[med-svn] [Git][med-team/libbpp-raa][upstream] New upstream version 2.4.0
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Mar 28 08:02:02 UTC 2018
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-raa
Commits:
afa6b0ca by Julien Y. Dutheil at 2018-03-28T09:31:58+02:00
New upstream version 2.4.0
- - - - -
7 changed files:
- CMakeLists.txt
- ChangeLog
- Doxyfile
- bpp-raa.spec
- src/Bpp/Raa/RAA.cpp
- src/Bpp/Raa/RAA.h
- src/Bpp/Raa/RAA_acnuc.c
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -36,7 +36,7 @@ ELSE(NO_DEP_CHECK)
# library implements.
# In other words, the library implements all the interface numbers in the
# range from number current - age to current.
-SET(${PROJECT_NAME}_VERSION_CURRENT "3")
+SET(${PROJECT_NAME}_VERSION_CURRENT "4")
SET(${PROJECT_NAME}_VERSION_REVISION "0")
SET(${PROJECT_NAME}_VERSION_AGE "0")
@@ -54,7 +54,7 @@ if (CMAKE_INSTALL_PREFIX)
endif (CMAKE_INSTALL_PREFIX)
include (GNUInstallDirs)
-find_package (bpp-seq 11.0.0 REQUIRED)
+find_package (bpp-seq 12.0.0 REQUIRED)
# Find the zlib installation (define zlib imported target)
find_package(ZLIB REQUIRED)
@@ -104,10 +104,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-raa")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.3.1")
+SET(CPACK_PACKAGE_VERSION "2.4.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "4")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -116,6 +116,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
# /!\ This assumes that an external build is used
SET(CPACK_SOURCE_IGNORE_FILES
"/build/"
+ "/html/"
+ "/BppRaa.tag"
"/\\\\.git/"
"/\\\\.gitignore"
${CPACK_SOURCE_IGNORE_FILES}
=====================================
ChangeLog
=====================================
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+25/02/18 -*- version 2.4.0 -*-
+
+25/02/18 Julien Dutheil
+
+* Removed all dynamic exception specifications
+* Increased inerface number to 4.
+
10/05/17 -*- version 2.3.0 -*-
28/09/14 -*- Version 2.2.0 -*-
=====================================
Doxyfile
=====================================
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-raa
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.3.0
+PROJECT_NUMBER = 2.4.0
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=====================================
bpp-raa.spec
=====================================
--- a/bpp-raa.spec
+++ b/bpp-raa.spec
@@ -1,28 +1,25 @@
-%define _basename bpp-raa
-%define _version 2.3.1
-%define _release 1
%define _prefix /usr
-URL: http://biopp.univ-montp2.fr/
+URL: https://github.com/BioPP/bpp-raa
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bpp-raa
+Version: 2.4.0
+Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
Summary: Bio++ Remote Acnuc Access library
Group: Development/Libraries/C and C++
-Requires: bpp-core = %{_version}
-Requires: bpp-seq = %{_version}
+Requires: bpp-core = %{version}
+Requires: bpp-seq = %{version}
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
-BuildRequires: libbpp-core3 = %{_version}
-BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-seq11 = %{_version}
-BuildRequires: libbpp-seq-devel = %{_version}
+BuildRequires: libbpp-core4 = %{version}
+BuildRequires: libbpp-core-devel = %{version}
+BuildRequires: libbpp-seq12 = %{version}
+BuildRequires: libbpp-seq-devel = %{version}
BuildRequires: zlib >= 1.2.3
BuildRequires: zlib-devel >= 1.2.3
@@ -33,28 +30,30 @@ AutoProv: yes
This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.
It is part of the Bio++ project.
-%package -n libbpp-raa3
+%package -n libbpp-raa4
Summary: Bio++ Remote Acnuc Access library
Group: Development/Libraries/C and C++
-%description -n libbpp-raa3
+%description -n libbpp-raa4
This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.
It is part of the Bio++ project.
%package -n libbpp-raa-devel
Summary: Libraries, includes to develop applications with %{_basename}
Group: Development/Libraries/C and C++
-Requires: libbpp-raa3 = %{_version}
-Requires: libbpp-seq11 = %{_version}
-Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core3 = %{_version}
-Requires: libbpp-core-devel = %{_version}
+Requires: libbpp-raa4 = %{version}
+Requires: libbpp-seq12 = %{version}
+Requires: libbpp-seq-devel = %{version}
+Requires: libbpp-core4 = %{version}
+Requires: libbpp-core-devel = %{version}
Requires: zlib >= 1.2.3
Requires: zlib-devel >= 1.2.3
%description -n libbpp-raa-devel
The libbpp-raa-devel package contains the header files and static libraries for
-building applications which use %{_basename}.
+building applications which use %{name}.
+
+%global debug_package %{nil}
%prep
%setup -q
@@ -71,11 +70,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
%clean
rm -rf $RPM_BUILD_ROOT
-%post -n libbpp-raa3 -p /sbin/ldconfig
+%post -n libbpp-raa4 -p /sbin/ldconfig
-%postun -n libbpp-raa3 -p /sbin/ldconfig
+%postun -n libbpp-raa4 -p /sbin/ldconfig
-%files -n libbpp-raa3
+%files -n libbpp-raa4
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
%{_prefix}/%{_lib}/lib*.so.*
@@ -91,6 +90,9 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Mon Feb 26 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.0-1
+- Increased interface number
+- Removed dynamic exceptions specifications.
* Tue Jun 06 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.1-1
- Increased interface number
* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.0-1
=====================================
src/Bpp/Raa/RAA.cpp
=====================================
--- a/src/Bpp/Raa/RAA.cpp
+++ b/src/Bpp/Raa/RAA.cpp
@@ -15,7 +15,7 @@ int sock_printf(raa_db_access* raa_current_db, const char* fmt, ...);
using namespace std;
using namespace bpp;
-RAA::RAA(const string& dbname, int port, const string& server) throw (int)
+RAA::RAA(const string& dbname, int port, const string& server)
{
kw_pattern = NULL;
current_address.div = -1;
@@ -27,7 +27,7 @@ RAA::RAA(const string& dbname, int port, const string& server) throw (int)
}
-RAA::RAA(int port, const string& server) throw (int)
+RAA::RAA(int port, const string& server)
{
kw_pattern = NULL;
int error = raa_open_socket((char*)server.c_str(), port, (char*)"Bio++", &raa_data);
@@ -241,7 +241,7 @@ string RAA::getAnnotLineAtAddress(RaaAddress address)
}
-Sequence* RAA::translateCDS(int seqrank) throw (BadCharException)
+Sequence* RAA::translateCDS(int seqrank)
{
char* descript;
if (seqrank < 2 || seqrank > raa_data->nseq)
@@ -276,7 +276,7 @@ Sequence* RAA::translateCDS(int seqrank) throw (BadCharException)
}
-Sequence* RAA::translateCDS(const string& name) throw (BadCharException)
+Sequence* RAA::translateCDS(const string& name)
{
int rank;
rank = raa_isenum(raa_data, (char*)name.c_str());
@@ -303,7 +303,7 @@ char RAA::translateInitCodon(int seqrank)
}
-RaaList* RAA::processQuery(const string& query, const string& listname) throw (string)
+RaaList* RAA::processQuery(const string& query, const string& listname)
{
char* message;
int type, rank;
@@ -329,7 +329,7 @@ RaaList* RAA::processQuery(const string& query, const string& listname) throw (s
}
-RaaList* RAA::createEmptyList(const string& listname, const string& kind) throw (int)
+RaaList* RAA::createEmptyList(const string& listname, const string& kind)
{
int err, lrank;
char type, * p = 0, * q = 0;
@@ -552,7 +552,7 @@ struct extract_data
};
-void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey) throw (string)
+void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey)
{
char* p, * line;
int l;
=====================================
src/Bpp/Raa/RAA.h
=====================================
--- a/src/Bpp/Raa/RAA.h
+++ b/src/Bpp/Raa/RAA.h
@@ -97,7 +97,7 @@ public:
* 4: database is currently not available for remote connection\n
* 7: not enough memory
*/
- RAA(const std::string& dbname, int port = 5558, const std::string& server = "pbil.univ-lyon1.fr") throw (int);
+ RAA(const std::string& dbname, int port = 5558, const std::string& server = "pbil.univ-lyon1.fr");
/**
* @brief Direct constructor: opens a network connection to a database server, without specifying a database.
@@ -113,7 +113,7 @@ public:
* 2: cannot create connection with server\n
* 7: not enough memory
*/
- RAA(int port = 5558, const std::string& server = "pbil.univ-lyon1.fr") throw (int);
+ RAA(int port = 5558, const std::string& server = "pbil.univ-lyon1.fr");
/**
* @brief Destructor: closes both the database access, if any, and the network connection.
@@ -272,7 +272,7 @@ public:
* @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
* exception when translated to protein.
*/
- Sequence* translateCDS(int seqrank) throw (BadCharException); // TODO add comment to Sequence
+ Sequence* translateCDS(int seqrank); // TODO add comment to Sequence
/**
* @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.
@@ -285,7 +285,7 @@ public:
* @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
* exception when translated to protein.
*/
- Sequence* translateCDS(const std::string& name) throw (BadCharException);
+ Sequence* translateCDS(const std::string& name);
/**
* @brief Returns the amino acid translation of the first codon of a protein-coding (sub)sequence.
@@ -316,7 +316,7 @@ public:
* @return The resulting list of matching database elements.
* @throw string If error, the string is a message describing the error cause.
*/
- RaaList* processQuery(const std::string& query, const std::string& listname) throw (std::string);
+ RaaList* processQuery(const std::string& query, const std::string& listname);
/**
* @brief Creates an empty list with specified name.
@@ -328,7 +328,7 @@ public:
* @throw int 3: a list with same name already existed; it is left unchanged.\n
* 4: the server cannot create more lists.
*/
- RaaList* createEmptyList(const std::string& listname, const std::string& kind = RaaList::LIST_SEQUENCES) throw (int);
+ RaaList* createEmptyList(const std::string& listname, const std::string& kind = RaaList::LIST_SEQUENCES);
/**
* @brief Deletes a list and calls its destructor.
@@ -406,7 +406,7 @@ public:
* @return An opaque pointer to be transmitted to functions getNextFeature() or interruptGetAnyFeature().
* @throw string A message indicating the cause of the error.
*/
- void* prepareGetAnyFeature(int seqrank, const std::string& featurekey) throw (std::string);
+ void* prepareGetAnyFeature(int seqrank, const std::string& featurekey);
/**
* @brief Successively returns features specified in a previous prepareGetAnyFeature() call.
=====================================
src/Bpp/Raa/RAA_acnuc.c
=====================================
--- a/src/Bpp/Raa/RAA_acnuc.c
+++ b/src/Bpp/Raa/RAA_acnuc.c
@@ -3192,7 +3192,7 @@ char* raa_translate_cds(raa_db_access* raa_current_db, int seqnum)
char raa_translate_init_codon(raa_db_access* raa_current_db, int numseq)
{
char codon[4];
- int point, special_init = TRUE, val, gc, phase, rank = 0;
+ int point, special_init = TRUE, val, gc = 0, phase = 0, rank = 0;
if (raa_current_db->num_5_partial == 0)
raa_current_db->num_5_partial = raa_iknum(raa_current_db, "5'-PARTIAL", raa_key);
View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/afa6b0cab780f93aa3852c865520abc72db41511
---
View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/afa6b0cab780f93aa3852c865520abc72db41511
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