[med-svn] [Git][med-team/ncbi-blastplus][master] 8 commits: improve reproducibility
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Dec 4 20:19:52 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / ncbi-blastplus
Commits:
84d05697 by Michael R. Crusoe at 2019-12-04T13:10:42Z
improve reproducibility
- - - - -
91a37091 by Michael R. Crusoe at 2019-12-04T13:38:55Z
fix some spelling typos
- - - - -
804c97bf by Michael R. Crusoe at 2019-12-04T13:38:55Z
remove some __FILE__ references
- - - - -
53531b4f by Michael R. Crusoe at 2019-12-04T13:40:16Z
debian/watch: use a secure URL
- - - - -
a3dd5f49 by Michael R. Crusoe at 2019-12-04T14:05:50Z
more optional build-deps
- - - - -
38e317d5 by Michael R. Crusoe at 2019-12-04T14:09:35Z
reprobuild fixup
- - - - -
373bce9a by Michael R. Crusoe at 2019-12-04T19:21:09Z
delete spurious usr/bin/windowmasker_2.2.22_adapter.bak
- - - - -
1dc1e25c by Michael R. Crusoe at 2019-12-04T20:05:07Z
set up a HOME directory
- - - - -
6 changed files:
- debian/control
- + debian/patches/reprobuild
- debian/patches/series
- + debian/patches/spelling
- debian/rules
- debian/watch
Changes:
=====================================
debian/control
=====================================
@@ -15,7 +15,11 @@ Build-Depends-Arch: 2to3,
libmbedtls-dev,
libpcre3-dev,
time,
- zlib1g-dev
+ zlib1g-dev,
+ procps,
+ libbackward-cpp-dev,
+ libdw-dev,
+ libmsgsl-dev
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git
=====================================
debian/patches/reprobuild
=====================================
@@ -0,0 +1,732 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: make the build more reproducible
+--- ncbi-blastplus.orig/c++/src/build-system/configure.ac
++++ ncbi-blastplus/c++/src/build-system/configure.ac
+@@ -2826,13 +2826,13 @@
+ linux*)
+ kver=`uname -r | sed -e 's/-.*//'`
+ libcver=`ldd --version | awk 'NR == 1 { print $NF }'`
+- verbose_host=$host_cpu-$host_vendor-linux$kver-gnu$libcver
++ verbose_host=$host_cpu-$host_vendor-linux-gnu$libcver
+ ;;
+ *) verbose_host=$host ;;
+ esac
+
+ #### Overall configuration mode summary
+-signature_hostname=`(hostname || uname -n) 2>/dev/null \
++signature_hostname=`echo debian_build 2>/dev/null \
+ | sed 's/\..*//; s/-/_/g; 1q'`
+ signature="${signature_compiler}_${signature_compiler_version}-${release_debug}${mt_sfx}${dll_sfx}${bit64_sfx}${prof_sfx}--${verbose_host}-${signature_hostname}"
+ AC_DEFINE_UNQUOTED(NCBI_SIGNATURE, "$signature",
+--- ncbi-blastplus.orig/c++/include/algo/blast/core/blast_message.h
++++ ncbi-blastplus/c++/include/algo/blast/core/blast_message.h
+@@ -117,7 +117,7 @@
+
+ /** Convenient define to call the function Blast_PerrorEx. */
+ #define Blast_PerrorWithLocation(msg, error_code, context) \
+-Blast_PerrorEx(msg, error_code, __FILE__, __LINE__, context)
++Blast_PerrorEx(msg, error_code, "c++/include/algo/blast/core/blast_message.h", __LINE__, context)
+
+ /** Extended version of Blast_Perror which includes parameters for the file
+ * name and line number where the error/warning occurred. This function should
+--- ncbi-blastplus.orig/c++/include/connect/ncbi_util.h
++++ ncbi-blastplus/c++/include/connect/ncbi_util.h
+@@ -113,7 +113,7 @@
+ */
+ #define LOG_WRITE(lg, code, subcode, level, message) \
+ LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION, \
+- __FILE__, __LINE__, message, 0, 0)
++ "c++/include/connect/ncbi_util.h", __LINE__, message, 0, 0)
+
+ #ifdef LOG_DATA
+ /* AIX's <pthread.h> defines LOG_DATA to be an integer constant;
+@@ -122,7 +122,7 @@
+ #endif
+ #define LOG_DATA(lg, code, subcode, level, data, size, message) \
+ LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION, \
+- __FILE__, __LINE__, message, data, size)
++ "c++/include/connect/ncbi_util.h", __LINE__, message, data, size)
+
+
+ /** Default for THIS_MODULE.
+--- ncbi-blastplus.orig/c++/include/corelib/impl/ncbi_java.h
++++ ncbi-blastplus/c++/include/corelib/impl/ncbi_java.h
+@@ -63,7 +63,7 @@
+
+ #define JAVA_ABORT(msg) \
+ { \
+- NcbiCerr << __FILE__ << ": " << NCBI_CURRENT_FUNCTION << ": " msg << endl; \
++ NcbiCerr << "c++/include/corelib/impl/ncbi_java.h" << ": " << NCBI_CURRENT_FUNCTION << ": " msg << endl; \
+ abort(); \
+ }
+
+--- ncbi-blastplus.orig/c++/include/corelib/ncbidiag.hpp
++++ ncbi-blastplus/c++/include/corelib/ncbidiag.hpp
+@@ -167,7 +167,7 @@
+ /// @sa
+ /// CDiagCompileInfo
+ #define DIAG_COMPILE_INFO \
+- NCBI_NS_NCBI::CDiagCompileInfo(__FILE__, \
++ NCBI_NS_NCBI::CDiagCompileInfo("c++/include/corelib/ncbidiag.hpp", \
+ __LINE__, \
+ NCBI_CURRENT_FUNCTION, \
+ NCBI_MAKE_MODULE(NCBI_MODULE))
+--- ncbi-blastplus.orig/c++/include/corelib/test_boost.hpp
++++ ncbi-blastplus/c++/include/corelib/test_boost.hpp
+@@ -249,7 +249,7 @@
+ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \
+ boost::unit_test::make_test_case( \
+ &BOOST_AUTO_TC_INVOKER( test_name ), #test_name, \
+- __FILE__, __LINE__ ), \
++ "c++/include/corelib/test_boost.hpp", __LINE__ ), \
+ ::NCBI_NS_NCBI::SNcbiTestTCTimeout< \
+ BOOST_AUTO_TC_UNIQUE_ID( test_name )>::instance()->value(), \
+ decorators ); \
+--- ncbi-blastplus.orig/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
++++ ncbi-blastplus/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
+@@ -1124,7 +1124,7 @@
+ #define SEQDB_FILE_ASSERT(YESNO) \
+ do { \
+ if (! (YESNO)) { \
+- SeqDB_FileIntegrityAssert(__FILE__, __LINE__, (#YESNO)); \
++ SeqDB_FileIntegrityAssert("c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp", __LINE__, (#YESNO)); \
+ } \
+ } while(0)
+
+--- ncbi-blastplus.orig/c++/include/util/ddump_viewer.hpp
++++ ncbi-blastplus/c++/include/util/ddump_viewer.hpp
+@@ -49,7 +49,7 @@
+ //
+
+ #define DEBUGDUMP_BPT(name,obj) \
+- do {CDebugDumpViewer().Bpt(name,&(obj),__FILE__,__LINE__);} while (0)
++ do {CDebugDumpViewer().Bpt(name,&(obj),"c++/include/util/ddump_viewer.hpp",__LINE__);} while (0)
+
+
+ //---------------------------------------------------------------------------
+--- ncbi-blastplus.orig/c++/include/util/static_set.hpp
++++ ncbi-blastplus/c++/include/util/static_set.hpp
+@@ -886,17 +886,17 @@
+ static const Type Var
+
+ #define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array) \
+- static const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__)
++ static const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__)
+
+ #define DEFINE_CLASS_STATIC_ARRAY_MAP(Type, Var, Array) \
+- const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__)
++ const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__)
+
+ #define DEFINE_STATIC_ARRAY_MAP_WITH_COPY(Type, Var, Array) \
+- static const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__, \
++ static const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__, \
+ NCBI_NS_NCBI::NStaticArray::eCopyWarn_hide)
+
+ #define DEFINE_CLASS_STATIC_ARRAY_MAP_WITH_COPY(Type, Var, Array) \
+- const Type (Var)((Array), sizeof(Array), __FILE__, __LINE__, \
++ const Type (Var)((Array), sizeof(Array), "c++/include/util/static_set.hpp", __LINE__, \
+ NCBI_NS_NCBI::NStaticArray::eCopyWarn_hide)
+
+
+--- ncbi-blastplus.orig/c++/src/connect/mbedtls/mbedtls/debug.h
++++ ncbi-blastplus/c++/src/connect/mbedtls/mbedtls/debug.h
+@@ -40,28 +40,28 @@
+ #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_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 )
+
+ #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 )
+ #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 )
+ #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 )
+ #endif
+
+ #else /* MBEDTLS_DEBUG_C */
+--- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos_cxx.cpp
++++ ncbi-blastplus/c++/src/connect/ncbi_lbos_cxx.cpp
+@@ -145,7 +145,7 @@
+ {
+ /* 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);
+@@ -217,7 +217,7 @@
+ 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);
+ }
+@@ -248,7 +248,7 @@
+ /* 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);
+@@ -307,7 +307,7 @@
+ 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 + "\"",
+@@ -315,7 +315,7 @@
+ }
+ 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 + "\"",
+@@ -623,7 +623,7 @@
+ /* 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);
+@@ -679,7 +679,7 @@
+ 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);
+@@ -706,7 +706,7 @@
+ 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",
+@@ -718,7 +718,7 @@
+ 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, "
+@@ -759,7 +759,7 @@
+ 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",
+@@ -793,7 +793,7 @@
+ 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",
+@@ -824,7 +824,7 @@
+ 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",
+@@ -870,7 +870,7 @@
+ 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, "
+--- ncbi-blastplus.orig/c++/src/connect/ncbi_monkey.cpp
++++ ncbi-blastplus/c++/src/connect/ncbi_monkey.cpp
+@@ -83,7 +83,7 @@
+ const string kSeedField = "seed";
+
+ #define PARAM_TWICE_EXCEPTION(param) \
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__), \
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__), \
+ NULL, CMonkeyException::e_MonkeyInvalidArgs, \
+ string("Parameter \"" param "\" is set " \
+ "twice in [") + GetSection() + "]" + \
+@@ -371,7 +371,7 @@
+ case eMonkey_Send:
+ return "write";
+ default:
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Unknown EMonkeyActionType value"));
+ }
+@@ -390,7 +390,7 @@
+ case eMonkey_Connect:
+ return "connect()";
+ default:
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Unknown EMonkeyActionType value"));
+ }
+@@ -467,7 +467,7 @@
+ {
+ if (m_RunPos.find(sock) == m_RunPos.end()) {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ "The socket provided has not been registered with current rule");
+ }
+@@ -511,7 +511,7 @@
+ m_ReturnStatus = eIO_Closed;
+ } else if (eIOStatus == "eio_invalidarg") {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Unsupported 'return_status': ") + eIOStatus_in);
+ } else if (eIOStatus == "eio_interrupt") {
+@@ -526,7 +526,7 @@
+ m_ReturnStatus = eIO_NotSupported;
+ } else {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Could not parse 'return_status': ") + eIOStatus_in);
+ }
+@@ -543,7 +543,7 @@
+ split it on commas*/
+ vector<string> runs_list = s_Monkey_Split(runs, ',');
+ if (runs_list.size() == 0)
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Parameter \"runs\" is empty in [")
+ + m_Section + "]" +
+@@ -573,7 +573,7 @@
+ if (m_RunMode == eMonkey_RunProbability) {
+ if (*run.rbegin() != '%') {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ "Value is not percentage: " + run +
+ ", values have to be either only percentages or "
+@@ -593,7 +593,7 @@
+ size_t last_step = m_Runs.size();
+ if (last_step == 0 && step != 1) {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ "In the string of runs: " + runs + " the first "
+ "element MUST set value for the first run");
+@@ -610,7 +610,7 @@
+ assert(run_format == eMonkey_RunSequence);
+ if (*run.rbegin() == '%') {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Value is percentage: ") + run +
+ string(", values have to be either only percentages or "
+@@ -619,7 +619,7 @@
+ int val = NStr::StringToInt(run);
+ if (m_Runs.size() > 0 && val <= *m_Runs.rbegin()) {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("\"runs\" should contain values in "
+ "increasing order"));
+@@ -815,7 +815,7 @@
+ string value = name_value[1];
+ if (name == "allow") {
+ if (allow_set) {
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL,
+ CMonkeyException::e_MonkeyInvalidArgs,
+ string("Parameter \"allow\" is set "
+@@ -827,7 +827,7 @@
+ }
+ }
+ if (!allow_set)
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Parameter \"allow\" not set in [")
+ + GetSection() + "]" +
+@@ -902,7 +902,7 @@
+ string value = name_value[1];
+ if (name == "ignore") {
+ if (ignore_set) {
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL,
+ CMonkeyException::e_MonkeyInvalidArgs,
+ string("Parameter \"ignore\" is set "
+@@ -914,7 +914,7 @@
+ }
+ }
+ if (!ignore_set) {
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ string("Parameter \"ignore\" not set in [")
+ + GetSection() + "]" +
+@@ -1032,7 +1032,7 @@
+ ".*" , "");
+ if (filtered.find_first_of("[]()+^?{}$.*\\") != string::npos) {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL,
+ CMonkeyException::e_MonkeyInvalidArgs,
+ exception_message);
+@@ -1051,7 +1051,7 @@
+ }
+ else {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL,
+ CMonkeyException::e_MonkeyInvalidArgs,
+ exception_message);
+@@ -1179,7 +1179,7 @@
+ ss << "Probability below zero for write rule in plan " << m_Name
+ << ". Check config!";
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ ss.str());
+ }
+@@ -1221,7 +1221,7 @@
+ stringstream ss;
+ ss << "Probability below zero for write rule in plan " << m_Name
+ << ". Check config!";
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ ss.str());
+ }
+@@ -1270,7 +1270,7 @@
+ stringstream ss;
+ ss << "Probability below zero for write rule in plan " << m_Name
+ << ". Check config!";
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ ss.str());
+ }
+@@ -1313,7 +1313,7 @@
+ ss << "Probability below zero for write rule in plan " << m_Name
+ << ". Check config!";
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ ss.str());
+ }
+@@ -1372,7 +1372,7 @@
+ {
+ if (sm_HookSwitch == NULL) {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ "Launch CONNECT_Init() before initializing CMonkey instance");
+ }
+@@ -1458,7 +1458,7 @@
+ prob = (int)(NStr::StringToDouble(prob_str) * 100);
+ }
+ if (prob < 0 || prob > 100) {
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL,
+ CMonkeyException::e_MonkeyInvalidArgs,
+ "Parameter \"probability\"=" + prob_str
+@@ -1469,7 +1469,7 @@
+ m_Probability = (unsigned short)prob;
+ }
+ catch (const CStringException&) {
+- throw CMonkeyException(CDiagCompileInfo(__FILE__, __LINE__),
++ throw CMonkeyException(CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ "Parameter \"probability\"=" + prob_str
+ + " for section [" + monkey_section
+@@ -1757,7 +1757,7 @@
+ << " has been already registered in CMonkey and cannot be used again";
+ if (m_RegisteredTokens.find(token) != m_RegisteredTokens.end()) {
+ throw CMonkeyException(
+- CDiagCompileInfo(__FILE__, __LINE__),
++ CDiagCompileInfo("c++/src/connect/ncbi_monkey.cpp", __LINE__),
+ NULL, CMonkeyException::e_MonkeyInvalidArgs,
+ ss.str());
+ }
+--- ncbi-blastplus.orig/c++/src/connect/ncbi_priv.h
++++ ncbi-blastplus/c++/src/connect/ncbi_priv.h
+@@ -223,7 +223,7 @@
+ _mess.level = _xx_level; \
+ _mess.module = THIS_MODULE; \
+ _mess.func = CORE_CURRENT_FUNCTION; \
+- _mess.file = __FILE__; \
++ _mess.file = "c++/src/connect/ncbi_priv.h"; \
+ _mess.line = __LINE__; \
+ _mess.raw_data = (_raw_data); \
+ _mess.raw_size = (_raw_size); \
+--- ncbi-blastplus.orig/c++/src/objects/seqfeat/BioSource.cpp
++++ ncbi-blastplus/c++/src/objects/seqfeat/BioSource.cpp
+@@ -938,7 +938,7 @@
+ };
+
+ typedef CStaticArraySet<const char*, PNocase_CStr> TCIgnoreCaseQualsSet;
+-static const TCIgnoreCaseQualsSet s_IgnoreCaseQualsSet(s_IgnoreCaseQuals, sizeof(s_IgnoreCaseQuals), __FILE__, __LINE__);
++static const TCIgnoreCaseQualsSet s_IgnoreCaseQualsSet(s_IgnoreCaseQuals, sizeof(s_IgnoreCaseQuals), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);
+
+ bool s_MayIgnoreCase(const string& value)
+ {
+@@ -960,7 +960,7 @@
+ };
+
+ typedef CStaticArraySet<const char*, PNocase_CStr> TCTaxNameElementQualsSet;
+-static const TCTaxNameElementQualsSet s_TaxNameElementQualsSet(s_TaxNameElementQuals, sizeof(s_TaxNameElementQuals), __FILE__, __LINE__);
++static const TCTaxNameElementQualsSet s_TaxNameElementQualsSet(s_TaxNameElementQuals, sizeof(s_TaxNameElementQuals), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);
+
+ bool s_IsTaxNameElement(const string& value)
+ {
+@@ -1364,7 +1364,7 @@
+ };
+
+ typedef CStaticArraySet<const char*, PNocase_CStr> TCStopWordStrSet;
+-static const TCStopWordStrSet s_StopWordsSet(s_StopWords, sizeof(s_StopWords), __FILE__, __LINE__);
++static const TCStopWordStrSet s_StopWordsSet(s_StopWords, sizeof(s_StopWords), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);
+
+
+ bool CBioSource::IsStopWord(const string& value)
+--- ncbi-blastplus.orig/c++/src/objects/seqfeat/SubSource.cpp
++++ ncbi-blastplus/c++/src/objects/seqfeat/SubSource.cpp
+@@ -3043,7 +3043,7 @@
+ "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__);
+
+ // former legal country names, must be in alphabetical order (case sensitive)
+ static const char* const s_Former_Countries[] = {
+@@ -3061,7 +3061,7 @@
+ "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)
+ {
+--- ncbi-blastplus.orig/c++/src/serial/datatool/classstr.cpp
++++ ncbi-blastplus/c++/src/serial/datatool/classstr.cpp
+@@ -850,7 +850,7 @@
+ " if (!CanGet"<< mem_cName<<"()) {\n"
+ " ThrowUnassigned("<<member_index;
+ #if 0
+- code.Methods(inl) << ", __FILE__, __LINE__";
++ code.Methods(inl) << ", "c++/src/serial/datatool/classstr.cpp", __LINE__";
+ #endif
+ code.Methods(inl) << ");\n"
+ " }\n";
+--- ncbi-blastplus.orig/c++/src/serial/serialobject.cpp
++++ ncbi-blastplus/c++/src/serial/serialobject.cpp
+@@ -295,7 +295,7 @@
+ // set temporary diag compile info to use argument file name and line
+ #undef DIAG_COMPILE_INFO
+ #define DIAG_COMPILE_INFO \
+- NCBI_NS_NCBI::CDiagCompileInfo(file_name? file_name: __FILE__, \
++ NCBI_NS_NCBI::CDiagCompileInfo(file_name? file_name: "c++/src/serial/serialobject.cpp", \
+ file_line? file_line: __LINE__, \
+ NCBI_CURRENT_FUNCTION, \
+ NCBI_MAKE_MODULE(NCBI_MODULE))
+@@ -303,7 +303,7 @@
+ // restore original diag compile info definition
+ #undef DIAG_COMPILE_INFO
+ #define DIAG_COMPILE_INFO \
+- NCBI_NS_NCBI::CDiagCompileInfo(__FILE__, \
++ NCBI_NS_NCBI::CDiagCompileInfo("c++/src/serial/serialobject.cpp", \
+ __LINE__, \
+ NCBI_CURRENT_FUNCTION, \
+ NCBI_MAKE_MODULE(NCBI_MODULE))
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mdb.c
++++ ncbi-blastplus/c++/src/util/lmdb/mdb.c
+@@ -1523,7 +1523,7 @@
+
+ #ifndef NDEBUG
+ # define mdb_assert0(env, expr, expr_txt) ((expr) ? (void)0 : \
+- mdb_assert_fail(env, expr_txt, mdb_func_, __FILE__, __LINE__))
++ mdb_assert_fail(env, expr_txt, mdb_func_, "c++/src/util/lmdb/mdb.c", __LINE__))
+
+ static void ESECT
+ mdb_assert_fail(MDB_env *env, const char *expr_txt,
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest.c
++++ ncbi-blastplus/c++/src/util/lmdb/mtest.c
+@@ -19,7 +19,7 @@
+ #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
+ #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
+ #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \
+- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))
++ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest.c", __LINE__, msg, mdb_strerror(rc)), abort()))
+
+ int main(int argc,char * argv[])
+ {
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest2.c
++++ ncbi-blastplus/c++/src/util/lmdb/mtest2.c
+@@ -22,7 +22,7 @@
+ #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
+ #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
+ #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \
+- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))
++ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest2.c", __LINE__, msg, mdb_strerror(rc)), abort()))
+
+ int main(int argc,char * argv[])
+ {
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest3.c
++++ ncbi-blastplus/c++/src/util/lmdb/mtest3.c
+@@ -22,7 +22,7 @@
+ #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
+ #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
+ #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \
+- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))
++ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest3.c", __LINE__, msg, mdb_strerror(rc)), abort()))
+
+ int main(int argc,char * argv[])
+ {
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest4.c
++++ ncbi-blastplus/c++/src/util/lmdb/mtest4.c
+@@ -22,7 +22,7 @@
+ #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
+ #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
+ #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \
+- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))
++ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest4.c", __LINE__, msg, mdb_strerror(rc)), abort()))
+
+ int main(int argc,char * argv[])
+ {
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest5.c
++++ ncbi-blastplus/c++/src/util/lmdb/mtest5.c
+@@ -22,7 +22,7 @@
+ #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
+ #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
+ #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \
+- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))
++ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest5.c", __LINE__, msg, mdb_strerror(rc)), abort()))
+
+ int main(int argc,char * argv[])
+ {
+--- ncbi-blastplus.orig/c++/src/util/lmdb/mtest6.c
++++ ncbi-blastplus/c++/src/util/lmdb/mtest6.c
+@@ -22,7 +22,7 @@
+ #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
+ #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
+ #define CHECK(test, msg) ((test) ? (void)0 : ((void)fprintf(stderr, \
+- "%s:%d: %s: %s\n", __FILE__, __LINE__, msg, mdb_strerror(rc)), abort()))
++ "%s:%d: %s: %s\n", "c++/src/util/lmdb/mtest6.c", __LINE__, msg, mdb_strerror(rc)), abort()))
+
+ char dkbuf[1024];
+
+--- ncbi-blastplus.orig/c++/src/util/regexp/pcre_scanner_unittest.cc
++++ ncbi-blastplus/c++/src/util/regexp/pcre_scanner_unittest.cc
+@@ -51,7 +51,7 @@
+ #define CHECK_EQ(a, b) do { \
+ if ( (a) != (b) ) { \
+ fprintf(stderr, "%s:%d: Check failed because %s != %s\n", \
+- __FILE__, __LINE__, #a, #b); \
++ "c++/src/util/regexp/pcre_scanner_unittest.cc", __LINE__, #a, #b); \
+ exit(1); \
+ } \
+ } while (0)
+--- ncbi-blastplus.orig/c++/src/util/regexp/pcre_stringpiece_unittest.cc
++++ ncbi-blastplus/c++/src/util/regexp/pcre_stringpiece_unittest.cc
+@@ -19,7 +19,7 @@
+ #define CHECK(condition) do { \
+ if (!(condition)) { \
+ fprintf(stderr, "%s:%d: Check failed: %s\n", \
+- __FILE__, __LINE__, #condition); \
++ "c++/src/util/regexp/pcre_stringpiece_unittest.cc", __LINE__, #condition); \
+ exit(1); \
+ } \
+ } while (0)
+--- ncbi-blastplus.orig/c++/src/util/static_set.cpp
++++ ncbi-blastplus/c++/src/util/static_set.cpp
+@@ -87,7 +87,7 @@
+ TParamStaticArrayCopyWarning::GetDefault()) ) {
+ // report incorrect usage
+ CDiagCompileInfo diag_compile_info
+- (file? file: __FILE__,
++ (file? file: "c++/src/util/static_set.cpp",
+ file? line: __LINE__,
+ NCBI_CURRENT_FUNCTION,
+ NCBI_MAKE_MODULE(NCBI_MODULE));
+@@ -122,7 +122,7 @@
+ if ( TParamStaticArrayUnsafeTypeWarning::GetDefault() ) {
+ // report incorrect usage
+ CDiagCompileInfo diag_compile_info
+- (file? file: __FILE__,
++ (file? file: "c++/src/util/static_set.cpp",
+ file? line: __LINE__,
+ NCBI_CURRENT_FUNCTION,
+ NCBI_MAKE_MODULE(NCBI_MODULE));
+@@ -145,7 +145,7 @@
+ {
+ { // report incorrect usage
+ CDiagCompileInfo diag_compile_info
+- (file? file: __FILE__,
++ (file? file: "c++/src/util/static_set.cpp",
+ file? line: __LINE__,
+ NCBI_CURRENT_FUNCTION,
+ NCBI_MAKE_MODULE(NCBI_MODULE));
=====================================
debian/patches/series
=====================================
@@ -11,3 +11,5 @@ suppress_gnutls_version_check
optionally_keep_sequence
fix_unit_tests
system_mbedtls_only
+reprobuild
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,239 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Spelling fixes
+--- ncbi-blastplus.orig/c++/include/objtools/alnmgr/seqids_extractor.hpp
++++ ncbi-blastplus/c++/include/objtools/alnmgr/seqids_extractor.hpp
+@@ -232,7 +232,7 @@
+ else if (*id_vec[i] != *id) {
+ string err("Inconsistent Seq-ids found in seg ");
+ err += NStr::NumericToString(i) +
+- ". Excpected " + id_vec[i]->AsString() +
++ ". Expected " + id_vec[i]->AsString() +
+ ", encountered " + id->AsString() + ".";
+ NCBI_THROW(CAlnException, eInvalidSeqId, err);
+ }
+--- ncbi-blastplus.orig/c++/src/algo/blast/api/blast_setup_cxx.cpp
++++ ncbi-blastplus/c++/src/algo/blast/api/blast_setup_cxx.cpp
+@@ -784,7 +784,7 @@
+ if(warning != kEmptyStr){
+ warning += ": ";
+ }
+- warning += "Subject sequence contians no data";
++ warning += "Subject sequence contains no data";
+ ERR_POST(Warning << warning);
+ continue;
+ }
+--- ncbi-blastplus.orig/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
++++ ncbi-blastplus/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
+@@ -75,7 +75,7 @@
+ }
+ else NCBI_THROW( CSeqMaskerOstatFactoryException,
+ eBadName,
+- "unkown unit counts format" );
++ "unknown unit counts format" );
+ }
+ catch( CException & e ) {
+ NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
+@@ -113,7 +113,7 @@
+ }
+ else NCBI_THROW( CSeqMaskerOstatFactoryException,
+ eBadName,
+- "unkown unit counts format" );
++ "unknown unit counts format" );
+ }
+ catch( CException & e ) {
+ NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
+--- ncbi-blastplus.orig/c++/src/app/blastdb/blastdbcheck.cpp
++++ ncbi-blastplus/c++/src/app/blastdb/blastdbcheck.cpp
+@@ -232,7 +232,7 @@
+ "Require that all sequences in the database have taxid set.");
+
+ arg_desc->AddFlag
+- ("cdd_delta", "Do aditional tests for a CDD database for DELTA-BLAST");
++ ("cdd_delta", "Do additional tests for a CDD database for DELTA-BLAST");
+
+ // Setup arg.descriptions for this application
+ SetupArgDescriptions(arg_desc.release());
+--- ncbi-blastplus.orig/c++/src/app/blastdb/makeprofiledb.cpp
++++ ncbi-blastplus/c++/src/app/blastdb/makeprofiledb.cpp
+@@ -546,13 +546,13 @@
+
+ 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);
+ }
+
+@@ -605,13 +605,13 @@
+
+ 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);
+ }
+
+@@ -1563,7 +1563,7 @@
+ if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)
+ {
+ *m_LogFile << filename +
+- " was excluded: it conatins an invalid CD \n";
++ " was excluded: it contains an invalid CD \n";
+ return false;
+ }
+
+--- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos.c
++++ ncbi-blastplus/c++/src/connect/ncbi_lbos.c
+@@ -951,7 +951,7 @@
+ sizeof(char) * (strlen(buf) + 1))) )
+ {
+ CORE_LOG(eLOG_Warning, "s_LBOS_UrlReadAll: Buffer shrink error, using "
+- "original stirng");
++ "original string");
+ } else {
+ buf = realloc_result;
+ }
+--- ncbi-blastplus.orig/c++/src/objects/seqalign/Dense_seg.cpp
++++ ncbi-blastplus/c++/src/objects/seqalign/Dense_seg.cpp
+@@ -988,7 +988,7 @@
+ if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {
+ NCBI_THROW(CSeqalignException, eInvalidInputData,
+ "CDense_seg::RemapToLoc():"
+- " The strand should be the same accross"
++ " The strand should be the same across"
+ " the input seq-loc");
+ }
+ }
+--- ncbi-blastplus.orig/c++/src/objects/seqalign/Seq_align.cpp
++++ ncbi-blastplus/c++/src/objects/seqalign/Seq_align.cpp
+@@ -872,7 +872,7 @@
+ if (dim != ss.GetDim() || row != dim) {
+ NCBI_THROW(CSeqalignException, eInvalidInputAlignment,
+ "CreateDensegFromStdseg(): "
+- "Inconsistent dimentions!");
++ "Inconsistent dimensions!");
+ }
+
+ if (widths_determined[seg]) {
+--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.inc
++++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.inc
+@@ -661,7 +661,7 @@
+ "BPS\ts\tCalifornia Department of Food and Agriculture\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",
++"BR<BRA>\tc\tJohanna Dobereiner Biological Resource Center (CRB-JD)\t\t\t",
+ "BRA\ts\tSlovak National Museum, Botany Department\t\t\t",
+ "BRAD\ts\tUniversity of Bradford, Biology Department\t\t\t",
+ "BRC\ts\tBotanical Record Club\t\t\t",
+--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.txt
++++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.txt
+@@ -628,7 +628,7 @@
+ BPS s California Department of Food and Agriculture
+ 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)
++BR<BRA> c Johanna Dobereiner Biological Resource Center (CRB-JD)
+ BRA s Slovak National Museum, Botany Department
+ BRAD s University of Bradford, Biology Department
+ BRC s Botanical Record Club
+--- ncbi-blastplus.orig/c++/src/objmgr/util/sequence.cpp
++++ ncbi-blastplus/c++/src/objmgr/util/sequence.cpp
+@@ -274,7 +274,7 @@
+ if ( best_feats.empty() ) {
+ NCBI_THROW_FMT(CObjMgrException, eFindFailed,
+ "GetProteinName("<<GetId(seq, eGetId_Best)<<"): "
+- "the sequence does't have prot feature");
++ "the sequence doesn't have prot feature");
+ }
+ if ( best_feats.size() > 1 ) {
+ NCBI_THROW_FMT(CObjMgrException, eFindConflict,
+--- ncbi-blastplus.orig/c++/src/objtools/align_format/taxFormat.cpp
++++ ncbi-blastplus/c++/src/objtools/align_format/taxFormat.cpp
+@@ -587,7 +587,7 @@
+ }
+ }
+ if (!tax_load_ok) {
+- NCBI_THROW(CException, eUnknown,"Taxonomic load was not successfull.");
++ NCBI_THROW(CException, eUnknown,"Taxonomic load was not successful.");
+ }
+ m_TaxTreeLoaded = true;
+
+--- ncbi-blastplus.orig/c++/src/objtools/format/flat_file_config.cpp
++++ ncbi-blastplus/c++/src/objtools/format/flat_file_config.cpp
+@@ -614,7 +614,7 @@
+
+ // from
+ arg_desc->AddOptionalKey("from", "From",
+- "Begining of shown range", CArgDescriptions::eInteger);
++ "Beginning of shown range", CArgDescriptions::eInteger);
+
+ // to
+ arg_desc->AddOptionalKey("to", "To",
+--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_converter.cpp
++++ ncbi-blastplus/c++/src/objtools/readers/agp_converter.cpp
+@@ -728,7 +728,7 @@
+ submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo());
+ submit_block_writer.Flush();
+ seq_sub_header_strm << "," << endl;
+- seq_sub_header_strm << "data entrys {" << endl;
++ seq_sub_header_strm << "data entries {" << endl;
+
+ out_sObjectOpeningString = seq_sub_header_strm.str();
+ out_sObjectClosingString = "} }" + out_sObjectClosingString;
+--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_util.cpp
++++ ncbi-blastplus/c++/src/objtools/readers/agp_util.cpp
+@@ -67,7 +67,7 @@
+
+ "object_beg != previous object_end + 1",
+ "no valid AGP lines",
+- "consequtive gaps lines with the same type and linkage",
++ "consecutive gaps lines with the same type and linkage",
+ "in \"Scaffold from component\" file, invalid scaffold-breaking gap",
+ "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",
+
+@@ -88,7 +88,7 @@
+ // Content Warnings
+ "gap at the end of object (OK if X is the circular chromosome/plasmid)",
+ "gap at the beginning of object ",
+- "two consequtive gap lines (e.g. a gap at the end of "
++ "two consecutive gap lines (e.g. a gap at the end of "
+ "a scaffold, two non scaffold-breaking gaps, ...)",
+ "no components in object",
+ "the span overlaps a previous span for this component",
+--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_validate_reader.cpp
++++ ncbi-blastplus/c++/src/objtools/readers/agp_validate_reader.cpp
+@@ -295,7 +295,7 @@
+ int prev_comp_file=spans.rbegin()->file_num;
+ int prev_comp_line=spans.rbegin()->line_num;
+ if(prev_comp_file < m_last_scaf_start_file || prev_comp_line < m_last_scaf_start_line) {
+- sameComId_otherScaf="; previous occurance at ";
++ sameComId_otherScaf="; previous occurrence at ";
+ if(prev_comp_file && prev_comp_file!=m_AgpErr->GetFileNum()) {
+ sameComId_otherScaf += m_AgpErr->GetFile(prev_comp_file);
+ sameComId_otherScaf += ":";
+--- ncbi-blastplus.orig/c++/src/util/compress/api/compress.cpp
++++ ncbi-blastplus/c++/src/util/compress/api/compress.cpp
+@@ -160,7 +160,7 @@
+ while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) {
+ os.write(buf.get(), nread);
+ if ( !os.good() ) {
+- SetError(-1, "Error writing to ouput file");
++ SetError(-1, "Error writing to output file");
+ return false;
+ }
+ }
=====================================
debian/rules
=====================================
@@ -4,6 +4,8 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+export HOME=$(CURDIR)/fakehome
+
NUMJOBS=1
ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
@@ -62,6 +64,7 @@ endif
override_dh_auto_configure-indep:;
override_dh_auto_configure-arch: $(PREBUILT_DATATOOL_EXE)
+ mkdir -p $(HOME)
cd c++ && CONFIG_SHELL=/bin/bash \
./configure $(DEB_CONFIGURE_EXTRA_FLAGS) \
|| (tail -v -n +0 config.log BUILD/status/config.log; exit 1)
@@ -102,7 +105,7 @@ override_dh_install-arch:
> $(instroot)/bin/windowmasker_2.2.22_adapter
2to3 -w $(instroot)/bin/windowmasker_2.2.22_adapter
chmod +x $(instroot)/bin/windowmasker_2.2.22_adapter
- rm $(instroot)/bin/windowmasker_2.2.22_adapter.py
+ rm $(instroot)/bin/windowmasker_2.2.22_adapter.py*
# Clean up tests, demos, and internal build tools
rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
$(instroot)/bin/datatool $(instroot)/bin/run_with_lock \
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=3
-opts=pasv,filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \
- ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate
+opts=filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \
+ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/compare/c9708099df9d4c4fe606593325d92451caf972bc...1dc1e25c9484588b31f1c756ec26c7330fdf56e6
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