Debian Patches

Status for ncbi-blast+/2.16.0+ds-6

Patch Description Author Forwarded Bugs Origin Last update
system_mbedtls_only Omit convenience mbed TLS copy Aaron M. Ucko <amu@ucko.debian.net> no 2021-12-01
support_mbedtls3 [PATCH] Accommodate Mbed TLS 3.x (specifically, 3.6.0 LTS).
- Conditionally pass mbedtls_pk_parse_key the existing pRNG and its state.
- Call psa_crypto_init during setup, as PSA may be in play even when not
explicitly enabled. Documentation suggests calling it as early as
possible; in practice, though, holding off until after pRNG
initialization avoids "insufficient entropy" errors under 2.x (at least
2.28.8 LTS on Linux) and still works fine as of 3.6.0.
- At least for now, ensure that MBEDTLS_SSL_VERIFY_NONE remains effective
by additionally capping the TLS version at 1.2; as of 1.3, certificate
checking has become mandatory, and Mbed TLS respects that requirement.
- Additional tuneups to ncbi_mbedtls.c-only code:
-- Account for error-code macro repertoire changes by conditionalizing
major-version-specific macros on their availability and specifically
checking for or emitting MBEDTLS_ERR_PLATFORM_FEATURE_UNSUPPORTED (new)
as appropriate,
-- x_ErrorToStatus: Conditionally use MBEDTLS_PRIVATE for p_bio, which has
no accessor.
-- x_MbedTlsWrite: Substitute mbedtls_ssl_get_max_out_record_payload for
mbedtls_ssl_get_output_max_frag_len, which didn't account for other
relevant considerations and is now fully private.

https://github.com/Mbed-TLS/mbedtls/blob/development/docs/3.0-migration-guide.md
supplied useful guidance. JIRA: CXX-13565.
ucko <ucko@ncbi.nlm.nih.gov> no 2024-04-23
allow_pcre2 [PATCH] Allow substituting PCRE2 for legacy PCRE by explicit request.
- For now, require opt-in via --with-components="...;PCRE2;..." (CMake),
--with-pcre2 (traditional Unix build system), or uncommenting the
relevant ThirdParty_PCRE2 setting in project_tree_builder.ini
(traditional Windows build system).
- Likewise, hold off on switching the bundled copy to PCRE2 or checking
for any functions or headers that will become of interest.
- Redundantly (for now) shun external PCRE2 in bin-release configurations.
- Otherwise favor (allowed!) external installations over the bundled
copy, preferring PCRE2 over legacy PCRE when both are found and
allowed but (in due course) external legacy PCRE over bundled PCRE2 in
the absence of external PCRE2.
- In the traditional build system, have the widely used PCRE_LIBS macro
correspond to whichever PCRE is default (when not falling back on a
bundled copy), and add a PCRE_LEGACY_LIBS macro for the sake of
anything using legacy PCRE directly (very occasionally seen).



Irrelevant (and inapplicable) changes to c++/src/build-system/cmake/,
c++/src/build-system/configure (which will be regenerated anyway), and
c++/src/build-system/project_tree_builder.ini elided.
ucko <ucko@ncbi.nlm.nih.gov> no 2024-07-18
optin_usage_report this patch change strategy to optin ie user asks per config/env vars to send reports, else it is disabled by default.
Not a bug by itself but default strategy update to send info over internet.
Olivier Sallou <osallou@debian.org> no
enable_clean_after_failed_compile Enable clean Tim Booth no
hurd_fixes fix portability issues that led to Hurd build failures
* src/build-system/configure(.ac):
- Reflect the Hurd's support for -Wl,rpath,... .
* src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
cope with missing PATH_MAX everywhere, not just under Windows.
Aaron M. Ucko <ucko@debian.org> no 2020-09-19
legacy_rename_rpsblast rename binary as blast+ for package coherency. Olivier Sallou <olivier.sallou@irisa.fr> no
fix_lib_deps ensure that all libraries link against all direct dependencies
* src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
loop between libxblast and libxalgoblastdbindex by having the former
provide only the C++ BLAST API, leaving the C core only in libblast.
* src/build-system/library_relations.txt: Change xblast's
relationship to blast from includes to needs, accordingly.
* src/algo/blast/Makefile.blast_macros.mk: Add blast to BLAST_LIBS.
* src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
rather than libconnect for consistency with libblast, which uses the
former to keep the aforementioned cycle-breaking from causing
inconsistency elsewhere.
Aaron M. Ucko <ucko@debian.org> no 2016-12-05
no_multiarch_rpath avoid redundant rpath entries on multiarch systems
* src/build-system/configure(.ac): when ensuring that executables
will be able to find libstdc++, don't add rpath entries that files
under /etc/ld.so.conf.d already specify, even if they don't resemble
traditional single-architecture or biarch locations.
Aaron M. Ucko <ucko@debian.org> no 2011-08-28
use_pie_for_apps build executables with -fPIE, not -fPIC
* -fPIC is only useful for shared libraries; substitute -fPIE (along
with -pie at link time) when building executables.
Aaron M. Ucko <ucko@debian.org> no 2012-05-10
skip_services_unit_test test require internet connection Tim Booth no
fix_configure Debian build is not done in configure directory, need to update way to get relative configure.orig script Olivier Sallou <osallou@debian.org> no
support_x32 Support x32
Avoid picking up wrong inline assembly.
Aaron M. Ucko <ucko@debian.org> no 2021-12-01
suppress_tls_version_checks suppress gnu TLS and mbed TLS version checks
Prevent bailing when the exact compile-time and runtime GNU TLS versions
differ; trust dpkg to disallow combinations that are actually incompatible.
Likewise for mbed TLS.
Aaron M. Ucko <ucko@debian.org> no 2021-12-01
optionally_keep_sequence Hang on to sequence data even if -parse_deflines recognized a non-local ID, on the condition that the environment variable BLAST_ALWAYS_KEEP_SEQUENCE
(or configuration parameter [BLAST] always_keep_sequence) is set to a
"true" value (English-only, case-insensitive true, t, yes, y, or 1).
Aaron M. Ucko <ucko@debian.org> no 2016-12-14
fix_unit_tests unit_test need blast lib to compile Olivier Sallou <osallou@debian.org> not-needed
spelling Spelling fixes Michael R. Crusoe <michael.crusoe@gmail.com> no
support_gcc10 Support GCC 10+.
* ncbifile.cpp (s_GetFileSystemInfo): Formally cast st.f_type to avoid
narrowing errors for cases with the high bit set when that field is
a 32-bit signed integer (as on i386).
Aaron M. Ucko <ucko@debian.org> no 2020-09-06
run_perl_directly Bypass env in Perl script shebangs. Aaron M. Ucko <ucko@debian.org> no 2021-12-01
tune_lmdb_defaults no
2to3 no
big_endian_workaround no

All known versions for source package 'ncbi-blast+'

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