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

+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

@@ -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

-%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@univ-montp2.fr> 2.4.0-1
+- Increased interface number
+- Removed dynamic exceptions specifications.
 * Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
 - Increased interface number
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

debian/changelog

+libbpp-raa (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Wed, 28 Mar 2018 09:33:22 +0200
+
 libbpp-raa (2.3.2-1) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.80),
                zlib1g-dev,
-               libbpp-seq-dev (>= 2.3.2)
+               libbpp-seq-dev (>= 2.4.0)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-raa.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-raa.git
@@ -17,9 +17,9 @@ Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 Package: libbpp-raa-dev
 Architecture: any
 Section: libdevel
-Depends: libbpp-raa3 (= ${binary:Version}),
+Depends: libbpp-raa4 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-seq-dev (>= 2.3.2)
+         libbpp-seq-dev (>= 2.4.0)
 Description: Bio++ Remote Acnuc Access library development files
  This library contains utilitary and classes to query public databases
  (GenBank, EMBL, SwissProt, etc) using acnuc.
@@ -27,12 +27,12 @@ Description: Bio++ Remote Acnuc Access library development files
  .
  This package contains header files and static library.
 
-Package: libbpp-raa3
+Package: libbpp-raa4
 Architecture: any
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libbpp-seq11 (>= 2.3.2)
+         libbpp-seq12 (>= 2.4.0)
 Description: Bio++ Remote Acnuc Access library
  This library contains utilitary and classes to query public databases
  (GenBank, EMBL, SwissProt, etc) using acnuc.

debian/copyright

 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Raa
+Upstream-Name: Bpp-Raa
 Upstream-Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-raa/
 
 Files: *
 Copyright: 2010-2016 Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>

debian/libbpp-raa4.symbols

+libbpp-raa.so.4 libbpp-raa4 #MINVER#
+ _ZN3bpp14RaaSpeciesTree10firstChildEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree11nextSynonymEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree5countEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree5labelB5cxx11Ei@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree6getTidEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree6parentEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree7getNameB5cxx11Ei@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree7isChildEii@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree8findNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree8findNodeEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree8getMajorEi@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree9nextChildEii@Base 2.4.0
+ _ZN3bpp16BadCharExceptionC1ERKS0_@Base 2.4.0
+ _ZN3bpp16BadCharExceptionC2ERKS0_@Base 2.4.0
+ _ZN3bpp16BadCharExceptionD0Ev@Base 2.4.0
+ _ZN3bpp16BadCharExceptionD1Ev@Base 2.4.0
+ _ZN3bpp16BadCharExceptionD2Ev@Base 2.4.0
+ _ZN3bpp17AlphabetExceptionD0Ev@Base 2.4.0
+ _ZN3bpp17AlphabetExceptionD1Ev@Base 2.4.0
+ _ZN3bpp17AlphabetExceptionD2Ev@Base 2.4.0
+ _ZN3bpp3RAA10deleteListEPNS_7RaaListE@Base 2.4.0
+ _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_@Base 2.4.0
+ _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAA11getSeq_bothERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEii@Base 2.4.0
+ _ZN3bpp3RAA12openDatabaseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFPcPvESA_@Base 2.4.0
+ _ZN3bpp3RAA12processQueryERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
+ _ZN3bpp3RAA12translateCDSERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAA12translateCDSEi@Base 2.4.0
+ _ZN3bpp3RAA13closeDatabaseEv@Base 2.4.0
+ _ZN3bpp3RAA13getAttributesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAA13getAttributesEi@Base 2.4.0
+ _ZN3bpp3RAA14getNextFeatureEPv@Base 2.4.0
+ _ZN3bpp3RAA14keywordPatternERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAA14knownDatabasesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESA_@Base 2.4.0
+ _ZN3bpp3RAA15createEmptyListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
+ _ZN3bpp3RAA15freeSpeciesTreeEPNS_14RaaSpeciesTreeE@Base 2.4.0
+ _ZN3bpp3RAA15loadSpeciesTreeEb@Base 2.4.0
+ _ZN3bpp3RAA16getDirectFeatureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_S8_@Base 2.4.0
+ _ZN3bpp3RAA16getNextAnnotLineB5cxx11Ev@Base 2.4.0
+ _ZN3bpp3RAA17getFirstAnnotLineB5cxx11Ei@Base 2.4.0
+ _ZN3bpp3RAA18listAllFeatureKeysB5cxx11Ev@Base 2.4.0
+ _ZN3bpp3RAA18translateInitCodonEi@Base 2.4.0
+ _ZN3bpp3RAA19nextMatchingKeywordERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAA20prepareGetAnyFeatureEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAA21getAnnotLineAtAddressB5cxx11ENS_10RaaAddressE@Base 2.4.0
+ _ZN3bpp3RAA21listDirectFeatureKeysB5cxx11Ev@Base 2.4.0
+ _ZN3bpp3RAA22getCurrentAnnotAddressEv@Base 2.4.0
+ _ZN3bpp3RAA22interruptGetAnyFeatureEPv@Base 2.4.0
+ _ZN3bpp3RAA6getSeqERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi@Base 2.4.0
+ _ZN3bpp3RAA6getSeqEii@Base 2.4.0
+ _ZN3bpp3RAAC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_@Base 2.4.0
+ _ZN3bpp3RAAC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAAC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_@Base 2.4.0
+ _ZN3bpp3RAAC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZN3bpp3RAAD1Ev@Base 2.4.0
+ _ZN3bpp3RAAD2Ev@Base 2.4.0
+ _ZN3bpp7RaaList10addElementEi@Base 2.4.0
+ _ZN3bpp7RaaList11nextElementEv@Base 2.4.0
+ _ZN3bpp7RaaList11parentsOnlyEv@Base 2.4.0
+ _ZN3bpp7RaaList12LIST_SPECIESB5cxx11E@Base 2.4.0
+ _ZN3bpp7RaaList12firstElementEv@Base 2.4.0
+ _ZN3bpp7RaaList12modifyByDateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
+ _ZN3bpp7RaaList12residueCountB5cxx11Ev@Base 2.4.0
+ _ZN3bpp7RaaList13LIST_KEYWORDSB5cxx11E@Base 2.4.0
+ _ZN3bpp7RaaList13removeElementEi@Base 2.4.0
+ _ZN3bpp7RaaList14LIST_SEQUENCESB5cxx11E@Base 2.4.0
+ _ZN3bpp7RaaList14modifyByLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
+ _ZN3bpp7RaaList7setFromEi@Base 2.4.0
+ _ZN3bpp7RaaList8getCountEv@Base 2.4.0
+ _ZN3bpp7RaaList8isInListEi@Base 2.4.0
+ _ZN3bpp7RaaList8zeroListEv@Base 2.4.0
+ _ZN3bpp7RaaListC1Ev@Base 2.4.0
+ _ZN3bpp7RaaListC2Ev@Base 2.4.0
+ _ZNK3bpp17AlphabetException11getAlphabetEv@Base 2.4.0
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.0
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm@Base 2.4.0
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.0
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.0
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.0
+ _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
+ ajout_reponse@Base 2.4.0
+ aminoacids@Base 2.4.0
+ atoi_u@Base 2.4.0
+ calc_codon_number@Base 2.4.0
+ chg_acnuc@Base 2.4.0
+ clear_reponse@Base 2.4.0
+ close_sock_gz_r@Base 2.4.0
+ codaa@Base 2.4.0
+ compact@Base 2.4.0
+ compch@Base 2.4.0
+ complementer_base@Base 2.4.0
+ complementer_seq@Base 2.4.0
+ genetic_code@Base 2.4.0
+ get_acnuc_gc_number@Base 2.4.0
+ get_code_descr@Base 2.4.0
+ get_ncbi_gc_number@Base 2.4.0
+ gets_no_echo@Base 2.4.0
+ init_codon_to_aa@Base 2.4.0
+ initreponse@Base 2.4.0
+ majuscules@Base 2.4.0
+ mycalloc@Base 2.4.0
+ notrail2@Base 2.4.0
+ padtosize@Base 2.4.0
+ parse@Base 2.4.0
+ prepare_sock_gz_r@Base 2.4.0
+ prepch@Base 2.4.0
+ print_raa_long@Base 2.4.0
+ raa_1_coordinate_set@Base 2.4.0
+ raa_MD5String@Base 2.4.0
+ raa_acnucclose@Base 2.4.0
+ raa_acnucopen@Base 2.4.0
+ raa_acnucopen_alt@Base 2.4.0
+ raa_alllistranks@Base 2.4.0
+ raa_bcount@Base 2.4.0
+ raa_bit0@Base 2.4.0
+ raa_bit1@Base 2.4.0
+ raa_btest@Base 2.4.0
+ raa_copylist@Base 2.4.0
+ raa_countfilles@Base 2.4.0
+ raa_decode_address@Base 2.4.0
+ raa_error_mess_proc@Base 2.4.0
+ raa_fcode@Base 2.4.0
+ raa_followshrt2@Base 2.4.0
+ raa_get_taxon_info@Base 2.4.0
+ raa_getattributes@Base 2.4.0
+ raa_getemptylist@Base 2.4.0
+ raa_getlistrank@Base 2.4.0
+ raa_getliststate@Base 2.4.0
+ raa_gfrag@Base 2.4.0
+ raa_ghelp@Base 2.4.0
+ raa_iknum@Base 2.4.0
+ raa_isenum@Base 2.4.0
+ raa_knowndbs@Base 2.4.0
+ raa_loadtaxonomy@Base 2.4.0
+ raa_modifylist@Base 2.4.0
+ raa_next_annots@Base 2.4.0
+ raa_nexteltinlist@Base 2.4.0
+ raa_nexteltinlist_annots@Base 2.4.0
+ raa_nextmatchkey@Base 2.4.0
+ raa_open_socket@Base 2.4.0
+ raa_opendb@Base 2.4.0
+ raa_opendb_pw@Base 2.4.0
+ raa_prep_acnuc_query@Base 2.4.0
+ raa_prep_coordinates@Base 2.4.0
+ raa_proc_query@Base 2.4.0
+ raa_read_annots@Base 2.4.0
+ raa_read_first_rec@Base 2.4.0
+ raa_readacc@Base 2.4.0
+ raa_readext@Base 2.4.0
+ raa_readkey@Base 2.4.0
+ raa_readlng@Base 2.4.0
+ raa_readloc@Base 2.4.0
+ raa_readshrt@Base 2.4.0
+ raa_readsmj@Base 2.4.0
+ raa_readspec@Base 2.4.0
+ raa_readsub@Base 2.4.0
+ raa_readsub_pannots@Base 2.4.0
+ raa_releaselist@Base 2.4.0
+ raa_residuecount@Base 2.4.0
+ raa_savelist@Base 2.4.0
+ raa_seq_to_annots@Base 2.4.0
+ raa_seqrank_attributes@Base 2.4.0
+ raa_setlistname@Base 2.4.0
+ raa_setliststate@Base 2.4.0
+ raa_short_descr@Base 2.4.0
+ raa_translate_cds@Base 2.4.0
+ raa_translate_init_codon@Base 2.4.0
+ raa_zerolist@Base 2.4.0
+ read_sock@Base 2.4.0
+ read_sock_timeout@Base 2.4.0
+ scan_raa_long@Base 2.4.0
+ sock_flush@Base 2.4.0
+ sock_fputs@Base 2.4.0
+ sock_printf@Base 2.4.0
+ strcmptrail@Base 2.4.0
+ totcodes@Base 2.4.0
+ trim_key@Base 2.4.0
+ unprotect_quotes@Base 2.4.0
+ val@Base 2.4.0
+ z_getc@Base 2.4.0
+ z_gets@Base 2.4.0
+ z_read_sock@Base 2.4.0

debian/patches/unforce-cxxflags.patch

@@ -11,7 +11,7 @@ Comment: Upstream version 2.3.0 now has additional -std=c++11 which might
  
  # Compile options
 -set (CMAKE_CXX_FLAGS "-std=c++11 -Wall")
-+set (CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated -g")
++#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
 -set (CMAKE_C_FLAGS "-Wall")
 +# set (CMAKE_C_FLAGS "-Wall")
  

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

@@ -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

@@ -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);