[Debian-med-packaging] Bug#1097575: phast: ftbfs with GCC-15

[Matthias Klose]

Package: src:phast
Version: 1.7+dfsg-2
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
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