| 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 |