Your message dated Fri, 19 Sep 2025 22:05:28 +0000
with message-id <[email protected]>
and subject line Bug#1097575: fixed in phast 1.7+dfsg-3
has caused the Debian Bug report #1097575,
regarding phast: 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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--
1097575: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097575
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:phast
Version: 1.7+dfsg-2
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/phast_1.7+dfsg-2_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
[...]
| |
| char *
In file included from
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
from
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
from msa_view.c:14:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56:
note: expected ‘const unsigned char *’ but argument is of type ‘char *’
386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
<command-line>: warning: ‘PHAST_HOME’ redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: ‘PHAST_HOME’ redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3
-Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\"
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall
-I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\"
-fno-strict-aliasing -c refeature.c -o refeature.o
<command-line>: warning: ‘PHAST_HOME’ redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3
-Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\"
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall
-I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\"
-fno-strict-aliasing -c stringiphy.c -o stringiphy.o
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3
-Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\"
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall
-I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\"
-fno-strict-aliasing -c treeGen.c -o treeGen.o
<command-line>: warning: ‘PHAST_HOME’ redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: ‘PHAST_HOME’ redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3
-Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\"
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall
-I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include
-DPHAST_VERSION=\"v1.6\"
-DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\"
-fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o
<command-line>: warning: ‘PHAST_HOME’ redefined
<command-line>: note: this is the location of the previous definition
tree_doctor.c: In function ‘main’:
tree_doctor.c:348:19: warning: the comparison will always evaluate as ‘true’
for the address of ‘name’ will never be NULL [-Waddress]
348 | if (n->name != NULL && n->name[0] != '\0' &&
| ^~
In file included from
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26,
from tree_doctor.c:14:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/trees.h:47:8:
note: ‘name’ declared here
47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila
23' usually one of the sequence names */
| ^~~~
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o
/build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists
all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro
-Wl,-z,now
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o
/build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve
base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro
-Wl,-z,now
/usr/bin/ld: all_dists.o: in function `main':
./src/util/./src/util/all_dists.c:70:(.text.startup+0x15d): undefined reference
to `tr_new_from_file'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:68:(.text.startup+0x181):
undefined reference to `tr_new_from_string'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:106:(.text.startup+0x25b):
undefined reference to `tr_new_from_file'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:100:(.text.startup+0x2b5):
undefined reference to `tm_new_from_file'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:101:(.text.startup+0x2c2):
undefined reference to `tr_create_copy'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:102:(.text.startup+0x2d4):
undefined reference to `tm_free'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:157:(.text.startup+0x8ad):
undefined reference to `tr_total_len'
/usr/bin/ld:
/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o):
in function `tm_rmp_protect':
./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360):
undefined reference to `tm_get_nparams'
/usr/bin/ld:
./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185):
undefined reference to `tm_get_nparams'
/usr/bin/ld:
./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac):
undefined reference to `tm_get_nparams'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:20:
/build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists] Error 1
make[3]: *** Waiting for unfinished jobs....
/usr/bin/ld: base_evolve.o: in function `main':
./src/util/./src/util/base_evolve.c:68:(.text.startup+0x2f4): undefined
reference to `tm_new_from_file'
/usr/bin/ld: ./src/util/./src/util/base_evolve.c:98:(.text.startup+0x413):
undefined reference to `tm_new_from_file'
/usr/bin/ld: ./src/util/./src/util/base_evolve.c:110:(.text.startup+0x476):
undefined reference to `tm_generate_msa'
/usr/bin/ld: ./src/util/./src/util/base_evolve.c:136:(.text.startup+0x55a):
undefined reference to `tm_generate_msa'
/usr/bin/ld: ./src/util/./src/util/base_evolve.c:110:(.text.startup+0x663):
undefined reference to `tm_generate_msa'
/usr/bin/ld:
/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o):
in function `tm_rmp_protect':
./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360):
undefined reference to `tm_get_nparams'
/usr/bin/ld:
./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185):
undefined reference to `tm_get_nparams'
/usr/bin/ld:
./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac):
undefined reference to `tm_get_nparams'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:20:
/build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve] Error 1
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util'
make[2]: *** [Makefile:9: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src'
make[1]: *** [Makefile:6: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned
exit code 2
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: phast
Source-Version: 1.7+dfsg-3
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
phast, 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.
Nilesh Patra <[email protected]> (supplier of updated phast 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: Sat, 20 Sep 2025 03:01:50 +0530
Source: phast
Architecture: source
Version: 1.7+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1097575
Changes:
phast (1.7+dfsg-3) unstable; urgency=medium
.
* Team Upload.
* Fixup FTBFS with gcc-15 (Closes: #1097575)
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