dgit.raspbian.org Git - ncbi-blast+.git/log

Declare fast forward from 2.16.0+ds-5

[dgit --quilt=gbp --overwrite]

big_endian_workaround

Gbp-Pq: Name big_endian_workaround

to3

Gbp-Pq: Name 2to3

tune_lmdb_defaults

Gbp-Pq: Name tune_lmdb_defaults

Bypass env in Perl script shebangs.

Gbp-Pq: Name run_perl_directly

Support GCC 10+.

Debian-Bug: 957581.

* 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).

Gbp-Pq: Name support_gcc10

Spelling fixes

Gbp-Pq: Name spelling

add missing lib for tests

Forwarded: Not-Needed
Last-Updated: 2018-02-11

Gbp-Pq: Name fix_unit_tests

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).

Gbp-Pq: Name optionally_keep_sequence

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.

Gbp-Pq: Name suppress_tls_version_checks

Support x32

Avoid picking up wrong inline assembly.

Gbp-Pq: Name support_x32

fix path for debian build

Forwarded: no
Last-Updated: 2014-06-06

Gbp-Pq: Name fix_configure

remove network required test

Forwarded: no
Last-Updated: 2013-06-01

Gbp-Pq: Name skip_services_unit_test

build executables with -fPIE, not -fPIC

* -fPIC is only useful for shared libraries; substitute -fPIE (along
with -pie at link time) when building executables.

Author: Aaron M. Ucko <ucko@debian.org>
Last-Update: 2012-05-10

Gbp-Pq: Name use_pie_for_apps

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.

Debian-Bug: 633567.
Author: Aaron M. Ucko <ucko@debian.org>
Last-Update: 2011-08-28

Gbp-Pq: Name no_multiarch_rpath

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.

Debian-Bug: 633567.
Author: Aaron M. Ucko <ucko@debian.org>
Last-Update: 2016-12-05

Gbp-Pq: Name fix_lib_deps

rename binary as blast+ for package coherency.

Last-Updated: 2011-10-03

Gbp-Pq: Name legacy_rename_rpsblast

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.

Author: Aaron M. Ucko <ucko@debian.org>
Last-Update: 2020-09-19

Gbp-Pq: Name hurd_fixes

clean after failure

Last-Updated: 2013-06-01
Forwarded: no

Gbp-Pq: Name enable_clean_after_failed_compile

blast+ use optout to send usage reports over internet

Last-Updated: 202-02-10
Forwarded: no

Gbp-Pq: Name optin_usage_report

[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).

JIRA: CXX-12761,

git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@102806 78c7ea69-d796-4a43-9a09-de51944f1b03

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.

Gbp-Pq: Name allow_pcre2

[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.

git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@102329 78c7ea69-d796-4a43-9a09-de51944f1b03

Gbp-Pq: Name support_mbedtls3

Omit convenience mbed TLS copy

Gbp-Pq: Name system_mbedtls_only

Finalize ncbi-blast+ 2.16.0+ds-6 for unstable.

debian/rules: Try disabling optimization altogether on sh4.

Reinstate big-endian builds, with default blastdb_version 4.

* debian/control: Reinstate big-endian builds, which can be salvaged
  adequately well.
* debian/patches/big_endian_workaround (new): On big-endian
  architectures, roll makeblastdb's and makeprofiledb's default
  blastdb_version back to 4 pending a proper fix.  Some things,
  including in particular q2-feature-classifier, will still explicitly
  request version 5, but everything else should be OK.  (See #1077777.)

Start work on ncbi-blast+ 2.16.0+ds-6 (yet more arch tuneups).

Finalize ncbi-blast+ 2.16.0+ds-5 for unstable.

Declare fast forward from 2.16.0+ds-4

[dgit --quilt=gbp --overwrite]