Your message dated Sun, 04 May 2025 04:15:09 +0000
with message-id <[email protected]>
and subject line Bug#1097434: fixed in ncbi-blast+ 2.16.0+ds-7
has caused the Debian Bug report #1097434,
regarding ncbi-blast+: 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.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1097434: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097434
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:ncbi-blast+
Version: 2.16.0+ds-6
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/ncbi-blast+_2.16.0+ds-6_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
[...]
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/connect/ncbi_priv.h:224:33:
note: in expansion of macro ‘CORE_CURRENT_FUNCTION’
224 | _mess.func = CORE_CURRENT_FUNCTION;
\
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/connect/ncbi_priv.h:239:5:
note: in expansion of macro ‘DO_CORE_LOG_X’
239 | DO_CORE_LOG_X(code, subcode, level, message, dynamic, 0, 0, 0, 0)
| ^~~~~~~~~~~~~
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/connect/ncbi_priv.h:151:5:
note: in expansion of macro ‘DO_CORE_LOG’
151 | DO_CORE_LOG(NCBI_C_ERRCODE_X, subcode, level,
\
| ^~~~~~~~~~~
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/connect/ncbi_tls.c:212:5:
note: in expansion of macro ‘CORE_LOGF_X’
212 | CORE_LOGF_X(47, eLOG_Error,
| ^~~~~~~~~~~
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-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
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/usr/bin/g++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -fopenmp -g -O2
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-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
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/usr/bin/g++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -fopenmp -g -O2
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-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/html/commentdiag.cpp -o
commentdiag.o
/usr/bin/g++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -fopenmp -g -O2
-ffile-prefix-map=/build/reproducible-path/ncbi-blast+-2.16.0+ds=.
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indentstream.o
/usr/bin/g++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -fopenmp -g -O2
-ffile-prefix-map=/build/reproducible-path/ncbi-blast+-2.16.0+ds=.
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-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/inc
-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/html/writer_htmlenc.cpp
-o writer_htmlenc.o
/bin/rm -f libxhtml.so .libxhtml.so.stamp
/usr/bin/g++ -std=gnu++17 -shared -o libxhtml.so
-Wl,-rpath,/usr/lib/ncbi-blast+ -Wl,--enable-new-dtags -Wl,-export-dynamic
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writer_htmlenc.o
-Wl,-rpath-link,/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
-L/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib -lxncbi -lm
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/bin/bash
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/scripts/common/impl/if_diff.sh
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib/libxhtml.so
/bin/ln -f .xhtml.dep
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/status/.xhtml.dep
make[5]: Leaving directory
'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build/html'
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'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build/algo/blast/unit_tests/api'
make[5]: Entering directory
'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build/objtools/blast/gene_info_reader/unit_test'
/usr/bin/g++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -fopenmp -g -O2
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/objtools/blast/gene_info_reader/unit_test/gene_info_test.cpp
-o gene_info_test.o
/usr/bin/g++ -std=gnu++17 -Wl,-rpath,/usr/lib/ncbi-blast+
-Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp
-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now -gdwarf-3 -O2
-fPIE -pie gene_info_test.o
-Wl,-rpath-link,/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
-L/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib -ltest_boost
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/scripts/common/impl/if_diff.sh
/bin/ln -f gene_info_unit_test
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/bin
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_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_FORTIFY_SOURCE=2 -D_MT
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/connect/ncbi_tls.c -o
ncbi_tls.o
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/usr/bin/g++ -std=gnu++17 -shared -o libxconnect.so
-Wl,-rpath,/usr/lib/ncbi-blast+ -Wl,--enable-new-dtags -Wl,-export-dynamic
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-Wl,-z,now -gdwarf-3 -O2 -Wl,--as-needed -fPIC ncbi_lbsm.o ncbi_lbsm_ipc.o
ncbi_ansi_ext.o ncbi_types.o ncbi_core.o ncbi_priv.o ncbi_util.o ncbi_buffer.o
ncbi_socket.o ncbi_connector.o ncbi_connection.o ncbi_connutil.o ncbi_ipv6.o
ncbi_server_info.o ncbi_host_info.o ncbi_service.o ncbi_sendmail.o
ncbi_base64.o ncbi_heapmgr.o ncbi_lb.o ncbi_socket_connector.o
ncbi_file_connector.o ncbi_http_connector.o ncbi_memory_connector.o
ncbi_service_connector.o ncbi_ftp_connector.o ncbi_version.o ncbi_iprange.o
ncbi_local.o ncbi_lbsmd.o ncbi_dispd.o ncbi_linkerd.o ncbi_namerd.o parson.o
ncbi_localip.o ncbi_lbdns.o ncbi_socket_cxx.o ncbi_core_cxx.o
email_diag_handler.o ncbi_conn_streambuf.o ncbi_conn_stream.o ncbi_conn_test.o
ncbi_misc.o ncbi_namedpipe.o ncbi_namedpipe_connector.o ncbi_pipe.o ncbi_p
ipe_connector.o ncbi_conn_reader_writer.o ncbi_userhost.o ncbi_http_session.o
ncbi_monkey.o ncbi_service_cxx.o ncbi_localip_cxx.o ncbi_blowfish.o
ncbi_usage_report.o connect_misc.o ncbi_gnutls.o ncbi_mbedtls.o ncbi_tls.o
-Wl,-rpath-link,/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/scripts/common/impl/if_diff.sh
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
/bin/ln -f libxconnect.so
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib/libxconnect.so
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E -I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/inc
-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/cgi/cgi_entry_reader.cpp
-o cgi_entry_reader.o
/usr/bin/g++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -fopenmp -g -O2
-ffile-prefix-map=/build/reproducible-path/ncbi-blast+-2.16.0+ds=.
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-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/inc
-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/cgi/user_agent.cpp -o
user_agent.o
/bin/rm -f libxcgi.so .libxcgi.so.stamp
/usr/bin/g++ -std=gnu++17 -shared -o libxcgi.so
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ref_args.o cgi_run.o cgi_util.o cgi_serial.o cgi_session.o cgi_exception.o
cgiapp_cached.o cgi_entry_reader.o user_agent.o
-Wl,-rpath-link,/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
-L/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib -lxutil -lxncbi
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/bin/bash
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/scripts/common/impl/if_diff.sh
/bin/ln -f libxcgi.so
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
/bin/ln -f libxcgi.so
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib/libxcgi.so
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/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/status/.xcgi.dep
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=format-security -fcf-protection -fPIC -DNDEBUG -D_LARGEFILE_SOURCE
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-I/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/include
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/src/util/compress/api/archive_zip.cpp
-o archive_zip.o
/bin/rm -f libxcompress.so .libxcompress.so.stamp
/usr/bin/g++ -std=gnu++17 -shared -o libxcompress.so
-Wl,-rpath,/usr/lib/ncbi-blast+ -Wl,--enable-new-dtags -Wl,-export-dynamic
-pthread -fopenmp -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro
-Wl,-z,now -gdwarf-3 -O2 -fPIC compress.o stream.o streambuf.o stream_util.o
bzip2.o lzo.o zlib.o zstd.o reader_zlib.o tar.o archive.o archive_.o
archive_zip.o
-Wl,-rpath-link,/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
-L/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib -lxutil -lxncbi
-lbz2 -lz -lm -lpthread
/bin/bash
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/scripts/common/impl/if_diff.sh
/bin/ln -f libxcompress.so
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib
/bin/ln -f libxcompress.so
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/lib/libxcompress.so
/bin/ln -f .xcompress.dep
/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/status/.xcompress.dep
make[5]: Leaving directory
'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build/util/compress/api'
make[4]: Leaving directory
'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build/util/compress/api'
make[3]: Leaving directory
'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build'
make[2]: *** [Makefile.flat:415: ptb_all] Error 2
make[2]: Leaving directory
'/build/reproducible-path/ncbi-blast+-2.16.0+ds/c++/BUILD/build'
make[1]: *** [debian/rules:102: override_dh_auto_build-arch] Error 2
make[1]: Leaving directory '/build/reproducible-path/ncbi-blast+-2.16.0+ds'
make: *** [debian/rules:210: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: ncbi-blast+
Source-Version: 2.16.0+ds-7
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ncbi-blast+, 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.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-blast+ 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, 03 May 2025 23:42:51 -0400
Source: ncbi-blast+
Architecture: source
Version: 2.16.0+ds-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1097434 1100037
Changes:
ncbi-blast+ (2.16.0+ds-7) unstable; urgency=medium
.
* debian/control: Build-depend on libncbi-vdb-dev where available
(amd64, arm64, and x32).
* debian/copyright: Overhaul with much help from licenserecon (lrc).
* debian/patches/fix_bm_for_gcc15 (new): Cherry-pick a BitMagic fix
needed for modern compilers, adjusting the path appropriately.'
(Closes: #1097434.)
* debian/rules: Build against (packaged!) VDB where available, using
logic cribbed from ncbi-igblast. (Closes: #1100037.)
* Standards-Version: 4.7.2 (routine-update)
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