ncbi-blast+ (2.17.0+ds-1) UNRELEASED; urgency=medium
* New upstream release. (NOT RELEASED YET.)
+ * debian/patches: Update for new release, mostly formally.
+ * debian/patches/series: Comment out support_mbedtls3, allow_pcre2,
+ and fix_bm_for_gcc15, all incorporated upstream.
+ * debian/patches/system_mbedtls_only: Drop code changes (incorporated
+ upstream) and port Makefile.connssl.lib's changes.
- -- Aaron M. Ucko <ucko@debian.org> Sat, 27 Sep 2025 20:39:52 -0400
+ -- Aaron M. Ucko <ucko@debian.org> Sat, 27 Sep 2025 20:57:59 -0400
ncbi-blast+ (2.16.0+ds-7) unstable; urgency=medium
--- a/c++/src/app/blastdb/makeblastdb.cpp
+++ b/c++/src/app/blastdb/makeblastdb.cpp
-@@ -293,7 +293,13 @@ void CMakeBlastDBApp::Init()
+@@ -298,7 +298,13 @@ void CMakeBlastDBApp::Init()
arg_desc->AddDefaultKey("blastdb_version", "version",
"Version of BLAST database to be created",
CArgDescriptions::eInteger,
arg_desc->AddDefaultKey("max_file_sz", "number_of_bytes",
--- a/c++/src/app/blastdb/makeprofiledb.cpp
+++ b/c++/src/app/blastdb/makeprofiledb.cpp
-@@ -420,7 +420,13 @@ void CMakeProfileDBApp::x_SetupArgDescri
+@@ -418,7 +418,13 @@ void CMakeProfileDBApp::x_SetupArgDescri
arg_desc->AddDefaultKey("blastdb_version", "version",
"Version of BLAST database to be created",
CArgDescriptions::eInteger,
+++ b/c++/src/algo/blast/core/Makefile.blast.lib
@@ -23,6 +23,7 @@ CFLAGS = $(FAST_CFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
- WATCHERS = madden camacho fongah2
+ WATCHERS = camacho fongah2
+DLL_LIB = composition_adjustment xconnect tables
seqmasks_io
--- a/c++/src/build-system/library_relations.txt
+++ b/c++/src/build-system/library_relations.txt
-@@ -1369,7 +1369,7 @@ xassembly_svc needs gc_asn_access
+@@ -1481,7 +1481,7 @@ xassembly_svc needs gc_asn_access
xbiosample_util needs $(OBJEDIT_LIBS)
xbiosample_util needs xmlwrapp
xbiosample_util needs xobjutil
+++ b/c++/src/corelib/Makefile.test_mt.lib
@@ -3,6 +3,8 @@
SRC = test_mt
- LIB = test_mt
+ LIB = test_mt
+DLL_LIB = xncbi
+
LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS)
+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info taxon1 seqset seq general xser \
++ xobjmgr xnetblast blastdb taxon1 seqset seq general xser \
+ xcgi xhtml tables xncbi
+
### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
WATCHERS = camacho
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,10 @@ LIB_OR_DLL = both
+@@ -13,6 +13,10 @@ LIB_OR_DLL = both
# Dependencies for shared library
DLL_LIB = general ncbi_xreader$(DLL) $(GENBANK_PSG_CLIENT_LDEP)
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
--DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB)
-+DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) xutil xncbi
+-DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) zcf
++DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) zcf xutil xncbi
LIBS = $(BZ2_LIBS) $(LZO_LIBS) $(Z_LIBS) $(ZSTD_LIBS) $(ORIG_LIBS)
WATCHERS = ivanov
USES_LIBRARIES = \
xser
---- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -6,6 +6,7 @@ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG
- LIB = gene_info
- SRC = gene_info gene_info_reader file_utils
-
-+DLL_LIB = xncbi
-
- USES_LIBRARIES = \
- xncbi
--- a/c++/src/objects/medlars/Makefile.medlars.lib
+++ b/c++/src/objects/medlars/Makefile.medlars.lib
@@ -1,6 +1,7 @@
USES_LIBRARIES = \
biblio
---- a/c++/src/objects/mla/Makefile.mla.lib
-+++ b/c++/src/objects/mla/Makefile.mla.lib
-@@ -1,7 +1,7 @@
- LIB = mla
- SRC = mla__ mla___
-
--DLL_LIB = medlars
-+DLL_LIB = medlars pub pubmed xser xutil xncbi
-
- USES_LIBRARIES = \
- medlars pub pubmed
---- a/c++/src/objects/mla/Makefile.mlacli.lib
-+++ b/c++/src/objects/mla/Makefile.mlacli.lib
-@@ -5,5 +5,7 @@ SRC = mla_client mla_client_
-
- DLL_LIB = mla pubmed medlars xconnect
-
-+DLL_LIB = mla xconnect xser xutil xncbi
-+
- USES_LIBRARIES = \
- mla xconnect
--- a/c++/src/objects/pubmed/Makefile.pubmed.lib
+++ b/c++/src/objects/pubmed/Makefile.pubmed.lib
@@ -1,6 +1,7 @@
+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
@@ -13,6 +13,8 @@ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(ORIG_
- WATCHERS = jianye zaretska madden camacho fongah2
+ WATCHERS = jianye zaretska camacho fongah2
+DLL_LIB = xformat $(BLAST_LIBS) align_format blastxml blastxml2 \
+ xhtml xcgi xncbi
WATCHERS = dicuccio gotvyans
-+DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \
++DLL_LIB = xcleanup valid gbseq medlars pubmed submit xalnmgr \
+ xobjutil taxon3 $(SOBJMGR_LIBS)
USES_LIBRARIES = \
Last-Update: 2020-09-19
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -10806,7 +10806,7 @@ if test -z "$CONF_f_runpath" ; then
+@@ -10946,7 +10946,7 @@ if test -z "$CONF_f_runpath" ; then
CONF_f_runpath="-R"
;;
linux*:[GI]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \
irix*:* | linux*:KCC | *:Compaq )
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -2424,7 +2424,7 @@ if test -z "$CONF_f_runpath" ; then
+@@ -2470,7 +2470,7 @@ if test -z "$CONF_f_runpath" ; then
CONF_f_runpath="-R"
;;
linux*:[[GI]]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \
--- a/c++/src/connect/ncbi_localip.c
+++ b/c++/src/connect/ncbi_localip.c
-@@ -67,7 +67,7 @@
+@@ -68,7 +68,7 @@
# define INADDR_LOOPBACK 0x7F000001
#endif /*!INADDR_LOOPBACK*/
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -10912,7 +10912,7 @@ case "$compiler:$compiler_version:$with_
+@@ -11052,7 +11052,7 @@ case "$compiler:$compiler_version:$with_
break
;;
/* )
esac
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -2491,7 +2491,7 @@ case "$compiler:$compiler_version:$with_
+@@ -2537,7 +2537,7 @@ case "$compiler:$compiler_version:$with_
break
;;
/* )
Forwarded: no
--- a/c++/src/algo/blast/api/blast_usage_report.cpp
+++ b/c++/src/algo/blast/api/blast_usage_report.cpp
-@@ -190,6 +190,7 @@ void CBlastUsageReport::AddParam(EUsageP
+@@ -195,6 +195,7 @@ void CBlastUsageReport::AddParam(EUsageP
void CBlastUsageReport::x_CheckBlastUsageEnv()
{
char * blast_usage_env = getenv("BLAST_USAGE_REPORT");
if(blast_usage_env != NULL){
bool enable = NStr::StringToBool(blast_usage_env);
if (!enable) {
-@@ -198,6 +199,10 @@ void CBlastUsageReport::x_CheckBlastUsag
+@@ -203,6 +204,10 @@ void CBlastUsageReport::x_CheckBlastUsag
LOG_POST(Info <<"Phone home disabled");
return ;
}
}
CNcbiIstrstream empty_stream(kEmptyStr);
-@@ -210,10 +215,15 @@ void CBlastUsageReport::x_CheckBlastUsag
+@@ -215,10 +220,15 @@ void CBlastUsageReport::x_CheckBlastUsag
LOG_POST(Info <<"Phone home disabled by config setting");
return ;
}
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
- # $Id: update_blastdb.pl 681901 2024-04-17 13:16:37Z ivanov $
+ # $Id: update_blastdb.pl 697487 2025-05-14 13:03:33Z ivanov $
# ===========================================================================
#
system_mbedtls_only
-support_mbedtls3
-allow_pcre2
+# support_mbedtls3
+# allow_pcre2
optin_usage_report
enable_clean_after_failed_compile
hurd_fixes
tune_lmdb_defaults
2to3
big_endian_workaround
-fix_bm_for_gcc15
+# fix_bm_for_gcc15
+# This test requires an internet connection, shouldn't be run on a build server
+# CHECK_CMD = blast_services_unit_test
- WATCHERS = madden camacho
+ WATCHERS = camacho
SetupArgDescriptions(arg_desc.release());
--- a/c++/src/app/blastdb/makeprofiledb.cpp
+++ b/c++/src/app/blastdb/makeprofiledb.cpp
-@@ -1838,7 +1838,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co
+@@ -1811,7 +1811,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co
if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)
{
*m_LogFile << filename +
return true;
--- a/c++/src/objects/seqalign/Dense_seg.cpp
+++ b/c++/src/objects/seqalign/Dense_seg.cpp
-@@ -980,7 +980,7 @@ void CDense_seg::RemapToLoc(TDim row, co
+@@ -1001,7 +1001,7 @@ void CDense_seg::RemapToLoc(TDim row, co
if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {
NCBI_THROW(CSeqalignException, eInvalidInputData,
"CDense_seg::RemapToLoc():"
if (widths_determined[seg]) {
--- a/c++/src/objects/seqfeat/institution_codes.inc
+++ b/c++/src/objects/seqfeat/institution_codes.inc
-@@ -791,7 +791,7 @@ static const char* const kInstitutionCol
+@@ -832,7 +832,7 @@ static const char* const kInstitutionCol
"BPPT-ESC\tc\tBPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit\t\t\t",
"BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t",
"BR<BEL>\ts\tBotanic Garden Meise\t\t\t",
"BRB\ts\tBrassica Resource Bank\t\t\t",
--- a/c++/src/objects/seqfeat/institution_codes.txt
+++ b/c++/src/objects/seqfeat/institution_codes.txt
-@@ -755,7 +755,7 @@ BPM s Beipiao Paleontological Museum
+@@ -796,7 +796,7 @@ BPM s Beipiao Paleontological Museum
BPPT-ESC c BPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit
BPU s Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology
BR<BEL> s Botanic Garden Meise
NCBI_THROW_FMT(CObjMgrException, eFindConflict,
--- a/c++/src/objtools/align_format/taxFormat.cpp
+++ b/c++/src/objtools/align_format/taxFormat.cpp
-@@ -616,7 +616,7 @@ void CTaxFormat::x_LoadTaxTree(void)
+@@ -689,7 +689,7 @@ void CTaxFormat::x_LoadTaxTree(void)
}
}
if (!tax_load_ok) {
--- a/c++/src/objtools/format/flat_file_config.cpp
+++ b/c++/src/objtools/format/flat_file_config.cpp
-@@ -655,7 +655,7 @@ void CFlatFileConfig::AddArgumentDescrip
+@@ -656,7 +656,7 @@ void CFlatFileConfig::AddArgumentDescrip
// from
arg_desc->AddOptionalKey("from", "From",
out_sObjectClosingString = "} }" + out_sObjectClosingString;
--- a/c++/src/objtools/readers/agp_util.cpp
+++ b/c++/src/objtools/readers/agp_util.cpp
-@@ -173,7 +173,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
+@@ -174,7 +174,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
"object_beg != previous object_end + 1",
"no valid AGP lines",
"in \"Scaffold from component\" file, invalid scaffold-breaking gap",
"in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",
-@@ -193,7 +193,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
+@@ -194,7 +194,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
// Content Warnings
"gap at the end of object (OK if X is the circular chromosome/plasmid)",
"gap at the beginning of object ",
--- a/c++/src/connect/ncbi_gnutls.c
+++ b/c++/src/connect/ncbi_gnutls.c
-@@ -748,6 +748,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -769,6 +769,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
- assert(!s_GnuTlsCredAnon);
+ CORE_TRACE("GnuTlsInit(): Enter");
+#if 0
version = gnutls_check_version(0);
if (strcasecmp(GNUTLS_VERSION, version) != 0) {
CORE_LOGF_X(26, eLOG_Critical,
-@@ -755,6 +756,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -776,6 +777,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
GNUTLS_VERSION, version));
assert(0);
}
+#endif
- CORE_TRACE("GnuTlsInit(): Enter");
-
+ if (!pull || !push) {
+ status = eIO_InvalidArg;
--- a/c++/src/connect/ncbi_mbedtls.c
+++ b/c++/src/connect/ncbi_mbedtls.c
-@@ -739,12 +739,14 @@ static EIO_Status s_MbedTlsInit(FSSLPull
- psa_status_t psa_status;
+@@ -770,12 +770,14 @@ static EIO_Status s_MbedTlsInit(FSSLPull
+ CORE_TRACE("MbedTlsInit(): Enter");
mbedtls_version_get_string(version);
+#if 0
}
+#endif
- CORE_TRACE("MbedTlsInit(): Enter");
-
+ if (!pull || !push) {
+ status = eIO_InvalidArg;
Subject: Omit convenience mbed TLS copy
--- a/c++/src/connect/Makefile.connssl.lib
+++ b/c++/src/connect/Makefile.connssl.lib
-@@ -1,8 +1,10 @@
- # $Id: Makefile.connssl.lib 642488 2021-12-20 21:00:34Z ucko $
+@@ -1,6 +1,6 @@
+ # $Id: Makefile.connssl.lib 682178 2024-04-23 19:31:32Z ucko $
-CPPFLAGS = $(TLS_INCLUDE) -I$(srcdir)/mbedtls $(ORIG_CPPFLAGS)
+CPPFLAGS = $(TLS_INCLUDE) $(ORIG_CPPFLAGS)
--SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls \
-+SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls
-+
-+SRC_MBEDTLS_UNUSED = \
- mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/aria \
- mbedtls/asn1parse mbedtls/asn1write mbedtls/base64 mbedtls/bignum \
- mbedtls/blowfish mbedtls/camellia mbedtls/ccm mbedtls/chacha20 \
---- a/c++/src/connect/connect_misc_impl.hpp
-+++ b/c++/src/connect/connect_misc_impl.hpp
-@@ -30,11 +30,10 @@
- *
- */
-
--#include "mbedtls/mbedtls/ncbicxx_rename_mbedtls.h"
--#include "mbedtls/mbedtls/error.h"
--#include "mbedtls/mbedtls/ctr_drbg.h"
--#include "mbedtls/mbedtls/entropy.h"
--#include "mbedtls/mbedtls/ssl.h"
-+#include <mbedtls/error.h>
-+#include <mbedtls/ctr_drbg.h>
-+#include <mbedtls/entropy.h>
-+#include <mbedtls/ssl.h>
-
- #include <corelib/ncbimisc.hpp>
-
---- a/c++/src/connect/ncbi_mbedtls.c
-+++ b/c++/src/connect/ncbi_mbedtls.c
-@@ -43,7 +43,6 @@
-
- #if defined(HAVE_LIBMBEDTLS) || defined(NCBI_CXX_TOOLKIT)
-
--# ifdef HAVE_LIBMBEDTLS /* external */
- # include <mbedtls/ctr_drbg.h>
- # include <mbedtls/debug.h>
- # include <mbedtls/entropy.h>
-@@ -53,17 +52,6 @@
- # include <mbedtls/ssl.h>
- # include <mbedtls/threading.h>
- # include <mbedtls/version.h>
--# else /* embedded */
--# include "mbedtls/mbedtls/ctr_drbg.h"
--# include "mbedtls/mbedtls/debug.h"
--# include "mbedtls/mbedtls/entropy.h"
--# include "mbedtls/mbedtls/error.h"
--# include "mbedtls/mbedtls/pk.h"
--# include "mbedtls/mbedtls/net_sockets.h"
--# include "mbedtls/mbedtls/ssl.h"
--# include "mbedtls/mbedtls/threading.h"
--# include "mbedtls/mbedtls/version.h"
--# endif /*HAVE_LIBMBEDTLS*/
-
- # if defined(ENOTSUP)
- # define NCBI_NOTSUPPORTED ENOTSUP
+ SRC_MBED = aes aesce aesni aria asn1parse asn1write base64 bignum bignum_core \
+ bignum_mod bignum_mod_raw block_cipher camellia ccm chacha20 \
+@@ -21,7 +21,7 @@ SRC_MBED = aes aesce aesni aria asn1pars
+ ssl_tls13_client ssl_tls13_generic ssl_tls13_keys ssl_tls13_server \
+ threading timing version_features x509 x509_create x509_crl \
+ x509_crt x509_csr x509write x509write_crt x509write_csr
+-SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls $(SRC_MBED:%=mbedtls/%)
++SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls # $(SRC_MBED:%=mbedtls/%)
+
+ SRC = $(SRC_TLS)
+ LIB = connssl
--- a/c++/src/connect/Makefile.xxconnect2.lib
+++ b/c++/src/connect/Makefile.xxconnect2.lib
@@ -9,8 +9,7 @@ REQUIRES = LIBUV NGHTTP2
projects / ncbi-blast+.git / commitdiff