[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on an official ncbi-blast+ 2.7.1-2, mostly for #916000.
Aaron M. Ucko
gitlab at salsa.debian.org
Thu Dec 13 03:30:41 GMT 2018
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
cf1f6a35 by Aaron M. Ucko at 2018-12-13T03:13:49Z
Start work on an official ncbi-blast+ 2.7.1-2, mostly for #916000.
- - - - -
ad5ac4df by Aaron M. Ucko at 2018-12-13T03:19:19Z
Extend Boost support through at least v1.67, per upstream (#916000).
d/patches/support_boost_1_67: New patch to extend Boost support
(used for uninstalled tests) through at least version 1.67, per
upstream (https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B)
revisions 79910, 79926, 79928, and 79929.
- - - - -
c1d1759c by Aaron M. Ucko at 2018-12-13T03:24:19Z
d/control: Standards-Version: 4.2.1 (already compliant).
- - - - -
28b66a8a by Aaron M. Ucko at 2018-12-13T03:24:45Z
Finalize ncbi-blast+ 2.7.1-2 for unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/support_boost_1_67
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,16 @@
-ncbi-blast+ (2.7.1-1.1) UNRELEASED; urgency=medium
+ncbi-blast+ (2.7.1-2) unstable; urgency=medium
- * Non-maintainer upload.
+ [ David Miguel Susano Pinto ]
* d/control: fix Vcs-* links to point to salsa
- -- David Miguel Susano Pinto <carandraug+dev at gmail.com> Tue, 17 Jul 2018 12:43:08 +0100
+ [ Aaron M. Ucko ]
+ * d/control: Standards-Version: 4.2.1 (already compliant).
+ * d/patches/support_boost_1_67: New patch to extend Boost support
+ (used for uninstalled tests) through at least version 1.67, per
+ upstream (https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B)
+ revisions 79910, 79926, 79928, and 79929. (Closes: #916000.)
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 12 Dec 2018 22:24:45 -0500
ncbi-blast+ (2.7.1-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -15,7 +15,7 @@ Build-Depends: autotools-dev,
libpcre3-dev,
time,
zlib1g-dev
-Standards-Version: 4.1.3
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
=====================================
debian/patches/series
=====================================
@@ -12,3 +12,4 @@ support_x32
suppress_gnutls_version_check
optionally_keep_sequence
fix_unit_tests
+support_boost_1_67
=====================================
debian/patches/support_boost_1_67
=====================================
@@ -0,0 +1,274 @@
+--- a/c++/include/corelib/teamcity_messages.h
++++ b/c++/include/corelib/teamcity_messages.h
+@@ -33,9 +33,9 @@ protected:
+ std::ostream *m_out;
+
+ public:
+- std::string escape(std::string s);
++ std::string escape(const std::string &s);
+ void openMsg(const std::string &name);
+- void writeProperty(std::string name, std::string value);
++ void writeProperty(const std::string &name, const std::string &value);
+ void closeMsg();
+
+ public:
+@@ -46,14 +46,14 @@ public:
+
+ void setOutput(std::ostream &);
+
+- void suiteStarted(std::string name, std::string flowid = std::string());
+- void suiteFinished(std::string name, std::string flowid = std::string());
++ void suiteStarted(const std::string &name, const std::string &flowid = std::string());
++ void suiteFinished(const std::string &name, const std::string &flowid = std::string());
+
+- void testStarted(std::string name, std::string flowid = std::string(), bool captureStandardOutput = false);
+- void testFailed(std::string name, std::string message, std::string details, std::string flowid = std::string());
+- void testIgnored(std::string name, std::string message, std::string flowid = std::string());
+- void testOutput(std::string name, std::string output, std::string flowid, bool isStdErr = StdOut);
+- void testFinished(std::string name, int durationMs = -1, std::string flowid = std::string());
++ void testStarted(const std::string &name, const std::string &flowid = std::string(), bool captureStandardOutput = false);
++ void testFailed(const std::string &name, const std::string &message, const std::string &details, const std::string &flowid = std::string());
++ void testIgnored(const std::string &name, const std::string &message, const std::string &flowid = std::string());
++ void testOutput(const std::string &name, const std::string &output, const std::string &flowid, bool isStdErr = StdOut);
++ void testFinished(const std::string &name, int durationMs = -1, const std::string &flowid = std::string());
+ };
+
+ }
+--- a/c++/src/corelib/teamcity_boost.cpp
++++ b/c++/src/corelib/teamcity_boost.cpp
+@@ -83,6 +83,17 @@ public:
+ virtual void entry_context_start(std::ostream&, boost::unit_test::log_level);
+ virtual void log_entry_context(std::ostream&, boost::unit_test::const_string);
+ virtual void entry_context_finish(std::ostream&);
++
++#if BOOST_VERSION >= 106500
++ // Since v1.65.0 the log level is passed to the formatters for the contexts
++ // See boostorg/test.git:fcb302b66ea09c25f0682588d22fbfdf59eac0f7
++ void log_entry_context(std::ostream& os, boost::unit_test::log_level, boost::unit_test::const_string ctx) override {
++ log_entry_context(os, ctx);
++ }
++ void entry_context_finish(std::ostream& os, boost::unit_test::log_level) override {
++ entry_context_finish(os);
++ }
++#endif
+ };
+
+ // Fake fixture to register formatter
+@@ -90,14 +101,17 @@ struct TeamcityFormatterRegistrar {
+ TeamcityFormatterRegistrar() {
+ if (underTeamcity()) {
+ boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter());
+- boost::unit_test::unit_test_log.set_threshold_level
+- (RTCFG(but::log_level, LOG_LEVEL, log_level));
++ boost::unit_test::unit_test_log.set_threshold_level(boost::unit_test::log_test_units);
+ }
+ }
+ };
+
+ BOOST_GLOBAL_FIXTURE(TeamcityFormatterRegistrar);
+
++// Dummy method used to keep object file in case of static library linking
++// See README.md and https://github.com/JetBrains/teamcity-cpp/pull/19
++void TeamcityGlobalFixture() {}
++
+ // Formatter implementation
+ static std::string toString(boost::unit_test::const_string bstr) {
+ std::stringstream ss;
+--- a/c++/src/corelib/teamcity_messages.cpp
++++ b/c++/src/corelib/teamcity_messages.cpp
+@@ -26,7 +26,7 @@ namespace jetbrains {
+ namespace teamcity {
+
+ std::string getFlowIdFromEnvironment() {
+-#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)) && 0
++#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32)) && !defined(__CYGWIN__) && !defined(__MINGW32__) && 0
+ char *flowId = NULL;
+ size_t sz = 0;
+ std::string result;
+@@ -43,7 +43,7 @@ std::string getFlowIdFromEnvironment() {
+ }
+
+ bool underTeamcity() {
+-#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32) && !defined(__CYGWIN__)) && 0
++#if (defined(WIN32) || defined(_WIN32) || defined(__WIN32)) && !defined(__CYGWIN__) && !defined(__MINGW32__) && 0
+ char *teamCityProjectName = 0;
+ size_t sz = 0;
+ bool result = false;
+@@ -66,8 +66,9 @@ void TeamcityMessages::setOutput(std::os
+ m_out = &out;
+ }
+
+-std::string TeamcityMessages::escape(std::string s) {
++std::string TeamcityMessages::escape(const std::string &s) {
+ std::string result;
++ result.reserve(s.length());
+
+ for (size_t i = 0; i < s.length(); i++) {
+ char c = s[i];
+@@ -86,8 +87,7 @@ std::string TeamcityMessages::escape(std
+ }
+
+ void TeamcityMessages::openMsg(const std::string &name) {
+- // endl for http://jetbrains.net/tracker/issue/TW-4412
+- *m_out << std::endl << "##teamcity[" << name;
++ *m_out << "##teamcity[" << name;
+ }
+
+ void TeamcityMessages::closeMsg() {
+@@ -96,11 +96,11 @@ void TeamcityMessages::closeMsg() {
+ *m_out << std::endl;
+ }
+
+-void TeamcityMessages::writeProperty(std::string name, std::string value) {
++void TeamcityMessages::writeProperty(const std::string &name, const std::string &value) {
+ *m_out << " " << name << "='" << escape(value) << "'";
+ }
+
+-void TeamcityMessages::suiteStarted(std::string name, std::string flowid) {
++void TeamcityMessages::suiteStarted(const std::string &name, const std::string &flowid) {
+ openMsg("testSuiteStarted");
+ writeProperty("name", name);
+ if(flowid.length() > 0) {
+@@ -110,7 +110,7 @@ void TeamcityMessages::suiteStarted(std:
+ closeMsg();
+ }
+
+-void TeamcityMessages::suiteFinished(std::string name, std::string flowid) {
++void TeamcityMessages::suiteFinished(const std::string &name, const std::string &flowid) {
+ openMsg("testSuiteFinished");
+ writeProperty("name", name);
+ if(flowid.length() > 0) {
+@@ -120,7 +120,7 @@ void TeamcityMessages::suiteFinished(std
+ closeMsg();
+ }
+
+-void TeamcityMessages::testStarted(std::string name, std::string flowid, bool captureStandardOutput) {
++void TeamcityMessages::testStarted(const std::string &name, const std::string &flowid, bool captureStandardOutput) {
+ openMsg("testStarted");
+ writeProperty("name", name);
+ if(flowid.length() > 0) {
+@@ -134,7 +134,7 @@ void TeamcityMessages::testStarted(std::
+ closeMsg();
+ }
+
+-void TeamcityMessages::testFinished(std::string name, int durationMs, std::string flowid) {
++void TeamcityMessages::testFinished(const std::string &name, int durationMs, const std::string &flowid) {
+ openMsg("testFinished");
+
+ writeProperty("name", name);
+@@ -152,7 +152,7 @@ void TeamcityMessages::testFinished(std:
+ closeMsg();
+ }
+
+-void TeamcityMessages::testFailed(std::string name, std::string message, std::string details, std::string flowid) {
++void TeamcityMessages::testFailed(const std::string &name, const std::string &message, const std::string &details, const std::string &flowid) {
+ openMsg("testFailed");
+ writeProperty("name", name);
+ writeProperty("message", message);
+@@ -164,7 +164,7 @@ void TeamcityMessages::testFailed(std::s
+ closeMsg();
+ }
+
+-void TeamcityMessages::testIgnored(std::string name, std::string message, std::string flowid) {
++void TeamcityMessages::testIgnored(const std::string &name, const std::string &message, const std::string &flowid) {
+ openMsg("testIgnored");
+ writeProperty("name", name);
+ writeProperty("message", message);
+@@ -175,7 +175,7 @@ void TeamcityMessages::testIgnored(std::
+ closeMsg();
+ }
+
+-void TeamcityMessages::testOutput(std::string name, std::string output, std::string flowid, bool isStdError) {
++void TeamcityMessages::testOutput(const std::string &name, const std::string &output, const std::string &flowid, bool isStdError) {
+ openMsg(isStdError ? "testStdErr" : "testStdOut");
+ writeProperty("name", name);
+ writeProperty("out", output);
+--- a/c++/src/corelib/test_boost.cpp
++++ b/c++/src/corelib/test_boost.cpp
+@@ -95,8 +95,15 @@
+
+ #if BOOST_VERSION >= 106000
+ # define attr_value utils::attr_value
+-# define RTCFG(type, new_name, old_name) \
+- but::runtime_config::get<type >(but::runtime_config::new_name)
++# if BOOST_VERSION >= 106400
++ // Everything old is new again, apparently...
++# define RTCFG(type, new_name, old_name) \
++ but::runtime_config::get<type >(but::runtime_config::btrt_##old_name)
++# define CONFIGURED_FILTERS RTCFG(std::vector<std::string>, _, run_filters)
++# else
++# define RTCFG(type, new_name, old_name) \
++ but::runtime_config::get<type >(but::runtime_config::new_name)
++# endif
+ #else
+ # define RTCFG(type, new_name, old_name) but::runtime_config::old_name()
+ # if BOOST_VERSION >= 105900
+@@ -112,8 +119,10 @@
+ # endif
+ #endif
+
+-#define CONFIGURED_FILTERS \
++#ifndef CONFIGURED_FILTERS
++ #define CONFIGURED_FILTERS \
+ RTCFG(std::vector<std::string>, RUN_FILTERS, test_to_run)
++#endif
+
+ #ifdef NCBI_COMPILER_MSVC
+ # pragma warning(pop)
+@@ -278,11 +287,19 @@ public:
+ virtual
+ void entry_context_start(ostream& ostr, but::log_level l);
+
++# if BOOST_VERSION >= 106500
++ virtual
++ void log_entry_context(ostream& os, but::log_level l, but::const_string v);
++
++ virtual
++ void entry_context_finish(ostream& os, but::log_level l);
++# else
+ virtual
+ void log_entry_context(ostream& ostr, but::const_string value);
+
+ virtual
+ void entry_context_finish (ostream& ostr);
++# endif
+ #endif
+
+ private:
+@@ -2124,6 +2141,19 @@ void CNcbiBoostLogger::entry_context_sta
+ m_Upper->entry_context_start(ostr, l);
+ }
+
++# if BOOST_VERSION >= 106500
++void CNcbiBoostLogger::log_entry_context(ostream& ostr,
++ but::log_level l,
++ but::const_string value)
++{
++ m_Upper->log_entry_context(ostr, l, value);
++}
++
++void CNcbiBoostLogger::entry_context_finish(ostream& ostr, but::log_level l)
++{
++ m_Upper->entry_context_finish(ostr, l);
++}
++# else
+ void CNcbiBoostLogger::log_entry_context(ostream& ostr,
+ but::const_string value)
+ {
+@@ -2134,6 +2164,7 @@ void CNcbiBoostLogger::entry_context_fin
+ {
+ m_Upper->entry_context_finish(ostr);
+ }
++# endif
+ #endif
+
+ void
+@@ -2316,7 +2347,7 @@ main(int argc, char* argv[])
+
+ if (
+ #if BOOST_VERSION >= 106000
+- runtime_config::get<bool>( runtime_config::RESULT_CODE )
++ RTCFG(bool, RESULT_CODE, result_code)
+ #else
+ !runtime_config::no_result_code()
+ #endif
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/compare/ce0452afb7cb412c7fc7588c72ebe2149ae6054f...28b66a8a37157836b90be700a66d392eef60cc84
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/compare/ce0452afb7cb412c7fc7588c72ebe2149ae6054f...28b66a8a37157836b90be700a66d392eef60cc84
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20181213/a61aabdd/attachment-0001.html>
More information about the debian-med-commit
mailing list