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| author |   Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2023-05-02 14:10:02 +0200 |
|---|---|---|
| committer | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2023-05-02 14:15:14 +0200 |
| commit | 7e108279bb4d8cacad16e51875e704c885edc2e7 (patch) | |
| tree | 380b9c56f8812d6a773c5c02f8d8f36d4b12838f /sci-biology | |
| parent | sci-biology/ncbi-genome-download: treeclean (diff) | |
| download | sci-7e108279bb4d8cacad16e51875e704c885edc2e7.tar.gz sci-7e108279bb4d8cacad16e51875e704c885edc2e7.tar.bz2 sci-7e108279bb4d8cacad16e51875e704c885edc2e7.zip | |
sci-biology/ncbi-tools++: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Diffstat (limited to 'sci-biology')
50 files changed, 0 insertions, 3361 deletions
diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest deleted file mode 100644 index 9dd3a53d8..000000000 --- a/sci-biology/ncbi-tools++/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed -DIST ncbi_cxx--18_0_0.tar.gz 69807228 BLAKE2B 2221232e4ab38845708a9ec5601a94f1dd25c5dd6fff265bde3c3d64b9108eec00b8480a1888d2517881f25abe9127e547ba88528b95398480ecd09d133482a7 SHA512 70dd07597aafa3f48881640530bf2aeebcac6fa13843fada4c590ca101cb8fdfa1aabf240ed0177d371a1fc36c6d231d667125279096006cd1eba119ea9514f5 -DIST ncbi_cxx--22_0_0.tar.gz 56042079 BLAKE2B 8a358f9f09e2844c4007b99f4b1c5212e254f804237c26c2eb6620448755b88029d492ff124fff3fdb515189219400f3edaaa195eb4f0fa539ac7b122af4d7e1 SHA512 f6624b09aae1f27b30196b7036f3d962125f2c57e1369bef013b15c116828e2daf264e018a1c1e71fb57c55462d71c5df7580e429fcf9d736e02f89c71cbfbd0 diff --git a/sci-biology/ncbi-tools++/files/curl-types.patch b/sci-biology/ncbi-tools++/files/curl-types.patch deleted file mode 100644 index 3e6079057..000000000 --- a/sci-biology/ncbi-tools++/files/curl-types.patch +++ /dev/null @@ -1,24 +0,0 @@ -Index: libs/kns/url-fetcher-curl.c -=================================================================== ---- src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11878) -+++ src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11880) -@@ -38,7 +38,6 @@ - #include <string.h> - - #include <curl/curl.h> --#include <curl/types.h> - #include <curl/easy.h> - - /*-------------------------------------------------------------------------- -Index: tools/refseq-load/refseq-load.c -=================================================================== ---- src/sra/sdk/tools/refseq-load/refseq-load.c (revision 11878) -+++ src/sra/sdk/tools/refseq-load/refseq-load.c (revision 11880) -@@ -41,7 +41,6 @@ - #include <sysalloc.h> - - #include <curl/curl.h> --#include <curl/types.h> - #include <curl/easy.h> - - #include <stdlib.h> diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt deleted file mode 100644 index fa27aa13b..000000000 --- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt +++ /dev/null @@ -1,8 +0,0 @@ -.* --.*/test --.*/unit_test --.*/unit_tests --dbapi/driver/ftds.*/freetds/.*/unittests --sample --.*/demo --.*/samples diff --git a/sci-biology/ncbi-tools++/files/make_install.patch b/sci-biology/ncbi-tools++/files/make_install.patch deleted file mode 100644 index e98f1110d..000000000 --- a/sci-biology/ncbi-tools++/files/make_install.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- src/build-system/Makefile.in.top.old 2013-01-07 23:07:29.970141951 +0100 -+++ src/build-system/Makefile.in.top 2013-01-07 23:08:37.940990190 +0100 -@@ -39,7 +39,10 @@ - -$(RMDIR) $(pincludedir) - $(INSTALL) -d $(bindir) $(libdir) $(pincludedir) - $(INSTALL) $(lbindir)/* $(bindir) -- $(INSTALL) -m 644 $(llibdir)/* $(libdir) -+ $(INSTALL) -m 644 $(llibdir)/*.* $(libdir) -+ if test -d $(llibdir)/ncbi; then \ -+ cp -pPR $(llibdir)/ncbi $(libdir)/; \ -+ fi - -rm -f $(libdir)/lib*-static.a - cd $(libdir) && \ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done diff --git a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch b/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch deleted file mode 100644 index 4900e529a..000000000 --- a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch +++ /dev/null @@ -1,100 +0,0 @@ ---- trunk/c++/src/app/netcache/nc_memory.cpp 2011/12/16 17:42:54 52330 -+++ trunk/c++/src/app/netcache/nc_memory.cpp 2012/02/27 14:38:30 53136 -@@ -360,7 +360,7 @@ - m_ObjLock.Lock(); - ++m_SysFrees; - m_SystemMem -= alloced_size; -- m_LostMem -= alloced_size -= asked_size; -+ m_LostMem -= alloced_size - asked_size; - m_ObjLock.Unlock(); - } - -@@ -2539,7 +2539,7 @@ - bool - CNCMemManager::InitializeApp(void) - { -- try { -+ /*try { - CSQLITE_Global::SetCustomMallocFuncs(&s_NCMallocMethods); - } - catch (CSQLITE_Exception& ex) { -@@ -2547,13 +2547,15 @@ - return false; - } - -- return CNCMMCentral::RunLateInit(); -+ return CNCMMCentral::RunLateInit();*/ -+ g_InitNCThreadIndexes(); -+ return true; - } - - void - CNCMemManager::FinalizeApp(void) - { -- CNCMMCentral::PrepareToStop(); -+ //CNCMMCentral::PrepareToStop(); - } - - void -@@ -2571,28 +2573,29 @@ - void - CNCMemManager::PrintStats(CPrintTextProxy& proxy) - { -- CNCMMStats stats_sum; -+ /*CNCMMStats stats_sum; - CNCMMStats::CollectAllStats(&stats_sum); -- stats_sum.Print(proxy); -+ stats_sum.Print(proxy);*/ - } - - size_t - CNCMemManager::GetMemoryLimit(void) - { -- return CNCMMCentral::GetMemLimit(); -+ return 0;//CNCMMCentral::GetMemLimit(); - } - - size_t - CNCMemManager::GetMemoryUsed(void) - { -- CNCMMStats stat; -+ /*CNCMMStats stat; - CNCMMStats::CollectAllStats(&stat); -- return stat.GetSystemMem(); -+ return stat.GetSystemMem();*/ -+ return 0; - } - - END_NCBI_SCOPE - -- -+/* - void* - operator new (size_t size) - #ifndef NCBI_COMPILER_MSVC -@@ -2626,13 +2629,13 @@ - { - NCBI_NS_NCBI::CNCMMCentral::DeallocMemory(ptr); - } -- -+*/ - #ifdef __GLIBC__ - // glibc has special method of overriding C library allocation functions. - - #include <malloc.h> - -- -+/* - void* s_NCMallocHook(size_t size, const void* caller) - { - return NCBI_NS_NCBI::CNCMMCentral::AllocMemory(size); -@@ -2656,7 +2659,7 @@ - } - - void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook; -- -+*/ - #elif !defined(NCBI_OS_MSWIN) - // Changing of C library allocation functions on Windows is very tricky (if - // possible at all) and NetCache will never run in production on Windows. So - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch deleted file mode 100644 index 9589481d4..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch +++ /dev/null @@ -1,114 +0,0 @@ -Index: include/db/bdb/bdb_file.hpp -=================================================================== ---- include/db/bdb/bdb_file.hpp (revision 470126) -+++ include/db/bdb/bdb_file.hpp (working copy) -@@ -660,6 +660,9 @@ - void x_ConstructKeyBuf(); - void x_ConstructDataBuf(); - -+ static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t* locp); -+ - private: - auto_ptr<CBDB_BufferManager> m_KeyBuf; - auto_ptr<CBDB_BufferManager> m_DataBuf; -Index: src/db/bdb/bdb_blob.cpp -=================================================================== ---- src/db/bdb/bdb_blob.cpp (revision 470126) -+++ src/db/bdb/bdb_blob.cpp (working copy) -@@ -583,12 +583,31 @@ - return m_DBT_Data->size; - } - -+#if DB_VERSION_MAJOR >= 6 -+extern "C" { -+ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, -+ size_t*); -+ int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+ { return BDB_Uint4Compare(db, dbt1, dbt2); } -+ int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t*) -+ { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); } -+} -+#endif -+ - void CBDB_LobFile::SetCmp(DB*) - { -+#if DB_VERSION_MAJOR >= 6 -+ BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6; -+ if (IsByteSwapped()) { -+ func = BDB_ByteSwap_Uint4Compare_V6; -+ } -+#else - BDB_CompareFunction func = BDB_Uint4Compare; - if (IsByteSwapped()) { - func = BDB_ByteSwap_Uint4Compare; - } -+#endif - - _ASSERT(func); - int ret = m_DB->set_bt_compare(m_DB, func); -Index: src/db/bdb/bdb_file.cpp -=================================================================== ---- src/db/bdb/bdb_file.cpp (revision 470126) -+++ src/db/bdb/bdb_file.cpp (working copy) -@@ -1535,12 +1535,27 @@ - } - - -+#if DB_VERSION_MAJOR >= 6 -+int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+{ -+ const CBDB_BufferManager* key_buf -+ = static_cast<const CBDB_BufferManager*>(db->app_private); -+ _ASSERT(key_buf); -+ return (key_buf->GetCompareFunction())(db, dbt1, dbt2); -+} -+#endif -+ -+ - void CBDB_File::SetCmp(DB* db) - { - _ASSERT(m_DB_Type == eBtree); -+#if DB_VERSION_MAJOR >= 6 -+ int ret = db->set_bt_compare(db, x_CompareShim); -+#else - BDB_CompareFunction func = m_KeyBuf->GetCompareFunction(); - _ASSERT(func); - int ret = db->set_bt_compare(db, func); -+#endif - BDB_CHECK(ret, 0); - - if (m_PrefixCompress) { -@@ -2056,12 +2071,31 @@ - BindKey("id", &IdKey); - } - -+#if DB_VERSION_MAJOR >= 6 -+extern "C" { -+ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, -+ size_t*); -+ int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+ { return BDB_Int4Compare(db, dbt1, dbt2); } -+ int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t*) -+ { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); } -+} -+#endif -+ - void CBDB_IdFile::SetCmp(DB* /* db */) - { -+#if DB_VERSION_MAJOR >= 6 -+ BDB_CompareFunction_V6 func = BDB_Int4Compare_V6; -+ if (IsByteSwapped()) { -+ func = BDB_ByteSwap_Int4Compare_V6; -+ } -+#else - BDB_CompareFunction func = BDB_Int4Compare; - if (IsByteSwapped()) { - func = BDB_ByteSwap_Int4Compare; - } -+#endif - - _ASSERT(func); - int ret = m_DB->set_bt_compare(m_DB, func); diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch deleted file mode 100644 index 3ed3e7d5f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch +++ /dev/null @@ -1,64 +0,0 @@ - src/build-system/configure.ac | 17 ++++++++++++++--- - 1 file changed, 14 insertions(+), 3 deletions(-) - -diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac -index 03e34b4..336453d 100644 ---- a/src/build-system/configure.ac -+++ b/src/build-system/configure.ac -@@ -224,7 +224,7 @@ AC_ARG_WITH(ncbi-c, - AC_ARG_WITH(sss, - [ --without-sss do not use NCBI SSS libraries]) - AC_ARG_WITH(sssutils, -- [ --without-utils do not use NCBI SSS UTIL library]) -+ [ --without-sssutils do not use NCBI SSS UTIL library]) - AC_ARG_WITH(sssdb, - [ --without-sssdb do not use NCBI SSS DB library]) - AC_ARG_WITH(included-sss, -@@ -490,13 +490,13 @@ check ncbi-public strip pch caution ccache distcc \ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - changequote(, )dnl - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` -@@ -522,6 +522,7 @@ for x_arg in "$@" ; do - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) - ;; -@@ -532,6 +533,7 @@ for x_arg in "$@" ; do - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [[A-Z]*=*] \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -647,6 +649,15 @@ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) -+fi - - #### Always define this - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch deleted file mode 100644 index d44993da2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch +++ /dev/null @@ -1,216 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -927,7 +927,7 @@ - --without-distcc do not automatically use distcc if available - --without-ncbi-c do not use NCBI C Toolkit - --without-sss do not use NCBI SSS libraries -- --without-utils do not use NCBI SSS UTIL library -+ --without-sssutils do not use NCBI SSS UTIL library - --without-sssdb do not use NCBI SSS DB library - --with-included-sss use the in-tree copy of SSS - --with-z=DIR use zlib installation in DIR -@@ -2965,13 +2965,13 @@ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` - -@@ -2995,6 +2995,7 @@ - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 - echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} -@@ -3007,6 +3008,7 @@ - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [A-Z]*=* \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - -@@ -17878,68 +17891,6 @@ - fi - - --echo "$as_me:$LINENO: checking for std::is_sorted<> in <algorithm>" >&5 --echo $ECHO_N "checking for std::is_sorted<> in <algorithm>... $ECHO_C" >&6 --if test "${ncbi_cv_func_is_sorted+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ --#include <algorithm> --int --main () --{ --int a[2]; return std::is_sorted(a, a+2) ? 0 : 1; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_func_is_sorted=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_func_is_sorted=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_func_is_sorted" >&5 --echo "${ECHO_T}$ncbi_cv_func_is_sorted" >&6 --if test "$ncbi_cv_func_is_sorted" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_IS_SORTED 1 --_ACEOF -- --fi -- -- - - echo "$as_me:$LINENO: checking for SysV semaphores" >&5 - echo $ECHO_N "checking for SysV semaphores... $ECHO_C" >&6 -@@ -18550,7 +18501,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -18620,7 +18571,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -19046,67 +18997,6 @@ - _ACEOF - - fi -- --echo "$as_me:$LINENO: checking whether $CXX supports C++0x nullptr" >&5 --echo $ECHO_N "checking whether $CXX supports C++0x nullptr... $ECHO_C" >&6 --if test "${ncbi_cv_cxx_nullptr+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ -- --int --main () --{ --void * p = nullptr; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_cxx_nullptr=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_cxx_nullptr=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_cxx_nullptr" >&5 --echo "${ECHO_T}$ncbi_cv_cxx_nullptr" >&6 --if test "$ncbi_cv_cxx_nullptr" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_NULLPTR 1 --_ACEOF -- --fi - - ### Check for the availability of other packages - ### -------------------------------------------- diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch deleted file mode 100644 index fad02c38e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch +++ /dev/null @@ -1,44 +0,0 @@ ---- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2014-06-26 16:46:27.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app 2014-06-26 16:47:26.000000000 +0200 -@@ -9,7 +9,7 @@ - APP = speedtest - SRC = speedtest - LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ -- xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) - ---- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori 2014-06-26 16:47:53.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app 2014-06-26 16:48:07.000000000 +0200 -@@ -7,7 +7,7 @@ - - LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ - taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -- $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) -+ $(BLAST_LIBS) $(OBJMGR_LIBS) - - LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori 2014-06-26 17:45:11.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app 2014-06-26 17:48:26.000000000 +0200 -@@ -3,7 +3,7 @@ - APP = igblastp - SRC = igblastp_app - LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) --LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) -+LIB = blast_app_util igblast $(LIB_) - - # De-universalize Mac builds to work around a PPC toolchain limitation - CFLAGS = $(FAST_CFLAGS:ppc=i386) ---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori 2014-06-26 17:47:53.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app 2014-06-26 17:49:31.000000000 +0200 -@@ -3,7 +3,7 @@ - APP = igblastn - SRC = igblastn_app - LIB_ = $(BLAST_INPUT_LIBS) xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) --LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) -+LIB = blast_app_util igblast $(LIB_) - - # De-universalize Mac builds to work around a PPC toolchain limitation - CFLAGS = $(FAST_CFLAGS:ppc=i386) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch deleted file mode 100644 index fede70e51..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- src/app/agpconvert/Makefile.agpconvert.app.ori 2013-09-13 23:56:22.660032261 +0200 -+++ src/app/agpconvert/Makefile.agpconvert.app 2013-09-13 23:57:31.340032441 +0200 -@@ -6,13 +6,12 @@ - APP = agpconvert - SRC = agpconvert - --LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ -- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) --LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIB = $(OBJREAD_LIBS) taxon1 xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - --REQUIRES = objects algo -+REQUIRES = objects - - WATCHERS = xiangcha diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch deleted file mode 100644 index 46c2e83fb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- src/objtools/alnmgr/demo/Makefile.alnmrg.app.ori 2013-09-13 23:51:34.340031508 +0200 -+++ src/objtools/alnmgr/demo/Makefile.alnmrg.app 2013-09-13 23:51:36.660031514 +0200 -@@ -5,7 +5,7 @@ - SRC = alnmrg - - LIB = xalnmgr $(OBJREAD_LIBS) ncbi_xloader_blastdb seqdb xobjutil submit blastdb \ -- tables $(OBJMGR_LIBS) -+ tables creaders $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch deleted file mode 100644 index 97e845fdb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200 -@@ -48,7 +48,7 @@ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch deleted file mode 100644 index 8bba91f1d..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- scripts/common/new_project.sh (revision 408264) -+++ scripts/common/new_project.sh (working copy) -@@ -6,7 +6,7 @@ - svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"` - def_builddir="$NCBI/c++/Debug/build" - --repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' -+repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' - tmp_app_checkout_dir='tmp_app_sample' - stem='sample/app' diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch deleted file mode 100644 index 553e41d29..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori (revision 439078) -+++ ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app (working copy) -@@ -7,8 +7,8 @@ - SRC = agpconvert - - LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ -- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) --LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+ tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch deleted file mode 100644 index 86e96b865..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch +++ /dev/null @@ -1,421 +0,0 @@ -Index: src/algo/blast/format/Makefile.xblastformat.lib -=================================================================== ---- src/algo/blast/format/Makefile.xblastformat.lib (revision 439078) -+++ src/algo/blast/format/Makefile.xblastformat.lib (working copy) -@@ -7,6 +7,6 @@ - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - --DLL_LIB = align_format blastxml xhtml xcgi -+DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi - - WATCHERS = jianye zaretska madden camacho fongah2 -Index: src/app/compart/Makefile.compart.app -=================================================================== ---- src/app/compart/Makefile.compart.app (revision 439078) -+++ src/app/compart/Makefile.compart.app (working copy) -@@ -5,11 +5,11 @@ - APP = compart - SRC = compart - --LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -- $(OBJMGR_LIBS:%=%$(STATIC)) -+LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ -+ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/compart/Makefile.compartp.app -=================================================================== ---- src/app/compart/Makefile.compartp.app (revision 439078) -+++ src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/app/grid/util/Makefile.ncfetch.app -=================================================================== ---- src/app/grid/util/Makefile.ncfetch.app (revision 439078) -+++ src/app/grid/util/Makefile.ncfetch.app (working copy) -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = kazimird -Index: src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- src/app/hfilter/Makefile.hfilter.app (revision 439078) -+++ src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,9 +5,10 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/speedtest/Makefile.speedtest.app -=================================================================== ---- src/app/speedtest/Makefile.speedtest.app (revision 439078) -+++ src/app/speedtest/Makefile.speedtest.app (working copy) -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) -Index: src/app/splign/Makefile.splign.app -=================================================================== ---- src/app/splign/Makefile.splign.app (revision 439078) -+++ src/app/splign/Makefile.splign.app (working copy) -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) submit \ - $(OBJMGR_LIBS:%=%$(STATIC)) - -Index: src/connect/services/test/Makefile.test_nsstorage.app -=================================================================== ---- src/connect/services/test/Makefile.test_nsstorage.app (revision 439078) -+++ src/connect/services/test/Makefile.test_nsstorage.app (working copy) -@@ -2,7 +2,7 @@ - - APP = test_nsstorage - SRC = test_nsstorage --LIB = xconnserv xconnect xutil xncbi -+LIB = xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/misc/hgvs/test/Makefile.hgvs2variation.app -=================================================================== ---- src/misc/hgvs/test/Makefile.hgvs2variation.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.hgvs2variation.app (working copy) -@@ -6,7 +6,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation \ -+LIB_ = hgvs objcoords variation \ - entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - -Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app -=================================================================== ---- src/misc/hgvs/test/Makefile.test_hgvs_parser.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app (working copy) -@@ -5,7 +5,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \ -+LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \ - entrez2cli entrez2 $(OBJMGR_LIBS) - - LIB = $(LIB_:%=%$(STATIC)) -Index: src/objects/biblio/Makefile.biblio.lib -=================================================================== ---- src/objects/biblio/Makefile.biblio.lib (revision 439078) -+++ src/objects/biblio/Makefile.biblio.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = biblio - SRC = biblio__ biblio___ citation_base -+ -+DLL_LIB = general -Index: src/objects/blast/Makefile.blast.lib -=================================================================== ---- src/objects/blast/Makefile.blast.lib (revision 439078) -+++ src/objects/blast/Makefile.blast.lib (working copy) -@@ -1,4 +1,6 @@ - LIB = xnetblast - SRC = blast__ blast___ names - -+DLL_LIB = scoremat seqset -+ - WATCHERS = camacho -Index: src/objects/blast/Makefile.xnetblastcli.lib -=================================================================== ---- src/objects/blast/Makefile.xnetblastcli.lib (revision 439078) -+++ src/objects/blast/Makefile.xnetblastcli.lib (working copy) -@@ -2,3 +2,5 @@ - - LIB = xnetblastcli - SRC = blastclient blastclient_ -+ -+DLL_LIB = xnetblast xconnect -Index: src/objects/blastdb/Makefile.blastdb.lib -=================================================================== ---- src/objects/blastdb/Makefile.blastdb.lib (revision 439078) -+++ src/objects/blastdb/Makefile.blastdb.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = blastdb - SRC = blastdb__ blastdb___ -+ -+DLL_LIB = seq -Index: src/objects/general/Makefile.general.lib -=================================================================== ---- src/objects/general/Makefile.general.lib (revision 439078) -+++ src/objects/general/Makefile.general.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = general - SRC = general__ general___ uoconv -+ -+DLL_LIB = xser -Index: src/objects/medline/Makefile.medline.lib -=================================================================== ---- src/objects/medline/Makefile.medline.lib (revision 439078) -+++ src/objects/medline/Makefile.medline.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = medline - SRC = medline__ medline___ -+ -+DLL_LIB = biblio general -Index: src/objects/pub/Makefile.pub.lib -=================================================================== ---- src/objects/pub/Makefile.pub.lib (revision 439078) -+++ src/objects/pub/Makefile.pub.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = pub - SRC = pub__ pub___ -+ -+DLL_LIB = medline biblio -Index: src/objects/scoremat/Makefile.scoremat.lib -=================================================================== ---- src/objects/scoremat/Makefile.scoremat.lib (revision 439078) -+++ src/objects/scoremat/Makefile.scoremat.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = scoremat - SRC = scoremat__ scoremat___ -+ -+DLL_LIB = seqset -Index: src/objects/seq/Makefile.seq.lib -=================================================================== ---- src/objects/seq/Makefile.seq.lib (revision 439078) -+++ src/objects/seq/Makefile.seq.lib (working copy) -@@ -13,3 +13,5 @@ - seq_loc_from_string seq_loc_reverse_complementer - - WATCHERS = vasilche grichenk -+ -+DLL_LIB = seqcode pub biblio general xser sequtil -Index: src/objects/seqset/Makefile.seqset.lib -=================================================================== ---- src/objects/seqset/Makefile.seqset.lib (revision 439078) -+++ src/objects/seqset/Makefile.seqset.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = seqset - SRC = seqset__ seqset___ gb_release_file -+ -+DLL_LIB = xser -Index: src/objects/taxon1/Makefile.taxon1.lib -=================================================================== ---- src/objects/taxon1/Makefile.taxon1.lib (revision 439078) -+++ src/objects/taxon1/Makefile.taxon1.lib (working copy) -@@ -3,4 +3,6 @@ - LIB = taxon1 - SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont - -+DLL_LIB = xconnect -+ - WATCHERS = domrach -Index: src/objmgr/util/Makefile.util.lib -=================================================================== ---- src/objmgr/util/Makefile.util.lib (revision 439078) -+++ src/objmgr/util/Makefile.util.lib (working copy) -@@ -8,5 +8,7 @@ - SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util - LIB = xobjutil - -+DLL_LIB = xobjmgr -+ - WATCHERS = ucko vasilche - -Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -=================================================================== ---- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (revision 439078) -+++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (working copy) -@@ -29,4 +29,6 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xobjmgr blastdb -+ - WATCHERS = maning camacho -Index: src/objtools/blast/services/Makefile.blast_services.lib -=================================================================== ---- src/objtools/blast/services/Makefile.blast_services.lib (revision 439078) -+++ src/objtools/blast/services/Makefile.blast_services.lib (working copy) -@@ -13,3 +13,4 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xnetblastcli xconnect -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb seqset - -+DLL_LIB = seqdb -+ - WATCHERS = camacho -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb xnetblast - -+DLL_LIB = blast_services -+ - WATCHERS = camacho -Index: src/objtools/lds2/Makefile.lds2.lib -=================================================================== ---- src/objtools/lds2/Makefile.lds2.lib (revision 439078) -+++ src/objtools/lds2/Makefile.lds2.lib (working copy) -@@ -8,9 +8,9 @@ - SRC = lds2 lds2_db lds2_handlers - - # Dependencies for shared library --#DLL_LIB = sqlitewrapp -+DLL_LIB = sqlitewrapp $(COMPRESS_LIBS) - --LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) -+LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) - - CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS) - -Index: src/objtools/readers/Makefile.xobjread.lib -=================================================================== ---- src/objtools/readers/Makefile.xobjread.lib (revision 439078) -+++ src/objtools/readers/Makefile.xobjread.lib (working copy) -@@ -19,5 +19,6 @@ - best_feat_finder source_mod_parser fasta_exception - - --DLL_LIB = creaders -+DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil - -+ -Index: src/sample/app/cgi/Makefile.cgi_session_sample.app -=================================================================== ---- src/sample/app/cgi/Makefile.cgi_session_sample.app (revision 439078) -+++ src/sample/app/cgi/Makefile.cgi_session_sample.app (working copy) -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app -=================================================================== ---- src/sample/app/netcache/Makefile.netcache_cgi_sample.app (revision 439078) -+++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app (working copy) -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS -Index: src/serial/Makefile.serial.lib -=================================================================== ---- src/serial/Makefile.serial.lib (revision 439078) -+++ src/serial/Makefile.serial.lib (working copy) -@@ -19,3 +19,5 @@ - LIB = xser - - WATCHERS = gouriano -+ -+DLL_LIB = xutil xncbi -Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app -=================================================================== ---- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (revision 439078) -+++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (working copy) -@@ -7,7 +7,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \ -+ xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app -=================================================================== ---- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (revision 439078) -+++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (working copy) -@@ -5,7 +5,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \ -+ test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/readers/bam/test/Makefile.bam_test.app -=================================================================== ---- src/sra/readers/bam/test/Makefile.bam_test.app (revision 439078) -+++ src/sra/readers/bam/test/Makefile.bam_test.app (working copy) -@@ -9,7 +9,8 @@ - APP = bam_test - SRC = bam_test - --LIB = bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS) -+LIB = bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \ -+ $(OBJMGR_LIBS) - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - - REQUIRES = objects -Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib -=================================================================== ---- src/sra/sdk/libs/vfs/Makefile.vfs.lib (revision 16076) -+++ src/sra/sdk/libs/vfs/Makefile.vfs.lib (working copy) -@@ -8,6 +8,9 @@ - CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \ - $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS) - --DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) -+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \ -+ krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) - -+LIBS = $(SRA_SDK_SYSLIBS) -+ - LIB_OR_DLL = both diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch deleted file mode 100644 index 449bbc5a9..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch +++ /dev/null @@ -1,136 +0,0 @@ ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h 2013/09/30 14:10:44 59962 -@@ -62,10 +62,6 @@ - #define HAVE_SYS_TYPES_H 1 - #define HAVE_VSNPRINTF 1 - --#if _MSC_VER >= 1600 --# define HAVE_IS_SORTED 1 --#endif -- - #if _MSC_VER < 1500 - # define vsnprintf _vsnprintf - #endif -@@ -136,10 +132,6 @@ - - #endif - --#if _MSC_VER >= 1600 --# define HAVE_NULLPTR 1 --#endif -- - /* Windows XP and above */ - #define NCBI_WIN32_WINNT 0x0501 - #if !defined(_WIN32_WINNT) ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2013/09/30 14:10:44 59962 -@@ -258,9 +258,6 @@ - /* Define to 1 if you have `ios(_base)::register_callback'. */ - #define HAVE_IOS_REGISTER_CALLBACK 1 - --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ --/* #undef HAVE_IS_SORTED */ -- - /* Define to 1 if you have the `lchown' function. */ - /* #undef HAVE_LCHOWN */ - -@@ -595,9 +592,6 @@ - /* Define to 1 if wxWidgets is available. */ - /* #undef HAVE_WXWIDGETS */ - --/* Define to 1 if nullptr keyword is available. */ --/* #undef HAVE_NULLPTR */ -- - /* Define as const if the declaration of iconv() needs const. */ - #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */ - # define ICONV_CONST ---- ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h 2013/09/30 14:10:44 59962 -@@ -115,6 +115,11 @@ - || defined(__GXX_EXPERIMENTAL_CPP0X__) - # define NCBI_HAVE_CXX11 1 - # endif -+# if defined(NCBI_HAVE_CXX11) \ -+ || (defined(NCBI_COMPILER_MSVC) && _MSC_VER >= 1600) -+# define HAVE_IS_SORTED 1 -+# define HAVE_NULLPTR 1 -+# endif - #endif - - #include <common/ncbi_skew_guard.h> ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2013/09/30 14:10:44 59962 -@@ -179,9 +179,6 @@ - /* Define to 1 if you have `ios(_base)::register_callback'. */ - #undef HAVE_IOS_REGISTER_CALLBACK - --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ --#undef HAVE_IS_SORTED -- - /* Define to 1 if you have the `lchown' function. */ - #undef HAVE_LCHOWN - -@@ -391,9 +388,6 @@ - /* Define to 1 if `min'/`max' templates are not implemented. */ - #undef HAVE_NO_MINMAX_TEMPLATE - --/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */ --#undef HAVE_NULLPTR -- - /* Define to 1 if ODBC libraries are available. */ - #undef HAVE_ODBC - ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2013/09/30 14:10:44 59962 -@@ -3351,17 +3351,6 @@ - fi - - --AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM( -- [[#include <algorithm>]], -- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])], -- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])]) --if test "$ncbi_cv_func_is_sorted" = yes; then -- AC_DEFINE(HAVE_IS_SORTED, 1, -- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.]) --fi -- -- - - AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores, - AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h> -@@ -3498,7 +3487,7 @@ - AC_CACHE_CHECK([whether the C compiler supports C99 restrict], - ncbi_cv_c_restrict, - [ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], - [ncbi_cv_c_restrict=$restrict], []) -@@ -3518,7 +3507,7 @@ - AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict], - ncbi_cv_cxx_restrict, - [ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], - [ncbi_cv_cxx_restrict=$restrict], []) -@@ -3623,14 +3612,6 @@ - unaligned addresses.]) - fi - --AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])], -- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])]) --if test "$ncbi_cv_cxx_nullptr" = yes; then -- AC_DEFINE(HAVE_NULLPTR, 1, -- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.]) --fi -- - ### Check for the availability of other packages - ### -------------------------------------------- - - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch deleted file mode 100644 index 68baea046..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01 20:28:33.239758102 +0100 -+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659 +0100 -@@ -7,7 +7,7 @@ - ################################# - - USR_PROJ = precompile --LIB_PROJ = corelib test_mt test_boost -+LIB_PROJ = corelib test_mt - SUB_PROJ = test - PROJ_TAG = core - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch deleted file mode 100644 index 9047c3384..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch +++ /dev/null @@ -1,296 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/05 12:38:59 62744 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/05 13:59:33 62745 -@@ -1,126 +1,44 @@ --# Hacked up in various ways, since Autoconf's version doesn't quite --# suit our (unusual) conventions. (Originally from status.m4) --m4_define([_AC_SRCPATHS], --[#ac_builddir=. # Useless! --ac_builddir=$builddir --dnl Base source directories on path to *input* file. --if test -n "$ac_file_in"; then -- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])` -+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS) -+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly. -+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS]) -+m4_define([_AC_SRCDIRS], -+[# Base source directories on path to *input* file. -+if test -n "$ac_f"; then -+ ac_dir_in=`AS_DIRNAME(["$ac_f"])` - else - ac_dir_in=$1 - fi - --if test $ac_dir_in != .; then -- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'` -- # A "../" for each directory in $ac_dir_suffix. -- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'` --else -- ac_dir_suffix= ac_top_builddir= --fi -+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) - --case $srcdir in -- .) # No --srcdir option. We are building in place. -- ac_srcdir=. -- if test -z "$ac_top_builddir"; then -- ac_top_srcdir=. -- else -- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` -- fi ;; -- [[\\/]]* | ?:[[\\/]]* ) # Absolute path. -- ac_srcdir=$srcdir/$ac_dir_suffix; -- ac_top_srcdir=$srcdir ;; -- *) # Relative path. -- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix -- ac_top_srcdir=$ac_top_builddir$srcdir ;; --esac --# Do not use `cd foo && pwd` to compute absolute paths, because --# the directories may not exist. --AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1]) --AS_SET_CATFILE([ac_abs_top_builddir], -- [$ac_abs_builddir], [${ac_top_builddir}.]) --AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) --AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix]) --])# _AC_SRCPATHS -- -- --# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a --# last resort due to issues with sourcing .bashrc. --m4_define([_AS_LINENO_PREPARE], --[_AS_LINENO_WORKS || { -- # Find who we are. Look in the path if we contain no path at all -- # relative or not. -- case $[0] in -- *[[\\/]]* ) as_myself=$[0] ;; -- *) _AS_PATH_WALK([], -- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break]) -- ;; -- esac -- # We did not find ourselves, most probably we were run as `sh COMMAND' -- # in which case we are not to be found in the path. -- if test "x$as_myself" = x; then -- as_myself=$[0] -- fi -- if test ! -f "$as_myself"; then -- AS_ERROR([cannot find myself; rerun with an absolute path]) -- fi -- case $CONFIG_SHELL in -- '') -- AS_UNSET(ZSH_VERSION) -- for as_base in sh ksh sh5 bash; do -- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH], -- [case $as_dir in -- /*) -- if ("$as_dir/$as_base" -c \ -- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null -- then -- AS_UNSET(BASH_ENV) -- AS_UNSET(ENV) -- CONFIG_SHELL=$as_dir/$as_base -- export CONFIG_SHELL -- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"} -- fi;; -- esac -- done]);; -- esac -- -- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO -- # uniformly replaced by the line number. The first 'sed' inserts a -- # line-number line before each line; the second 'sed' does the real -- # work. The second script uses 'N' to pair each line-number line -- # with the numbered line, and appends trailing '-' during -- # substitution so that $LINENO is not a special case at line end. -- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the -- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) -- sed '=' <$as_myself | -- sed ' -- N -- s,$,-, -- : loop -- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3, -- t loop -- s,-$,, -- s,^[['$as_cr_digits']]*\n,, -- ' >$as_me.lineno && -- chmod +x $as_me.lineno || -- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell]) -- -- # Don't try to exec as it changes $[0], causing all sort of problems -- # (the dirname of $[0] is not the place where we might find the -- # original and so on. Autoconf is especially sensible to this). -- . ./$as_me.lineno -- # Exit status is that of the last command. -- exit --} --])# _AS_LINENO_PREPARE -+ac_builddir=$builddir -+]) -+ -+ -+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both -+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make -+# bash a last resort due to issues with sourcing .bashrc while entirely -+# avoiding zsh, which passes itself off as ksh on some systems but runs -+# parent shells' exit handlers from subshells, resulting in premature -+# cleanup of temporary files (notably confdefs.h). -+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL]) -+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN]) -+ -+m4_define([_AS_DETECT_BETTER_SHELL], -+ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]), -+ [sh bash ksh sh5], [sh ksh sh5 bash])]) -+m4_define([_AS_RUN], -+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl -+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])]) - - - # One more hack: suppress PACKAGE_*, as we don't use them and some - # third-party libraries expose their corresponding settings, leading - # to preprocessor warnings. --m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED])) -+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED]) - m4_define([AC_DEFINE_UNQUOTED], - [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [], -- [NCBI_ORIG_ACDU($@)])]) -+ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])]) - - - AC_DEFUN(NCBI_FIX_DIR, -@@ -158,7 +76,7 @@ - AC_MSG_WARN([Proceeding without questions per --without-caution]) ;; - * ) - echo "$1 [[y/N]]" -- read answer -+ read answer <& AS_ORIGINAL_STDIN_FD - case "$answer" in - [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;; - * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;; ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014/05/05 12:38:59 62744 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014/05/05 13:59:33 62745 -@@ -38,7 +38,7 @@ - # - ############################################################################# - --AC_PREREQ(2.59) -+AC_PREREQ(2.60) - - dnl Early setup, most crucially for locking. The diversion magic lets - dnl this occur before AC_INIT, which already interferes with other -@@ -493,6 +493,10 @@ - [***** See also HTML documentation in ./doc/index.html *****]) - - -+AC_DIVERT_PUSH(PARSE_ARGS) -+dnl As of Autoconf 2.60, this needs to run too early for config.log, -+dnl to which AC_MSG_ERROR normally copies its output, to be available. -+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD]) - #### Check the passed arguments against the list of available ones - x_with_list="\ - debug max-debug symbols optimization profiling tcheck dll static static-exe \ -@@ -564,7 +568,7 @@ - | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \ - | --x-includes=* | --x-libraries=* | --with-3psw=* \ - | --target=* | --with-runpath=* | --with-relative-runpath=* \ -- | --no-create | --no-recursion) -+ | --help | --no-create | --no-recursion) - ;; - - * ) -@@ -572,6 +576,8 @@ - ;; - esac - done -+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD]) -+AC_DIVERT_POP - - - if test "$with_gbench" = "yes" ; then -@@ -2176,7 +2182,7 @@ - fi - - AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) --AC_PATH_PROG(GREP, grep) -+dnl AC_PATH_PROG(GREP, grep) - AC_PROG_EGREP - AC_MSG_CHECKING([how to run $EGREP quietly]) - if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014/05/05 14:10:55 62749 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014/05/05 14:23:49 62750 -@@ -694,7 +694,7 @@ - /* Define to empty if `const' does not conform to ANSI C. */ - /* #undef const */ - --/* Define to `unsigned' if <sys/types.h> does not define. */ -+/* Define to `unsigned int' if <sys/types.h> does not define. */ - /* #undef size_t */ - - /* ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014/05/05 14:10:55 62749 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014/05/05 14:23:49 62750 -@@ -802,37 +802,37 @@ - by a signal. */ - #undef SELECT_UPDATES_TIMEOUT - --/* The size of a `char', as computed by sizeof. */ -+/* The size of `char', as computed by sizeof. */ - #undef SIZEOF_CHAR - --/* The size of a `double', as computed by sizeof. */ -+/* The size of `double', as computed by sizeof. */ - #undef SIZEOF_DOUBLE - --/* The size of a `float', as computed by sizeof. */ -+/* The size of `float', as computed by sizeof. */ - #undef SIZEOF_FLOAT - --/* The size of a `int', as computed by sizeof. */ -+/* The size of `int', as computed by sizeof. */ - #undef SIZEOF_INT - --/* The size of a `long', as computed by sizeof. */ -+/* The size of `long', as computed by sizeof. */ - #undef SIZEOF_LONG - --/* The size of a `long double', as computed by sizeof. */ -+/* The size of `long double', as computed by sizeof. */ - #undef SIZEOF_LONG_DOUBLE - --/* The size of a `long long', as computed by sizeof. */ -+/* The size of `long long', as computed by sizeof. */ - #undef SIZEOF_LONG_LONG - --/* The size of a `short', as computed by sizeof. */ -+/* The size of `short', as computed by sizeof. */ - #undef SIZEOF_SHORT - --/* The size of a `size_t', as computed by sizeof. */ -+/* The size of `size_t', as computed by sizeof. */ - #undef SIZEOF_SIZE_T - --/* The size of a `void*', as computed by sizeof. */ -+/* The size of `void*', as computed by sizeof. */ - #undef SIZEOF_VOIDP - --/* The size of a `__int64', as computed by sizeof. */ -+/* The size of `__int64', as computed by sizeof. */ - #undef SIZEOF___INT64 - - /* Define to 1 if the stack grows down. */ -@@ -873,5 +873,5 @@ - /* Define to empty if `const' does not conform to ANSI C. */ - #undef const - --/* Define to `unsigned' if <sys/types.h> does not define. */ -+/* Define to `unsigned int' if <sys/types.h> does not define. */ - #undef size_t ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/06 13:12:18 62759 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/06 13:42:48 62760 -@@ -11,6 +11,7 @@ - - NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) - -+AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) - ac_builddir=$builddir - ]) - - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch deleted file mode 100644 index b2d887c92..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch deleted file mode 100644 index c9428084d..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Index: c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app -=================================================================== ---- c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app (revision 523253) -+++ c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app (working copy) -@@ -8,8 +8,8 @@ - - APP = annotwriter - SRC = annotwriter --LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \ -- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS) -+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \ -+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch deleted file mode 100644 index 7a158dc5c..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch +++ /dev/null @@ -1,26 +0,0 @@ -Index: c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app -=================================================================== ---- c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app (revision 523253) -+++ c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app (working copy) -@@ -12,7 +12,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB_ = xobjsimple $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xobjsimple $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app -=================================================================== ---- c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app (revision 523253) -+++ c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app (working copy) -@@ -12,7 +12,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch deleted file mode 100644 index 749c2e57f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch +++ /dev/null @@ -1,29 +0,0 @@ -Index: c++.18.0.0/src/app/compart/Makefile.compart.app -=================================================================== ---- c++.18.0.0/src/app/compart/Makefile.compart.app (revision 523253) -+++ c++.18.0.0/src/app/compart/Makefile.compart.app (working copy) -@@ -5,8 +5,8 @@ - APP = compart - SRC = compart - --LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -+LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1 \ -+ $(BLAST_LIBS:%=%$(STATIC)) xqueryparse xregexp $(PCRE_LIB) \ - $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -Index: c++.18.0.0/src/app/compart/Makefile.compartp.app -=================================================================== ---- c++.18.0.0/src/app/compart/Makefile.compartp.app (revision 523253) -+++ c++.18.0.0/src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch deleted file mode 100644 index e495c9645..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app.ori 2017-03-23 19:24:31.534280319 +0100 -+++ ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app 2017-03-23 19:25:14.395360214 +0100 -@@ -2,7 +2,7 @@ - - APP = convert_seq - SRC = convert_seq --LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite \ -+LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite variation_utils \ - $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil tables xregexp \ - $(PCRE_LIB) $(OBJMGR_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch deleted file mode 100644 index 63bbcc45a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch +++ /dev/null @@ -1,14 +0,0 @@ -Index: c++.18.0.0/src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- c++.18.0.0/src/app/hfilter/Makefile.hfilter.app (revision 523253) -+++ c++.18.0.0/src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,7 +5,8 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch deleted file mode 100644 index ffd3f897f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch +++ /dev/null @@ -1,28 +0,0 @@ -Index: c++.18.0.0/src/app/igblast/Makefile.igblastn.app -=================================================================== ---- c++.18.0.0/src/app/igblast/Makefile.igblastn.app (revision 523253) -+++ c++.18.0.0/src/app/igblast/Makefile.igblastn.app (working copy) -@@ -2,7 +2,8 @@ - - APP = igblastn - SRC = igblastn_app --LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/igblast/Makefile.igblastp.app -=================================================================== ---- c++.18.0.0/src/app/igblast/Makefile.igblastp.app (revision 523253) -+++ c++.18.0.0/src/app/igblast/Makefile.igblastp.app (working copy) -@@ -2,7 +2,8 @@ - - APP = igblastp - SRC = igblastp_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch deleted file mode 100644 index fce7263b2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori 2017-03-26 18:49:50.431994978 +0200 -+++ ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app 2017-03-26 18:50:11.222552131 +0200 -@@ -2,7 +2,7 @@ - - APP = rmblastn - SRC = rmblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch deleted file mode 100644 index 222cb2c06..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app.ori 2017-03-27 00:41:58.742206850 +0200 -+++ ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app 2017-03-27 00:43:13.142206236 +0200 -@@ -12,8 +12,8 @@ - - LIB = xdiscrepancy xalgophytree fastme prosplign xalgoalignutil xalgoseq xmlwrapp \ - xvalidate xobjwrite xobjreadex valerr biotree macro \ -- $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) id2cli \ -- xregexp $(PCRE_LIB) $(SRAREAD_LIBS) $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS) -+ $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) taxon1 id2cli \ -+ xregexp $(PCRE_LIB) xqueryparse $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS) - - LIBS = $(LIBXSLT_LIBS) $(DATA_LOADERS_UTIL_LIBS) $(LIBXML_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) \ - $(SRA_SDK_SYSLIBS) \ diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch deleted file mode 100644 index 541dc2514..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori 2017-03-27 02:33:36.312151540 +0200 -+++ ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app 2017-03-27 02:34:19.372151184 +0200 -@@ -10,7 +10,7 @@ - SRC = tls - - LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \ -- xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+ xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS) - - LIBS = $(PCRE_LIBS) \ - $(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch deleted file mode 100644 index 898e3a70b..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ -Index: c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app -=================================================================== ---- c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app (revision 523253) -+++ c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app (working copy) -@@ -4,7 +4,7 @@ - - APP = vecscreen - SRC = vecscreen_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - # FIXME: do we need blast_app_util - #LIB = blast_app_util $(LIB_:%=%$(STATIC)) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch deleted file mode 100644 index e9dd1f710..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch +++ /dev/null @@ -1,130 +0,0 @@ -Index: c++.18.0.0/src/app/blast/Makefile.blast_formatter.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blast_formatter.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blast_formatter.app (working copy) -@@ -2,7 +2,7 @@ - - APP = blast_formatter - SRC = blast_formatter --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.blastp.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blastp.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blastp.app (working copy) -@@ -4,7 +4,7 @@ - - APP = blastp - SRC = blastp_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.blastx.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blastx.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blastx.app (working copy) -@@ -4,7 +4,7 @@ - - APP = blastx - SRC = blastx_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.deltablast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.deltablast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.deltablast.app (working copy) -@@ -1,7 +1,7 @@ - - APP = deltablast - SRC = deltablast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.psiblast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.psiblast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.psiblast.app (working copy) -@@ -2,7 +2,7 @@ - - APP = psiblast - SRC = psiblast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.rpsblast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.rpsblast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.rpsblast.app (working copy) -@@ -2,7 +2,7 @@ - - APP = rpsblast - SRC = rpsblast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.rpstblastn.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.rpstblastn.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.rpstblastn.app (working copy) -@@ -2,7 +2,7 @@ - - APP = rpstblastn - SRC = rpstblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.seedtop.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.seedtop.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.seedtop.app (working copy) -@@ -2,7 +2,7 @@ - - APP = seedtop - SRC = seedtop_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.tblastn.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.tblastn.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.tblastn.app (working copy) -@@ -4,7 +4,7 @@ - - APP = tblastn - SRC = tblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.tblastx.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.tblastx.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.tblastx.app (working copy) -@@ -4,7 +4,7 @@ - - APP = tblastx - SRC = tblastx_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch deleted file mode 100644 index 97e845fdb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200 -@@ -48,7 +48,7 @@ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch deleted file mode 100644 index aacb20a6c..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori 2017-03-23 21:12:52.028724998 +0100 -+++ ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app 2017-03-23 21:13:30.079737366 +0100 -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = sadyrovr diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch deleted file mode 100644 index e074046cf..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori 2017-03-23 21:16:18.824226906 +0100 -+++ ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app 2017-03-23 21:16:50.085058615 +0100 -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch deleted file mode 100644 index f237a86d8..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app.ori 2017-03-23 21:22:14.463688886 +0100 -+++ ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app 2017-03-23 21:22:48.854603873 +0100 -@@ -10,7 +10,7 @@ - REQUIRES = MT Linux - - --LIB = netstorage ncbi_xcache_netcache xconnserv \ -+LIB = netstorage ncbi_xcache_netcache xconnserv xthrserv \ - $(SDBAPI_LIB) xconnect connssl xutil xncbi - LIBS = $(SDBAPI_LIBS) $(NETWORK_LIBS) $(GNUTLS_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch deleted file mode 100644 index c45d4ad96..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori 2017-03-22 23:52:58.984696074 +0100 -+++ ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app 2017-03-22 23:53:54.746258126 +0100 -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch deleted file mode 100644 index 9435e8b6a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2017-03-23 21:41:31.084603405 +0100 -+++ ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app 2017-03-23 21:45:47.601428174 +0100 -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup taxon3 valid valerr $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil taxon1 xalgoseq xcleanup taxon3 valid valerr $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch deleted file mode 100644 index 56f213f08..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app.ori 2017-03-23 22:08:16.937327984 +0100 -+++ ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app 2017-03-23 22:09:19.208984755 +0100 -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) \ - $(OBJMGR_LIBS:%=%$(STATIC)) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch deleted file mode 100644 index 49a4adb4e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app -=================================================================== ---- c++.18.0.0/src/app/srcchk/Makefile.srcchk.app (revision 523253) -+++ c++.18.0.0/src/app/srcchk/Makefile.srcchk.app (working copy) -@@ -8,8 +8,8 @@ - - APP = srcchk - SRC = srcchk --LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \ -- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS) -+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \ -+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch deleted file mode 100644 index f0a27d85a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- work/ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib.ori 2017-03-17 22:33:51.569635396 +0100 -+++ ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib 2017-03-17 22:33:58.349811199 +0100 -@@ -4,6 +4,6 @@ - LIB = xthrserv - PROJ_TAG = core - LIBS = $(NETWORK_LIBS) --DLL_LIB = xutil xconnect -+DLL_LIB = xncbi xutil xconnect - - WATCHERS = vakatov diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch deleted file mode 100644 index 3c1cb0a9e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app.ori 2016-06-24 16:55:25.000000000 +0200 -+++ ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app 2017-03-21 14:07:31.070364301 +0100 -@@ -9,7 +9,7 @@ - APP = asn2fasta - SRC = asn2fasta - LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) \ -- xobjwrite xobjread $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \ -+ xobjwrite variation_utils $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \ - ncbi_xdbapi_ftds dbapi $(ncbi_xreader_pubseqos2) $(FTDS_LIB) \ - entrez2cli entrez2 tables $(OBJMGR_LIBS) $(PCRE_LIB) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch deleted file mode 100644 index 68baea046..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01 20:28:33.239758102 +0100 -+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659 +0100 -@@ -7,7 +7,7 @@ - ################################# - - USR_PROJ = precompile --LIB_PROJ = corelib test_mt test_boost -+LIB_PROJ = corelib test_mt - SUB_PROJ = test - PROJ_TAG = core - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch deleted file mode 100644 index 098a9ad1e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old 2017-03-26 19:01:58.101495278 +0200 -+++ ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in 2017-03-26 19:02:16.581990522 +0200 -@@ -13,6 +13,7 @@ - -a ! -d $(libdir)/64 ]; then \ - cd $(libdir) && $(LN_S) . 64; \ - fi -+ $(RM) $(LINK) - cd $(libdir) && $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK) - - clean:; diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch deleted file mode 100644 index 41240c330..000000000 --- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch +++ /dev/null @@ -1,64 +0,0 @@ ---- trunk/c++/src/build-system/configure.ac 2012/12/27 15:43:29 56694 -+++ trunk/c++/src/build-system/configure.ac 2013/01/03 03:16:14 56754 -@@ -605,7 +605,8 @@ - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - AC_MSG_NOTICE([using default projects file "projects".]) - with_projects=projects - AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") -@@ -623,6 +624,16 @@ - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) -+fi -+ - # Check for custom optimization flags before potentially going with defaults. - skip_fast_flags=no - if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -@@ -6379,7 +6390,7 @@ - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) - else - AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) -@@ -6982,11 +6993,9 @@ - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -7029,7 +7038,8 @@ - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF - diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch deleted file mode 100644 index 0c1b2d227..000000000 --- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch +++ /dev/null @@ -1,66 +0,0 @@ --- trunk/c++/src/build-system/configure 2012/12/27 15:43:29 56694 -+++ trunk/c++/src/build-system/configure 2013/01/03 03:16:14 56754 -@@ -3125,7 +3125,8 @@ - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 - echo "$as_me: using default projects file \"projects\"." >&6;} - with_projects=projects -@@ -3151,6 +3152,18 @@ - ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi -+ - # Check for custom optimization flags before potentially going with defaults. - skip_fast_flags=no - if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -@@ -33825,7 +33838,7 @@ - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 - echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} - { (exit 1); exit 1; }; } -@@ -36062,11 +36075,9 @@ - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -36110,7 +36121,8 @@ - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF - diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch deleted file mode 100644 index 89dae23ad..000000000 --- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- trunk/c++/src/build-system/configure.ac 2012/12/21 15:12:14 56664 -+++ trunk/c++/src/build-system/configure.ac 2012/12/27 15:43:29 56694 -@@ -623,6 +623,13 @@ - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - -+# Check for custom optimization flags before potentially going with defaults. -+skip_fast_flags=no -+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -+ case " $CFLAGS $CXXFLAGS" in -+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; -+ esac -+fi - - #### Always define this - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) -@@ -1431,7 +1438,7 @@ - wsrx="[[$wschars]]" - - #### Flags to enable (potentially unsafe) extra optimization. --if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then -+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then - case "$compiler:$compiler_version" in - GCC:2* | GCC:344 ) - # GCC 2.9x sometimes experiences internal errors at high optimization; -@@ -1502,8 +1509,6 @@ - DEF_FAST_FLAGS="-O" - ;; - esac --else -- DEF_FAST_FLAGS="-O" - fi - - : ${FAST_CFLAGS="$DEF_FAST_FLAGS"} -@@ -2608,9 +2613,15 @@ - CXXFLAGS="$CXXFLAGS -O" ; fi - if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then - LDFLAGS="$LDFLAGS -O" ; fi -- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -- FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ if test "$skip_fast_flags" = yes ; then -+ FAST_CFLAGS="$CFLAGS" -+ FAST_CXXFLAGS="$CXXFLAGS" -+ FAST_LDFLAGS="$LDFLAGS" -+ else -+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -+ FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ fi - fi - changequote([, ])dnl - fi - diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch deleted file mode 100644 index 669b31722..000000000 --- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch +++ /dev/null @@ -1,53 +0,0 @@ ---- trunk/c++/src/build-system/configure 2012/12/21 15:12:14 56664 -+++ trunk/c++/src/build-system/configure 2012/12/27 15:43:29 56694 -@@ -3151,6 +3151,13 @@ - ;; - esac - -+# Check for custom optimization flags before potentially going with defaults. -+skip_fast_flags=no -+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -+ case " $CFLAGS $CXXFLAGS" in -+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; -+ esac -+fi - - #### Always define this - -@@ -5715,7 +5722,7 @@ - wsrx="[$wschars]" - - #### Flags to enable (potentially unsafe) extra optimization. --if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then -+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then - case "$compiler:$compiler_version" in - GCC:2* | GCC:344 ) - # GCC 2.9x sometimes experiences internal errors at high optimization; -@@ -5786,8 +5793,6 @@ - DEF_FAST_FLAGS="-O" - ;; - esac --else -- DEF_FAST_FLAGS="-O" - fi - - : ${FAST_CFLAGS="$DEF_FAST_FLAGS"} -@@ -8936,9 +8941,15 @@ - CXXFLAGS="$CXXFLAGS -O" ; fi - if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then - LDFLAGS="$LDFLAGS -O" ; fi -- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -- FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ if test "$skip_fast_flags" = yes ; then -+ FAST_CFLAGS="$CFLAGS" -+ FAST_CXXFLAGS="$CXXFLAGS" -+ FAST_LDFLAGS="$LDFLAGS" -+ else -+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -+ FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ fi - fi - fi - diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml deleted file mode 100644 index fbf79d9b7..000000000 --- a/sci-biology/ncbi-tools++/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild deleted file mode 100644 index 009085d15..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ /dev/null @@ -1,364 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${MY_TAG/*_/}" -MY_PV="12_0_0" -MY_P="ncbi_cxx--${MY_PV}" -#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${P}-conf-opts.patch - "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch - "${FILESDIR}"/${P}-linkage-tuneups.patch - "${FILESDIR}"/${P}-more-patches.patch - "${FILESDIR}"/${P}-linkage-tuneups-addons.patch - "${FILESDIR}"/${P}-configure.patch - "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch - "${FILESDIR}"/${P}-fix-install.patch - "${FILESDIR}"/${P}-bdb6.patch - "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 - ) - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -# "${FILESDIR}"/${P}-as-needed.patch -# "${FILESDIR}"/${P}-fix-creaders-linking.patch -# "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch -# ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - # --without-downloaded-vdb - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild deleted file mode 100644 index 604c9c638..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild +++ /dev/null @@ -1,383 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${MY_TAG/*_/}" -MY_PV="18_0_0" -MY_P="ncbi_cxx--${MY_PV}" -#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${P}-configure.patch - "${FILESDIR}"/${P}-fix-install.patch - "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 - "${FILESDIR}"/${P}-fix-annotwriter-linking.patch - "${FILESDIR}"/${P}-fix-undefined-xobjread.patch - "${FILESDIR}"/${P}-fix-apps-blast-linking.patch - "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch - "${FILESDIR}"/${P}-fix-app-compartp-linking.patch - "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch - "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch - "${FILESDIR}"/${P}-fix-app-igblast-linking.patch - "${FILESDIR}"/${P}-fix-ncfetch-linking.patch - "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch - "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch - "${FILESDIR}"/${P}-fix-speedtest-linking.patch - "${FILESDIR}"/${P}-fix-splign-linking.patch - "${FILESDIR}"/${P}-fix-srcchk-linking.patch - "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch - "${FILESDIR}"/${P}-remove-old-symlinks.patch - "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch - "${FILESDIR}"/${P}-fix-app-tls-linking.patch - "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch - "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch - ) - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers - #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - --without-downloaded-vdb - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - # - # idfetch collides with idfetch from ncbi-tools-2.2.26 - # Although the two idfetch implementations do deliberately have several - # options in common, the C++ version is not yet a full drop-in replacement - # for the C version (and will never entirely be, due to fundamental - # differences between the two toolkits' argument-parsing conventions). - mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild deleted file mode 100644 index 4d0d6363e..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild +++ /dev/null @@ -1,388 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_TAG="Mar_28_2019" -MY_Y="${MY_TAG/*_/}" -MY_PV="22_0_0" -MY_P="ncbi_cxx--${MY_PV}" - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -# https://ncbi.github.io/cxx-toolkit/pages/release_notes -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( >=dev-db/sqlite-3.6.6:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( >=dev-libs/libxslt-1.1.14 ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - >=dev-libs/lzo-2.0 - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -# local PATCHES=( -# "${FILESDIR}"/${P}-configure.patch -# "${FILESDIR}"/${P}-fix-install.patch -# "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 -# "${FILESDIR}"/${P}-fix-annotwriter-linking.patch -# "${FILESDIR}"/${P}-fix-undefined-xobjread.patch -# "${FILESDIR}"/${P}-fix-apps-blast-linking.patch -# "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch -# "${FILESDIR}"/${P}-fix-app-compartp-linking.patch -# "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch -# "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch -# "${FILESDIR}"/${P}-fix-app-igblast-linking.patch -# "${FILESDIR}"/${P}-fix-ncfetch-linking.patch -# "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch -# "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch -# "${FILESDIR}"/${P}-fix-speedtest-linking.patch -# "${FILESDIR}"/${P}-fix-splign-linking.patch -# "${FILESDIR}"/${P}-fix-srcchk-linking.patch -# "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch -# "${FILESDIR}"/${P}-remove-old-symlinks.patch -# "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch -# "${FILESDIR}"/${P}-fix-app-tls-linking.patch -# "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch -# "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch -# ) - #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch -# epatch ${PATCHES[@]} - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - --without-downloaded-vdb - $(use_with debug) -# $(use_with debug max-debug) # broken in 22.0.0 as it triggers need for https://github.com/google/sanitizers/wiki/AddressSanitizer - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") -# $(use_with opengl glew-mx) can't find this with any version of media-libs/glew installed: explicitly specified, but no usable version found. - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - # - #if [ ! use static-libs -a ! use static ]; then - # rm -f "${ED}/usr/$(get_libdir)/${PN}"/*.a \ - # "${ED}/usr/$(get_libdir)/${PN}"/*-static.a || die - #fi - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - # - # idfetch collides with idfetch from ncbi-tools-2.2.26 - # Although the two idfetch implementations do deliberately have several - # options in common, the C++ version is not yet a full drop-in replacement - # for the C version (and will never entirely be, due to fundamental - # differences between the two toolkits' argument-parsing conventions). - mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} |