* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/files/, sci-biology/ncbi-blast+/
@ 2015-11-22 21:19 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2015-11-22 21:19 UTC (permalink / raw
To: gentoo-commits
commit: a6e8082dd9b651ba5114e1dbb08859e06d52f320
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Nov 22 21:18:31 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Nov 22 21:18:31 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6e8082d
sci-biology/ncbi-blast+-2.2.31: version bump, seems that some parts of the ncbi-blast+-2.2.30__fix_lib_deps.patch could/should be re-used
Package-Manager: portage-2.2.18
sci-biology/ncbi-blast+/ChangeLog | 8 ++++++++
...{fix_lib_deps.patch => ncbi-blast+-2.2.30__fix_lib_deps.patch} | 0
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 2 +-
.../{ncbi-blast+-2.2.30.ebuild => ncbi-blast+-2.2.31.ebuild} | 5 ++++-
4 files changed, 13 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog
index 4570694..4e01710 100644
--- a/sci-biology/ncbi-blast+/ChangeLog
+++ b/sci-biology/ncbi-blast+/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+*ncbi-blast+-2.2.31 (22 Nov 2015)
+
+ 22 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/ncbi-blast+-2.2.30__fix_lib_deps.patch, +ncbi-blast+-2.2.31.ebuild,
+ -files/fix_lib_deps.patch, ncbi-blast+-2.2.30.ebuild:
+ sci-biology/ncbi-blast+-2.2.31: version bump, seems that some parts of the
+ ncbi-blast+-2.2.30__fix_lib_deps.patch could/should be re-used
+
17 Jul 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml:
Add sqlite3 flag description.
diff --git a/sci-biology/ncbi-blast+/files/fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
similarity index 100%
rename from sci-biology/ncbi-blast+/files/fix_lib_deps.patch
rename to sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 31152c5..3008025 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -125,7 +125,7 @@ src_prepare() {
## epatch ${PATCHES[@]}
# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- epatch "${FILESDIR}"/fix_lib_deps.patch
+ epatch "${FILESDIR}"/"${P}"__fix_lib_deps.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
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
similarity index 98%
copy from sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
copy to sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 31152c5..9b3c9b2 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -125,7 +125,10 @@ src_prepare() {
## epatch ${PATCHES[@]}
# use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- epatch "${FILESDIR}"/fix_lib_deps.patch
+ # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
+ # it is still present, plus in a few places was something else patched
+ # staying without any patches for now and lets see is it works on Gentoo
+ # epatch "${FILESDIR}"/fix_lib_deps.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
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/files/, sci-biology/ncbi-blast+/
@ 2023-05-02 12:15 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:15 UTC (permalink / raw
To: gentoo-commits
commit: 90e60e2f6d4782f0dffc9996a07cc0bdcd24545b
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:09:35 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:15:13 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=90e60e2f
sci-biology/ncbi-blast+: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../files/disable-testsuite-compilation.txt | 3 -
.../files/ncbi-blast+-2.2.30__fix_lib_deps.patch | 668 ---------------------
sci-biology/ncbi-blast+/metadata.xml | 23 -
sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild | 360 -----------
sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 350 -----------
sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 350 -----------
sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 355 -----------
sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 360 -----------
8 files changed, 2469 deletions(-)
diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
deleted file mode 100644
index aeaf75e45..000000000
--- a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-.*
--.*/test
--.*/unit_test
diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
deleted file mode 100644
index 13dffeee7..000000000
--- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
+++ /dev/null
@@ -1,668 +0,0 @@
-Subject: ensure that all libraries link against all direct dependencies
-
- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
- loop between libxblast and libxalgoblastdbindex by having the former
- provide only the C++ BLAST API, leaving the C core only in libblast.
- * src/build-system/library_relations.txt: Change xblast's
- relationship to blast from includes to needs, accordingly.
- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
- rather than libconnect for consistency with libblast, which uses the
- former to keep the aforementioned cycle-breaking from causing
- inconsistency elsewhere.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2014-12-02
---- a/c++/src/algo/blast/core/Makefile.blast.lib
-+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,6 +21,7 @@ LIB = blast
- CFLAGS = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = composition_adjustment xconnect tables
-
- WATCHERS = madden camacho
-
---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi blastxml2
-
- WATCHERS = jianye zaretska madden camacho fongah2
-
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
--
-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
-
- USES_LIBRARIES = \
- seqmasks_io
---- a/c++/src/cgi/Makefile.cgi.lib
-+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
- user_agent
- LIB = xcgi
-
-+DLL_LIB = xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
-
- WATCHERS = vakatov
---- a/c++/src/html/Makefile.html.lib
-+++ b/c++/src/html/Makefile.html.lib
-@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se
- commentdiag indentstream html_exception writer_htmlenc
- LIB = xhtml
-
-+DLL_LIB = xncbi
-+
- WATCHERS = ivanov
-
-
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -3,6 +3,7 @@ ASN_DEP = xnetblast
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
-
- USES_LIBRARIES = \
- xconnect xnetblast
---- a/c++/src/objtools/align_format/Makefile.align_format.lib
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
-+ xcgi xhtml tables xncbi
-+
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
- # CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge
-
- WATCHERS = todorov dicuccio grichenk
-
--
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-
- USES_LIBRARIES = \
- tables xobjutil
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \
- message_listener line_error
-
-
--DLL_LIB = creaders
-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi
-
-
-
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,7 +12,7 @@ mask_writer_seqloc \
- mask_writer_blastdb_maskinfo
-
- ASN_DEP = seqset
--DLL_LIB = seqdb blastdb
-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
-
- WATCHERS = morgulis camacho
-
---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@ WATCHERS = jcherry
-
- ASN_DEP = seqset
-
-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
-+
- LIB = xobjsimple
- SRC = simple_om
-
---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -24,6 +24,8 @@ seqdbobj
-
- LIB = seqdb
-
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_
-
- ASN_DEP = blastdb seqset
-
-+DLL_LIB = seqdb xobjmgr seqset seq xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapt
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
-
- WATCHERS = camacho
---- a/c++/src/algo/blast/api/Makefile.xblast.lib
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,14 +74,15 @@ cdd_pssm_input \
- deltablast_options \
- deltablast
-
--SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
-
- LIB = xblast
-
- DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
- xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
- blastdb xnetblastcli xnetblast scoremat xconnect tables \
-- $(SOBJMGR_LIBS)
-+ $(SOBJMGR_LIBS) blast seqdb seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
-
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)
-
- LIB = blastinput
-
--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil
-+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
-+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
-+ scoremat seqset seq xser xutil xncbi
-
- # should be redundant, given the above :-/
- ASN_DEP = seqset xnetblast
---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgodustmask
-
- SRC = symdust
-
-+DLL_LIB = xobjmgr seq xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/connect/Makefile.xconnect.lib
-+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
- LIB = xconnect
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
-
- WATCHERS = lavr
---- a/c++/src/connect/ext/Makefile.xconnext.lib
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,6 +6,8 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper
-
- LIB = xconnext
-
-+DLL_LIB = xconnect xncbi
-+
- WATCHERS = lavr
-
-
---- a/c++/src/objects/blast/Makefile.blast.lib
-+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,6 +1,8 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
-
-+DLL_LIB = scoremat seqset seq xser xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objects/blastxml/Makefile.blastxml.lib
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
-@@ -1,6 +1,8 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,6 +1,8 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-
-+DLL_LIB = seqset seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,6 +1,7 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
--
-+
-+DLL_LIB = seqset seq general xser xncbi
-
-
- USES_LIBRARIES = \
---- a/c++/src/objects/submit/Makefile.submit.lib
-+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,6 +1,8 @@
- LIB = submit
- SRC = submit__ submit___
-
-+DLL_LIB = seqset seq biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objmgr/util/Makefile.util.lib
-+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,6 +8,8 @@ ASN_DEP = submit
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
- LIB = xobjutil
-
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche kornbluh
-
-
---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
-
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -8,6 +8,8 @@ SRC = blast_services
-
- LIB = blast_services
-
-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \
-+ id2 id1 ncbi_xreader xobjmgr seq xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -15,6 +15,9 @@ LIB_OR_DLL = both
- DLL_LIB =
- DLL_DLIB = $(GENBANK_READER_LDEP)
-
-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
-+ xser xconnect xcompress xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,7 +12,10 @@ LIB_OR_DLL = both
- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
-
- # Dependencies for shared library (disabled due to problems on Darwin)
--# DLL_LIB = xconnect ncbi_xreader$(DLL)
-+DLL_LIB = xconnect ncbi_xreader$(DLL)
-+
-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
-+
-
- WATCHERS = vasilche
-
---- a/c++/src/util/compress/api/Makefile.compress.lib
-+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -7,7 +7,7 @@ LIB = xcompress
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/util/sequtil/Makefile.sequtil.lib
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,6 +3,8 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
-
-
---- a/c++/src/corelib/Makefile.test_boost.lib
-+++ b/c++/src/corelib/Makefile.test_boost.lib
-@@ -3,6 +3,8 @@
- SRC = test_boost teamcity_messages
- LIB = test_boost
-
-+DLL_LIB = xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
-
- REQUIRES = Boost.Test.Included
---- a/c++/src/corelib/Makefile.test_mt.lib
-+++ b/c++/src/corelib/Makefile.test_mt.lib
-@@ -3,6 +3,8 @@
- SRC = test_mt
- LIB = test_mt
-
-+DLL_LIB = xncbi
-+
- # REQUIRES = MT
-
- USE_PCH = no
---- a/c++/src/objects/biblio/Makefile.biblio.lib
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,6 +1,8 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-
-+DLL_LIB = general xser xncbi
-+
-
- USES_LIBRARIES = \
- general
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,5 +1,7 @@
- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
-
-+
-+DLL_LIB = seq xser xncbi
- LIB = blastdb
- SRC = blastdb__ blastdb___
-
---- a/c++/src/objects/general/Makefile.general.lib
-+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,6 +1,8 @@
- LIB = general
- SRC = general__ general___ uoconv
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,6 +3,8 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
-
-
---- a/c++/src/objects/id1/Makefile.id1.lib
-+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,6 +3,8 @@ ASN_DEP = seq
- LIB = id1
- SRC = id1__ id1___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/id2/Makefile.id2.lib
-+++ b/c++/src/objects/id2/Makefile.id2.lib
-@@ -1,6 +1,8 @@
- LIB = id2
- SRC = id2__ id2___
-
-+DLL_LIB = seqsplit seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/medline/Makefile.medline.lib
-+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,6 +1,8 @@
- LIB = medline
- SRC = medline__ medline___
-
-+DLL_LIB = biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- biblio
---- a/c++/src/objects/pub/Makefile.pub.lib
-+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,6 +1,8 @@
- LIB = pub
- SRC = pub__ pub___
-
-+DLL_LIB = medline biblio xser xncbi
-+
-
- USES_LIBRARIES = \
- medline
---- a/c++/src/objects/seq/Makefile.seq.lib
-+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
- seq_loc_from_string seq_loc_reverse_complementer
-
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
-
-
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
-@@ -1,6 +1,8 @@
- LIB = seqcode
- SRC = seqcode__ seqcode___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/seqset/Makefile.seqset.lib
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,6 +1,8 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-
-+DLL_LIB = seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- $(SEQ_LIBS) pub
---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-@@ -1,6 +1,8 @@
- LIB = seqsplit
- SRC = seqsplit__ seqsplit___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/serial/Makefile.serial.lib
-+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,6 +18,8 @@ SRC = \
-
- LIB = xser
-
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
-
-
---- a/c++/src/util/Makefile.util.lib
-+++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s
- LIB = xutil
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
-
- WATCHERS = vakatov kornbluh
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@ LIB = xregexp
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
-
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgosegmask
-
- SRC = segmask
-
-+DLL_LIB = blast xobjmgr xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/objmgr/split/Makefile.id2_split.lib
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,7 +17,7 @@ LIB = id2_split
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
-
- WATCHERS = vasilche
-
---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum
-
- LIB = writedb
-
-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
-+ xser sequtil xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@ APP = makembindex
- SRC = main mkindex_app
-
- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
-- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)
-+ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
-
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/build-system/library_relations.txt
-+++ b/c++/src/build-system/library_relations.txt
-@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)
- xasmcompare needs pub
- xasn needs xhtml
- xasn needs3party $(NCBI_C_ncbi)
--xblast includes blast
-+xblast needs blast
- xblast needs xalgoblastdbindex
- xblast needs xalgodustmask
- xblast needs xalgowinmask
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
deleted file mode 100644
index 93556eaa7..000000000
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <use>
- <flag name="boost">Undocumented USE</flag>
- <flag name="cppunit">Undocumented USE</flag>
- <flag name="freetype">Undocumented USE</flag>
- <flag name="mesa">Undocumented USE</flag>
- <flag name="muparser">Undocumented USE</flag>
- <flag name="sablotron">Undocumented USE</flag>
- <flag name="xerces">Undocumented USE</flag>
- <flag name="xalan">Undocumented USE</flag>
- <flag name="xslt">Undocumented USE</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
deleted file mode 100644
index 527acfadf..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ /dev/null
@@ -1,360 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-single-r1 toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.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 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
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- berkdb? ( sys-libs/db:=[cxx(-)] )
- boost? ( dev-libs/boost )
- 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? ( ${PYTHON_DEPS} )
- cppunit? ( dev-util/cppunit )
- icu? ( dev-libs/icu )
- expat? ( dev-libs/expat )
- sablotron? ( app-text/sablotron )
- xml? ( dev-libs/libxml2 )
- xslt? ( dev-libs/libxslt )
- xerces? ( dev-libs/xerces-c )
- xalan? ( dev-libs/xalan-c )
- muparser? ( dev-cpp/muParser )
- hdf5? ( sci-libs/hdf5[cxx] )
- gif? ( media-libs/giflib )
- jpeg? ( media-libs/libjpeg-turbo:0= )
- png? ( media-libs/libpng:0= )
- tiff? ( media-libs/tiff:0= )
- xpm? ( x11-libs/libXpm )
- dev-libs/lzo
- app-arch/bzip2
- dev-libs/libpcre
- dev-db/lmdb"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-# The default (heavily patched) embedded copy should work, or you can
-# leave it off altogether -- the only public apps that make use of it are
-# samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# 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}"/${P}-conf-opts.patch
-## "${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}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.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
- default
-}
-
-# 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
- $(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")
- #
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
- # $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${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")
-# $(use_with X x) # there is no --with-x option
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
- --without-vdb
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${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 \
- ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${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 "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${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-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
deleted file mode 100644
index e90652f38..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ /dev/null
@@ -1,350 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${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 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"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- berkdb? ( sys-libs/db:=[cxx(-)] )
- boost? ( dev-libs/boost )
- 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}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-PATCHES=(
- "${FILESDIR}"/"${P}"__fix_lib_deps.patch
-)
-
-src_prepare() {
-# 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}"/${P}-conf-opts.patch
-## "${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}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # 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
- default
-}
-
-# 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
- $(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")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${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 \
- ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${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 "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${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-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
deleted file mode 100644
index ddeeac07d..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ /dev/null
@@ -1,350 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${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 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"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- berkdb? ( sys-libs/db:=[cxx(-)] )
- boost? ( dev-libs/boost )
- 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}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# 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}"/${P}-conf-opts.patch
-## "${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}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.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
- default
-}
-
-# 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
- $(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")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${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 \
- ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported"
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${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 "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${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-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
deleted file mode 100644
index 976ea3804..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ /dev/null
@@ -1,355 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${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 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"
-RESTRICT="!test? ( test )"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- berkdb? ( sys-libs/db:=[cxx(-)] )
- boost? ( dev-libs/boost )
- 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}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# 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}"/${P}-conf-opts.patch
-## "${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}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.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
- default
-}
-
-# 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
- $(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")
- #
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
- # $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${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")
-# $(use_with X x) # there is no --with-x option
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
- --without-vdb
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${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 "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${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-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
deleted file mode 100644
index 527acfadf..000000000
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ /dev/null
@@ -1,360 +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_P="ncbi-blast-${PV}+-src"
-# workdir/ncbi-blast-2.2.30+-src
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz
-
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
- debug static-libs static threads pch
- test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fltk freetype gif
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
- sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- <sys-devel/gcc-10:=
- !sci-biology/ncbi-tools++
- berkdb? ( sys-libs/db:=[cxx(-)] )
- boost? ( dev-libs/boost )
- 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? ( ${PYTHON_DEPS} )
- cppunit? ( dev-util/cppunit )
- icu? ( dev-libs/icu )
- expat? ( dev-libs/expat )
- sablotron? ( app-text/sablotron )
- xml? ( dev-libs/libxml2 )
- xslt? ( dev-libs/libxslt )
- xerces? ( dev-libs/xerces-c )
- xalan? ( dev-libs/xalan-c )
- muparser? ( dev-cpp/muParser )
- hdf5? ( sci-libs/hdf5[cxx] )
- gif? ( media-libs/giflib )
- jpeg? ( media-libs/libjpeg-turbo:0= )
- png? ( media-libs/libpng:0= )
- tiff? ( media-libs/tiff:0= )
- xpm? ( x11-libs/libXpm )
- dev-libs/lzo
- app-arch/bzip2
- dev-libs/libpcre
- dev-db/lmdb"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-# The default (heavily patched) embedded copy should work, or you can
-# leave it off altogether -- the only public apps that make use of it are
-# samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}/c++"
-# ncbi-blast-2.2.30+-src/c++
-
-src_prepare() {
-# 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}"/${P}-conf-opts.patch
-## "${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}-support-autoconf-2.60.patch
-## epatch ${PATCHES[@]}
-
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere
- # it is still present, plus in a few places was something else patched
- # staying without any patches for now and lets see is it works on Gentoo
- # epatch "${FILESDIR}"/fix_lib_deps.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
- default
-}
-
-# 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
- $(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")
- #
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
- # $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+
- $(usex odbc --with-odbc="${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")
-# $(use_with X x) # there is no --with-x option
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
- --without-vdb
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${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 \
- ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?"
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${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 "${S}"_build/build -f Makefile.flat
-}
-
-src_install() {
- rm -rvf "${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/'
-}
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2023-05-02 12:15 [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/files/, sci-biology/ncbi-blast+/ Andrew Ammerlaan
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2015-11-22 21:19 Martin Mokrejs
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