* New upstream release, which should be (more than) new enough for
recent q2-feature-classifier. (Closes: #1074316.) (NOT RELEASED YET.)
+ * debian/patches: Update for new release, mostly formally.
- -- Aaron M. Ucko <ucko@debian.org> Wed, 17 Jul 2024 21:23:09 -0400
+ -- Aaron M. Ucko <ucko@debian.org> Wed, 17 Jul 2024 21:39:28 -0400
ncbi-blast+ (2.12.0+ds-4) unstable; urgency=medium
Forwarded: no
--- a/c++/src/build-system/new_module.sh.in
+++ b/c++/src/build-system/new_module.sh.in
-@@ -198,7 +198,7 @@
+@@ -203,7 +203,7 @@ if test -z "$datatool"; then # keep look
if test -n "$DYLD_LIBRARY_PATH"; then
wrapper="DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH"
fi
Last-Update: 2016-12-05
--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -27,7 +27,9 @@ SRC = $(SRC_CXX)
+@@ -27,7 +27,8 @@ SRC = $(SRC_CXX)
LIB = blastinput
--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil
-+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
-+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
-+ scoremat seqset seq xser xutil xncbi
+-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil sqlitewrapp
++DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
++ seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) sqlitewrapp scoremat
# should be redundant, given the above :-/
ASN_DEP = seqset xnetblast
seqmasks_io
--- a/c++/src/build-system/library_relations.txt
+++ b/c++/src/build-system/library_relations.txt
-@@ -1603,7 +1603,7 @@ xbiosample_util needs mlacli
- xbiosample_util needs valid
+@@ -1369,7 +1369,7 @@ xassembly_svc needs gc_asn_access
+ xbiosample_util needs $(OBJEDIT_LIBS)
xbiosample_util needs xmlwrapp
xbiosample_util needs xobjutil
-xblast includes blast
+xblast needs blast
+ xblast needs utrtprof
xblast needs xalgoblastdbindex
xblast needs xalgodustmask
- xblast needs xalgowinmask
--- a/c++/src/cgi/Makefile.cgi.lib
+++ b/c++/src/cgi/Makefile.cgi.lib
@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
# CFLAGS = $(FAST_CFLAGS)
--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -29,6 +29,8 @@ LIB = seqdb
- DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB)
+@@ -27,9 +27,10 @@ seqidlist_reader \
+ tax4blastsqlite
+
+ LIB = seqdb
+-DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) sqlitewrapp
LIBS = $(BLAST_THIRD_PARTY_LIBS)
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++DLL_LIB = blastdb $(SOBJMGR_LIBS) $(LMDB_LIB) sqlitewrapp
+
CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(SQLITE3_INCLUDE) $(ORIG_CPPFLAGS) $(BLAST_THIRD_PARTY_INCLUDE)
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
+-DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB)
++DLL_LIB = $(BZ2_LIB) $(LZO_LIB) $(Z_LIB) $(ZSTD_LIB) xutil xncbi
+ LIBS = $(BZ2_LIBS) $(LZO_LIBS) $(Z_LIBS) $(ZSTD_LIBS) $(ORIG_LIBS)
WATCHERS = ivanov
--- a/c++/src/util/xregexp/Makefile.xregexp.lib
CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
+-DLL_LIB = $(PCRE_LIB) xutil
++DLL_LIB = $(PCRE_LIB) xutil xncbi
LIBS = $(PCRE_LIBS)
USES_LIBRARIES = \
--- a/c++/src/objtools/readers/Makefile.xobjread.lib
+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
@@ -29,6 +29,6 @@ SRC = reader_message reader_listener rea
- message_listener line_error
+ message_listener line_error
-DLL_LIB = submit seqset $(SEQ_LIBS) general xutil xlogging
biblio
--- a/c++/src/objects/mla/Makefile.mla.lib
+++ b/c++/src/objects/mla/Makefile.mla.lib
-@@ -1,6 +1,7 @@
+@@ -1,7 +1,7 @@
LIB = mla
SRC = mla__ mla___
+-DLL_LIB = medlars
+DLL_LIB = medlars pub pubmed xser xutil xncbi
USES_LIBRARIES = \
+++ b/c++/src/objects/taxon3/Makefile.taxon3.lib
@@ -8,6 +8,7 @@ DLL_LIB = xconnect
- WATCHERS = bollin holmesbr
+ WATCHERS = stakhovv holmesbr
+DLL_LIB = xconnect seq xser xutil xncbi
+++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib
@@ -11,7 +11,7 @@ SRC = autogenerated_cleanup autogenerate
cleanup_pub newcleanupp capitalization_string fix_feature_id \
- cleanup_message
+ cleanup_message huge_file_cleanup influenza_set
-DLL_LIB = $(OBJEDIT_LIBS) xregexp $(PCRE_LIB)
+DLL_LIB = $(OBJEDIT_LIBS) xobjutil valid xregexp $(PCRE_LIB) $(SOBJMGR_LIBS)
+++ b/c++/src/objtools/format/Makefile.xformat.lib
@@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect
- WATCHERS = ludwigf dicuccio
+ WATCHERS = dicuccio gotvyans
+DLL_LIB = xcleanup valid gbseq mlacli mla medlars pubmed submit xalnmgr \
+ xobjutil taxon3 $(SOBJMGR_LIBS)
USES_LIBRARIES = \
- gbseq mlacli xalnmgr xcleanup
+ gbseq xalnmgr xcleanup
--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
@@ -5,5 +5,7 @@ SRC = blastclient blastclient_
CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
--- a/c++/src/connect/Makefile.xconnect.lib
+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -13,6 +13,8 @@ UNIX_SRC = $(LOCAL_LBSM)
+@@ -12,6 +12,8 @@ SRC = $(SRC_C) $(SRC_CXX) $(SRC_TLS
LIB = xconnect
-DLL_LIB = seqcode pub general xser sequtil
+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
- WATCHERS = vasilche grichenk bollin ludwigf
+ WATCHERS = vasilche grichenk stakhovv gotvyans
--- a/c++/src/objects/seqset/Makefile.seqset.lib
+++ b/c++/src/objects/seqset/Makefile.seqset.lib
Last-Updated: 2018-02-11
--- a/c++/src/algo/blast/Makefile.blast_macros.mk
+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -21,7 +21,7 @@ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) v
- BLAST_LDEP = utrtprof xalgoblastdbindex composition_adjustment \
+@@ -22,7 +22,7 @@ BLAST_LDEP = utrtprof xalgoblastdbindex
xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
- xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables $(LMDB_LIB)
+ xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb \
+ sqlitewrapp scoremat tables $(LMDB_LIB)
-BLAST_LIBS = proteinkmer xblast $(BLAST_LDEP)
+BLAST_LIBS = proteinkmer xblast blast $(BLAST_LDEP)
Last-Update: 2020-09-19
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -10354,7 +10354,7 @@ if test -z "$CONF_f_runpath" ; then
+@@ -10806,7 +10806,7 @@ if test -z "$CONF_f_runpath" ; then
CONF_f_runpath="-R"
;;
linux*:[GI]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \
irix*:* | linux*:KCC | *:Compaq )
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -2213,7 +2213,7 @@ if test -z "$CONF_f_runpath" ; then
+@@ -2419,7 +2419,7 @@ if test -z "$CONF_f_runpath" ; then
CONF_f_runpath="-R"
;;
linux*:[[GI]]CC | linux*Clang | *bsd*:GCC | *bsd*Clang | cygwin*:GCC \
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -10126,7 +10126,7 @@
+@@ -10912,7 +10912,7 @@ case "$compiler:$compiler_version:$with_
break
;;
/* )
esac
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -2243,7 +2243,7 @@
+@@ -2486,7 +2486,7 @@ case "$compiler:$compiler_version:$with_
break
;;
/* )
Forwarded: no
--- a/c++/src/algo/blast/api/blast_usage_report.cpp
+++ b/c++/src/algo/blast/api/blast_usage_report.cpp
-@@ -184,6 +184,7 @@
+@@ -190,6 +190,7 @@ void CBlastUsageReport::AddParam(EUsageP
void CBlastUsageReport::x_CheckBlastUsageEnv()
{
char * blast_usage_env = getenv("BLAST_USAGE_REPORT");
if(blast_usage_env != NULL){
bool enable = NStr::StringToBool(blast_usage_env);
if (!enable) {
-@@ -192,6 +193,10 @@
+@@ -198,6 +199,10 @@ void CBlastUsageReport::x_CheckBlastUsag
LOG_POST(Info <<"Phone home disabled");
return ;
}
+ return;
}
- CNcbiIstrstream empty_stream(kEmptyCStr);
-@@ -204,10 +209,15 @@
+ CNcbiIstrstream empty_stream(kEmptyStr);
+@@ -210,10 +215,15 @@ void CBlastUsageReport::x_CheckBlastUsag
LOG_POST(Info <<"Phone home disabled by config setting");
return ;
}
"true" value (English-only, case-insensitive true, t, yes, y, or 1).
--- a/c++/src/algo/blast/api/search_strategy.cpp
+++ b/c++/src/algo/blast/api/search_strategy.cpp
-@@ -544,6 +544,11 @@
+@@ -560,6 +560,11 @@ void CExportStrategy::x_Process_Pssm(CRe
m_QueueSearchRequest->SetService(new_service);
}
void CExportStrategy::x_Process_Query(CRef<IQueryFactory> & query)
{
if (query.Empty())
-@@ -565,7 +570,7 @@
+@@ -581,7 +586,7 @@ void CExportStrategy::x_Process_Query(CR
// Check if there are any range restrictions applied and if local IDs are
// being used to determine how to specify the query sequence(s)
Description: make the build more reproducible
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -2914,13 +2914,13 @@ case "$host_os" in
+@@ -3138,13 +3138,13 @@ case "$host_os" in
linux*)
kver=`uname -r | sed -e 's/-.*//'`
libcver=`ldd --version | awk 'NR == 1 { print $NF }'`
NCBI_MAKE_MODULE(NCBI_MODULE))
--- a/c++/include/corelib/test_boost.hpp
+++ b/c++/include/corelib/test_boost.hpp
-@@ -273,7 +273,7 @@ static ::NCBI_NS_NCBI::SNcbiTestRegistra
+@@ -343,7 +343,7 @@ static ::NCBI_NS_NCBI::SNcbiTestRegistra
BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \
boost::unit_test::make_test_case( \
&BOOST_AUTO_TC_INVOKER( test_name ), #test_name, \
decorators ); \
--- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
+++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
-@@ -1124,7 +1124,7 @@ void SeqDB_FileIntegrityAssert(const str
+@@ -1123,7 +1123,7 @@ void SeqDB_FileIntegrityAssert(const str
#define SEQDB_FILE_ASSERT(YESNO) \
do { \
if (! (YESNO)) { \
--- a/c++/src/connect/mbedtls/mbedtls/debug.h
+++ b/c++/src/connect/mbedtls/mbedtls/debug.h
-@@ -41,28 +41,28 @@
- #define MBEDTLS_DEBUG_STRIP_PARENS( ... ) __VA_ARGS__
+@@ -39,33 +39,33 @@
+ #define MBEDTLS_DEBUG_STRIP_PARENS(...) __VA_ARGS__
- #define MBEDTLS_SSL_DEBUG_MSG( level, args ) \
-- mbedtls_debug_print_msg( ssl, level, __FILE__, __LINE__, \
-+ mbedtls_debug_print_msg( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, \
- MBEDTLS_DEBUG_STRIP_PARENS args )
+ #define MBEDTLS_SSL_DEBUG_MSG(level, args) \
+- mbedtls_debug_print_msg(ssl, level, __FILE__, __LINE__, \
++ mbedtls_debug_print_msg(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, \
+ MBEDTLS_DEBUG_STRIP_PARENS args)
- #define MBEDTLS_SSL_DEBUG_RET( level, text, ret ) \
-- mbedtls_debug_print_ret( ssl, level, __FILE__, __LINE__, text, ret )
-+ mbedtls_debug_print_ret( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, ret )
+ #define MBEDTLS_SSL_DEBUG_RET(level, text, ret) \
+- mbedtls_debug_print_ret(ssl, level, __FILE__, __LINE__, text, ret)
++ mbedtls_debug_print_ret(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, ret)
- #define MBEDTLS_SSL_DEBUG_BUF( level, text, buf, len ) \
-- mbedtls_debug_print_buf( ssl, level, __FILE__, __LINE__, text, buf, len )
-+ mbedtls_debug_print_buf( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, buf, len )
+ #define MBEDTLS_SSL_DEBUG_BUF(level, text, buf, len) \
+- mbedtls_debug_print_buf(ssl, level, __FILE__, __LINE__, text, buf, len)
++ mbedtls_debug_print_buf(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, buf, len)
#if defined(MBEDTLS_BIGNUM_C)
- #define MBEDTLS_SSL_DEBUG_MPI( level, text, X ) \
-- mbedtls_debug_print_mpi( ssl, level, __FILE__, __LINE__, text, X )
-+ mbedtls_debug_print_mpi( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X )
+ #define MBEDTLS_SSL_DEBUG_MPI(level, text, X) \
+- mbedtls_debug_print_mpi(ssl, level, __FILE__, __LINE__, text, X)
++ mbedtls_debug_print_mpi(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X)
#endif
#if defined(MBEDTLS_ECP_C)
- #define MBEDTLS_SSL_DEBUG_ECP( level, text, X ) \
-- mbedtls_debug_print_ecp( ssl, level, __FILE__, __LINE__, text, X )
-+ mbedtls_debug_print_ecp( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X )
+ #define MBEDTLS_SSL_DEBUG_ECP(level, text, X) \
+- mbedtls_debug_print_ecp(ssl, level, __FILE__, __LINE__, text, X)
++ mbedtls_debug_print_ecp(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, X)
#endif
#if defined(MBEDTLS_X509_CRT_PARSE_C)
- #define MBEDTLS_SSL_DEBUG_CRT( level, text, crt ) \
-- mbedtls_debug_print_crt( ssl, level, __FILE__, __LINE__, text, crt )
-+ mbedtls_debug_print_crt( ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, crt )
+ #define MBEDTLS_SSL_DEBUG_CRT(level, text, crt) \
+- mbedtls_debug_print_crt(ssl, level, __FILE__, __LINE__, text, crt)
++ mbedtls_debug_print_crt(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, text, crt)
+ #endif
+
+ #if defined(MBEDTLS_ECDH_C)
+ #define MBEDTLS_SSL_DEBUG_ECDH(level, ecdh, attr) \
+- mbedtls_debug_printf_ecdh(ssl, level, __FILE__, __LINE__, ecdh, attr)
++ mbedtls_debug_printf_ecdh(ssl, level, "c++/src/connect/mbedtls/mbedtls/debug.h", __LINE__, ecdh, attr)
#endif
#else /* MBEDTLS_DEBUG_C */
---- a/c++/src/connect/ncbi_lbos_cxx.cpp
-+++ b/c++/src/connect/ncbi_lbos_cxx.cpp
-@@ -146,7 +146,7 @@ std::string CLBOSIpCache::HostnameResolv
- {
- /* Hostname should not be empty in any case */
- if (hostname.empty()) {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eUnknown,
- "Internal error in LBOS Client IP Cache. Please contact developer",
- eLBOS_BadRequest);
-@@ -218,7 +218,7 @@ static void s_ProcessResult(unsigned sho
- if (lbos_answer != NULL) {
- message << " " << lbos_answer;
- }
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::s_HTTPCodeToEnum(result),
- message.str(), result);
- }
-@@ -249,7 +249,7 @@ void LBOS::Announce(const string& servi
- /* If we could not parse healthcheck URL, throw "Invalid Arguments" */
- if (cur_host.empty()) {
- ConnNetInfo_Destroy(healthcheck_info);
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- NStr::IntToString(eLBOS_InvalidArgs),
- eLBOS_InvalidArgs);
-@@ -308,7 +308,7 @@ void LBOS::AnnounceFromRegistry(const st
- port_int = NStr::StringToInt(port_str);
- }
- catch (...) {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "Could not parse port \"" + port_str +
- "\" in section \"" + reg_section + "\"",
-@@ -316,7 +316,7 @@ void LBOS::AnnounceFromRegistry(const st
- }
- if (port_int < 1 || port_int > 65535)
- {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "Invalid server port \"" + port_str +
- "\" in section \"" + reg_section + "\"",
-@@ -624,7 +624,7 @@ void LBOS::CMetaData::Set(const CTempStr
- /* Forbidden names for meta parameters */
- if (name == "version" || name == "ip" || name == "port" || name == "check"
- || name == "format" || name == "name") {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "This name cannot be used for metadata",
- eLBOS_InvalidArgs);
-@@ -680,7 +680,7 @@ void LBOS::CMetaData::SetRate(const stri
- SetRate(NStr::StringToInt(rate));
- }
- catch (const CStringException&) {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "Could not parse string value for SetRate",
- eLBOS_InvalidArgs);
-@@ -707,7 +707,7 @@ double LBOS::CMetaData::GetRate() const
- return NStr::StringToDouble(rate);
- }
- catch (const CStringException&) {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "Value in \"rate\" meta parameter cannot "
- "be represented as an integer",
-@@ -719,7 +719,7 @@ double LBOS::CMetaData::GetRate() const
- void LBOS::CMetaData::SetType(const string& host_type)
- {
- if (host_type.find_first_of(" \t\n\v\f\r") != string::npos) {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "This convenience function throws on whitespace characters "
- "in \"type\" meta parameter. If you know what you are doing, "
-@@ -760,7 +760,7 @@ void LBOS::CMetaData::SetType(EHostType
- SetType("");
- break;
- default:
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs, "Unknown EHostType "
- "value. If you are sure that a correct value is "
- "used, please tell the developer about this issue",
-@@ -794,7 +794,7 @@ void LBOS::CMetaData::SetType(ESERV_Type
- SetType("FIREWALL");
- break;
- default:
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs, "Unknown ESERV_Type "
- "value. If you are sure that a correct value is "
- "used, please tell the developer about this issue",
-@@ -825,7 +825,7 @@ void LBOS::CMetaData::SetType(int host_t
- SetType("");
- break;
- default:
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs, "Unknown EHostType "
- "value. If you are sure that a correct value is "
- "used, please tell the developer about this issue",
-@@ -871,7 +871,7 @@ LBOS::CMetaData::EHostType LBOS::CMetaDa
- void LBOS::CMetaData::SetExtra(const string& extra)
- {
- if (extra.find_first_of(" \t\n\v\f\r") != string::npos) {
-- throw CLBOSException(CDiagCompileInfo(__FILE__, __LINE__), NULL,
-+ throw CLBOSException(CDiagCompileInfo("c++/src/connect/ncbi_lbos_cxx.cpp", __LINE__), NULL,
- CLBOSException::eInvalidArgs,
- "This convenience function throws on whitespace characters "
- "in \"extra\" meta parameter. If you know what you are doing, "
--- a/c++/src/connect/ncbi_monkey.cpp
+++ b/c++/src/connect/ncbi_monkey.cpp
@@ -83,7 +83,7 @@ const string kEnablField
bool s_IsTaxNameElement(const string& value)
{
-@@ -1367,7 +1367,7 @@ static const char* const s_StopWords[] =
+@@ -1376,7 +1376,7 @@ static const char* const s_StopWords[] =
};
typedef CStaticArraySet<const char*, PNocase_CStr> TCStopWordStrSet;
bool CBioSource::IsStopWord(const string& value)
--- a/c++/src/objects/seqfeat/SubSource.cpp
+++ b/c++/src/objects/seqfeat/SubSource.cpp
-@@ -3120,7 +3120,7 @@ static const char* const s_Countries[] =
+@@ -3225,7 +3225,9 @@ static const char* const s_Countries[] =
+ "Zambia",
"Zimbabwe"
};
- typedef CStaticArraySet<const char*, PCase_CStr> TCStrSet;
-static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), __FILE__, __LINE__);
-+static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries), "c++/src/objects/seqfeat/SubSource.cpp", __LINE__);
++static const TCStrSet s_CountriesSet(s_Countries, sizeof(s_Countries),
++ "c+++/src/objects/seqfeat/SubSource.cpp",
++ __LINE__);
// former legal country names, must be in alphabetical order (case sensitive)
static const char* const s_Former_Countries[] = {
-@@ -3140,7 +3140,7 @@ static const char* const s_Former_Countr
+@@ -3246,7 +3248,7 @@ static const char* const s_Former_Countr
"Yugoslavia",
"Zaire"
};
-static const TCStrSet s_Former_CountriesSet(s_Former_Countries, sizeof(s_Former_Countries), __FILE__, __LINE__);
+static const TCStrSet s_Former_CountriesSet(s_Former_Countries, sizeof(s_Former_Countries), "c++/src/objects/seqfeat/SubSource.cpp", __LINE__);
- bool CCountries::IsValid(const string& country)
- {
+ // null term exemption values, must be in alphabetical order (case sensitive)
+ static const char* const s_Null_Countries[] = {
--- a/c++/src/serial/datatool/classstr.cpp
+++ b/c++/src/serial/datatool/classstr.cpp
@@ -850,7 +850,7 @@ mem_simple = false;
" }\n";
--- a/c++/src/serial/serialobject.cpp
+++ b/c++/src/serial/serialobject.cpp
-@@ -295,7 +295,7 @@ void CSerialObject::ThrowUnassigned(TMem
+@@ -299,7 +299,7 @@ void CSerialObject::ThrowUnassigned(TMem
// set temporary diag compile info to use argument file name and line
#undef DIAG_COMPILE_INFO
#define DIAG_COMPILE_INFO \
file_line? file_line: __LINE__, \
NCBI_CURRENT_FUNCTION, \
NCBI_MAKE_MODULE(NCBI_MODULE))
-@@ -303,7 +303,7 @@ void CSerialObject::ThrowUnassigned(TMem
+@@ -307,7 +307,7 @@ void CSerialObject::ThrowUnassigned(TMem
// restore original diag compile info definition
#undef DIAG_COMPILE_INFO
#define DIAG_COMPILE_INFO \
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
- # $Id: update_blastdb.pl 632592 2021-06-03 13:20:59Z ivanov $
+ # $Id: update_blastdb.pl 672917 2023-09-18 17:55:38Z ivanov $
# ===========================================================================
#
Last-Updated: 2013-06-01
--- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
+++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
-@@ -11,6 +11,7 @@
-
- LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS)
+@@ -12,6 +12,7 @@ LIB = test_boost blast_services xnetblas
+ LIBS = $(BLAST_THIRD_PARTY_LIBS) $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) \
+ $(ORIG_LIBS)
-CHECK_CMD = blast_services_unit_test
+# This test requires an internet connection, shouldn't be run on a build server
", encountered " + id->AsString() + ".";
NCBI_THROW(CAlnException, eInvalidSeqId, err);
}
---- a/c++/src/algo/blast/api/blast_setup_cxx.cpp
-+++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp
-@@ -784,7 +784,7 @@ SetupSubjects_OMF(IBlastQuerySource& sub
- if(warning != kEmptyStr){
- warning += ": ";
- }
-- warning += "Subject sequence contians no data";
-+ warning += "Subject sequence contains no data";
- ERR_POST(Warning << warning);
- continue;
- }
--- a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
@@ -75,7 +75,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory
SetupArgDescriptions(arg_desc.release());
--- a/c++/src/app/blastdb/makeprofiledb.cpp
+++ b/c++/src/app/blastdb/makeprofiledb.cpp
-@@ -609,13 +609,13 @@ CMakeProfileDBApp::x_CheckInputScoremat(
-
- if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength()))
- {
-- string err = filename + " contians no bioseq data";
-+ string err = filename + " contains no bioseq data";
- NCBI_THROW(CInputException, eInvalidInput, err);
- }
-
- if(!pssm.IsSetNumRows() || !pssm.IsSetNumColumns())
- {
-- string err = filename + " contians no info on num of columns or num of rows";
-+ string err = filename + " contains no info on num of columns or num of rows";
- NCBI_THROW(CInputException, eInvalidInput, err);
- }
-
-@@ -668,13 +668,13 @@ CMakeProfileDBApp::x_CheckInputScoremat(
-
- if(sm_invalid == sm)
- {
-- string err = filename + " contians no pssm or residue frequencies";
-+ string err = filename + " contains no pssm or residue frequencies";
- NCBI_THROW(CInputException, eInvalidInput, err);
- }
- }
- else
- {
-- string err = filename + " contians no scoremat";
-+ string err = filename + " contains no scoremat";
- NCBI_THROW(CInputException, eInvalidInput, err);
- }
-
-@@ -1816,7 +1816,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co
+@@ -1838,7 +1838,7 @@ bool CMakeProfileDBApp::x_CheckDelta( co
if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)
{
*m_LogFile << filename +
return false;
}
return true;
---- a/c++/src/connect/ncbi_lbos.c
-+++ b/c++/src/connect/ncbi_lbos.c
-@@ -951,7 +951,7 @@ static char * s_LBOS_UrlReadAll(SConnNet
- sizeof(char) * (strlen(buf) + 1))) )
- {
- CORE_LOG(eLOG_Warning, "s_LBOS_UrlReadAll: Buffer shrink error, using "
-- "original stirng");
-+ "original string");
- } else {
- buf = realloc_result;
- }
--- a/c++/src/objects/seqalign/Dense_seg.cpp
+++ b/c++/src/objects/seqalign/Dense_seg.cpp
-@@ -988,7 +988,7 @@ void CDense_seg::RemapToLoc(TDim row, co
+@@ -980,7 +980,7 @@ 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
-@@ -728,7 +728,7 @@ static const char* const kInstitutionCol
- "BPS\ts\tCalifornia Department of Food and Agriculture\t\t\t",
+@@ -788,7 +788,7 @@ 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",
-"BR<BRA>\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\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
-@@ -695,7 +695,7 @@ BPPT-ESC c BPPT Ethanol-Single Cell Prot
- BPS s California Department of Food and Agriculture
+@@ -752,7 +752,7 @@ 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
-BR<BRA> c Johanna Dobereiner Biological Resouce Center (CRB-JD)
BRB s Brassica Resource Bank
--- a/c++/src/objmgr/util/sequence.cpp
+++ b/c++/src/objmgr/util/sequence.cpp
-@@ -274,7 +274,7 @@ string GetProteinName(const CBioseq_Hand
+@@ -385,7 +385,7 @@ string GetProteinName(const CBioseq_Hand
if ( best_feats.empty() ) {
NCBI_THROW_FMT(CObjMgrException, eFindFailed,
"GetProteinName("<<GetId(seq, eGetId_Best)<<"): "
NCBI_THROW_FMT(CObjMgrException, eFindConflict,
--- a/c++/src/objtools/align_format/taxFormat.cpp
+++ b/c++/src/objtools/align_format/taxFormat.cpp
-@@ -588,7 +588,7 @@ void CTaxFormat::x_LoadTaxTree(void)
+@@ -616,7 +616,7 @@ 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
-@@ -639,7 +639,7 @@ void CFlatFileConfig::AddArgumentDescrip
+@@ -654,7 +654,7 @@ void CFlatFileConfig::AddArgumentDescrip
// from
arg_desc->AddOptionalKey("from", "From",
sameComId_otherScaf += ":";
--- a/c++/src/util/compress/api/compress.cpp
+++ b/c++/src/util/compress/api/compress.cpp
-@@ -160,7 +160,7 @@ bool CCompression::x_DecompressFile(CCom
- while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) {
+@@ -165,7 +165,7 @@ bool CCompression::x_DecompressFile(CCom
+ while ( (nread = src_file.Read(buf.get(), file_io_bufsize)) > 0 ) {
os.write(buf.get(), nread);
if ( !os.good() ) {
- SetError(-1, "Error writing to ouput file");
narrowing errors for cases with the high bit set when that field is
a 32-bit signed integer (as on i386).
-Index: b/c++/src/corelib/ncbifile.cpp
-===================================================================
--- a/c++/src/corelib/ncbifile.cpp
+++ b/c++/src/corelib/ncbifile.cpp
-@@ -5129,7 +5129,7 @@ void s_GetFileSystemInfo(const string&
+@@ -5178,7 +5178,7 @@ void s_GetFileSystemInfo(const string&
GET_STATFS_INFO;
if (flags & (fFSI_Type | fFSI_DiskSpace)) {
--- a/c++/src/connect/ncbi_gnutls.c
+++ b/c++/src/connect/ncbi_gnutls.c
-@@ -692,6 +692,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -748,6 +748,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
assert(!s_GnuTlsCredAnon);
+#if 0
version = gnutls_check_version(0);
if (strcasecmp(GNUTLS_VERSION, version) != 0) {
- CORE_LOGF(eLOG_Critical,
-@@ -699,6 +700,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
- GNUTLS_VERSION, version));
+ CORE_LOGF_X(26, eLOG_Critical,
+@@ -755,6 +756,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+ GNUTLS_VERSION, version));
assert(0);
}
+#endif
- if (!pull || !push)
- return eIO_InvalidArg;
+ CORE_TRACE("GnuTlsInit(): Enter");
+
--- a/c++/src/connect/ncbi_mbedtls.c
+++ b/c++/src/connect/ncbi_mbedtls.c
-@@ -665,12 +665,14 @@ static EIO_Status s_MbedTlsInit(FSSLPull
+@@ -728,12 +728,14 @@ static EIO_Status s_MbedTlsInit(FSSLPull
char buf[32];
mbedtls_version_get_string(version);
+#if 0
if (strcasecmp(MBEDTLS_VERSION_STRING, version) != 0) {
- CORE_LOGF(eLOG_Critical,
- ("%s version mismatch: %s headers vs. %s runtime",
- kMbedTls, MBEDTLS_VERSION_STRING, version));
+ CORE_LOGF_X(5, eLOG_Critical,
+ ("%s version mismatch: %s headers vs. %s runtime",
+ kMbedTls, MBEDTLS_VERSION_STRING, version));
assert(0);
}
+#endif
- if (!pull || !push)
- return eIO_InvalidArg;
+ CORE_TRACE("MbedTlsInit(): Enter");
+
Subject: Omit convenience mbed TLS copy
--- a/c++/src/connect/Makefile.connssl.lib
+++ b/c++/src/connect/Makefile.connssl.lib
-@@ -2,7 +2,9 @@
+@@ -1,8 +1,10 @@
+ # $Id: Makefile.connssl.lib 642488 2021-12-20 21:00:34Z ucko $
- CPPFLAGS = $(TLS_INCLUDE) $(ORIG_CPPFLAGS)
+-CPPFLAGS = $(TLS_INCLUDE) -I$(srcdir)/mbedtls $(ORIG_CPPFLAGS)
++CPPFLAGS = $(TLS_INCLUDE) $(ORIG_CPPFLAGS)
-SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls \
+SRC_TLS = ncbi_gnutls ncbi_mbedtls ncbi_tls
+
+SRC_MBEDTLS_UNUSED = \
- mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/asn1parse \
- mbedtls/asn1write mbedtls/base64 mbedtls/bignum mbedtls/blowfish \
- mbedtls/camellia mbedtls/ccm mbedtls/cipher mbedtls/cipher_wrap \
+ mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/aria \
+ mbedtls/asn1parse mbedtls/asn1write mbedtls/base64 mbedtls/bignum \
+ mbedtls/blowfish mbedtls/camellia mbedtls/ccm mbedtls/chacha20 \
--- a/c++/src/connect/connect_misc_impl.hpp
+++ b/c++/src/connect/connect_misc_impl.hpp
@@ -30,11 +30,10 @@
Last-Update: 2012-05-10
--- a/c++/src/build-system/Makefile.app.in
+++ b/c++/src/build-system/Makefile.app.in
-@@ -25,8 +25,8 @@
+@@ -25,8 +25,8 @@ default_rule: all
### C/C++ source file compilation setup
CPPFLAGS += -DNCBI_APP_BUILT_AS=$(APP)
SOURCES = @UNIX_SRC@ $(SRC)
### Standard application build rules
-@@ -57,7 +57,7 @@
+@@ -59,7 +59,7 @@ PROJ_TYPE = app
include $(builddir)/Makefile.$(Rules)
CMD_BASE = $(LINK_WRAPPER) $(LINK)
projects / ncbi-blast+.git / commitdiff