| ^~~~~~~~~~~~
src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer
target type [-Wdiscarded-qualifiers]
1576 | s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
| ^
src/index.c: In function ‘get_unique_merged_seqname’:
src/index.c:1643:22: error: assignment to ‘char **’ from incompatible pointer
type ‘const char **’ [-Wincompatible-pointer-types]
1643 | seqnames = ti_seqname(tbs[i]->idx,&len);
| ^
src/index.c: In function ‘flip_region’:
src/index.c:1744:19: warning: variable ‘split_pos’ set but not used
[-Wunused-but-set-variable]
1744 | int l, i, l2, split_pos;
| ^~~~~~~~~
src/index.c: In function ‘querys_2D_wrapper’:
src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards
‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
1911 | char *reg2 = flip_region(reg, get_region_split_character(tb));
| ^~~
src/index.c:1743:27: note: expected ‘char *’ but argument is of type ‘const
char *’
1743 | char *flip_region ( char* s, char region_split_character) {
| ~~~~~~^
src/index.c: In function ‘check_triangle’:
src/index.c:1971:23: error: initialization of ‘char **’ from incompatible
pointer type ‘const char **’ [-Wincompatible-pointer-types]
1971 | char **seqnames = ti_seqname(idx,&len);
| ^~~~~~~~~~
src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’
qualifier from pointer target type [-Wdiscarded-qualifiers]
1977 | if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2);
return(0); } // not a triangle
| ^~~~
In file included from src/khash.h:94,
from src/index.c:4:
/usr/include/stdlib.h:687:25: note: expected ‘void *’ but argument is of type
‘const char *’
687 | extern void free (void *__ptr) __THROW;
| ~~~~~~^~~~~
src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’
qualifier from pointer target type [-Wdiscarded-qualifiers]
1978 | free(reg2);
| ^~~~
/usr/include/stdlib.h:687:25: note: expected ‘void *’ but argument is of type
‘const char *’
687 | extern void free (void *__ptr) __THROW;
| ~~~~~~^~~~~
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1:
/usr/bin/python3 setup.py build
dh_auto_build: error: pybuild --build -i python{version} -p "3.11 3.12"
returned exit code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: python-pairix
Source-Version: 0.3.8-1
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-pairix, 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 python-pairix
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: Thu, 22 Aug 2024 23:02:54 +0200
Source: python-pairix
Architecture: source
Version: 0.3.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1075419
Changes:
python-pairix (0.3.8-1) unstable; urgency=medium
.
* New upstream version 0.3.8
* gcc-14.patch: new: fix various incompatible pointer types.
(Closes: #1075419)
* d/control: declare compliance to standards version 4.7.0.
* d/python3-pairix.lintian-overrides: refresh override.
* d/control: add myself to uploaders.
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