commit: 505486cbc011b906cb37e3af2376dc4deeba06d6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 22 22:35:40 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 22 22:35:40 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=505486cb
sci-biology/ncbi-tools++: fix plenty linking issues, still far from completeness
Package-Manager: Portage-2.3.3, Repoman-2.3.1
...bi-tools++-18.0.0-fix-annotwriter-linking.patch | 15 ++
...cbi-tools++-18.0.0-fix-apps-blast-linking.patch | 205 +++++++++++++++++++++
.../ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch | 10 +
...cbi-tools++-18.0.0-fix-undefined-xobjread.patch | 11 ++
.../ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 4 +
5 files changed, 245 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
new file mode 100644
index 000000000..3f1379223
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch
@@ -0,0 +1,15 @@
+--- ncbi_cxx--18_0_0/src/app/annotwriter/Makefile.annotwriter.app.ori
2017-03-20 18:13:08.087145846 +0100
++++ ncbi_cxx--18_0_0/src/app/annotwriter/Makefile.annotwriter.app
2017-03-20 18:14:10.988888851 +0100
+@@ -8,8 +8,8 @@
+
+ APP = annotwriter
+ SRC = annotwriter
+-LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \
+- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS)
++LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
++ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
new file mode 100644
index 000000000..43104976e
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
@@ -0,0 +1,205 @@
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blast_formatter.app.ori
2017-03-22 17:21:05.653409646 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blast_formatter.app
2017-03-22 17:22:25.755581547 +0100
+@@ -2,7 +2,7 @@
+
+ APP = blast_formatter
+ SRC = blast_formatter
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -11,6 +11,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blastn.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blastn.app 2017-03-22
19:58:28.925273217 +0100
+@@ -14,7 +14,7 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blastp.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blastp.app 2017-03-22
19:58:54.365962959 +0100
+@@ -4,7 +4,7 @@
+
+ APP = blastp
+ SRC = blastp_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -13,7 +13,7 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blastx.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blastx.app 2017-03-22
19:59:11.066415737 +0100
+@@ -4,7 +4,7 @@
+
+ APP = blastx
+ SRC = blastx_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -13,7 +13,7 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.deltablast.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.deltablast.app 2017-03-22
19:59:30.396939821 +0100
+@@ -1,7 +1,7 @@
+
+ APP = deltablast
+ SRC = deltablast_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -10,6 +10,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.psiblast.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.psiblast.app 2017-03-22
19:59:51.837521114 +0100
+@@ -2,7 +2,7 @@
+
+ APP = psiblast
+ SRC = psiblast_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -11,6 +11,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.rpsblast.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.rpsblast.app 2017-03-22
20:00:15.808170999 +0100
+@@ -2,7 +2,7 @@
+
+ APP = rpsblast
+ SRC = rpsblast_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -11,6 +11,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.rpstblastn.app.ori 2017-03-22
19:57:18.063352028 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.rpstblastn.app 2017-03-22
20:00:34.328673121 +0100
+@@ -2,7 +2,7 @@
+
+ APP = rpstblastn
+ SRC = rpstblastn_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -11,6 +11,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.seedtop.app.ori 2017-03-22
19:57:18.073352297 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.seedtop.app 2017-03-22
20:00:52.309160604 +0100
+@@ -2,7 +2,7 @@
+
+ APP = seedtop
+ SRC = seedtop_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -11,6 +11,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastn.app.ori 2017-03-22
19:57:18.073352297 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastn.app 2017-03-22
20:01:09.669631276 +0100
+@@ -4,7 +4,7 @@
+
+ APP = tblastn
+ SRC = tblastn_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -13,7 +13,7 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+
+--- ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastx.app.ori 2017-03-22
19:57:18.073352297 +0100
++++ ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastx.app 2017-03-22
20:01:23.860016002 +0100
+@@ -4,7 +4,7 @@
+
+ APP = tblastx
+ SRC = tblastx_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -13,7 +13,7 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
+
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
new file mode 100644
index 000000000..f0a27d85a
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
@@ -0,0 +1,10 @@
+--- work/ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib.ori
2017-03-17 22:33:51.569635396 +0100
++++ ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib 2017-03-17
22:33:58.349811199 +0100
+@@ -4,6 +4,6 @@
+ LIB = xthrserv
+ PROJ_TAG = core
+ LIBS = $(NETWORK_LIBS)
+-DLL_LIB = xutil xconnect
++DLL_LIB = xncbi xutil xconnect
+
+ WATCHERS = vakatov
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
new file mode 100644
index 000000000..3c1cb0a9e
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app.ori
2016-06-24 16:55:25.000000000 +0200
++++ ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app 2017-03-21
14:07:31.070364301 +0100
+@@ -9,7 +9,7 @@
+ APP = asn2fasta
+ SRC = asn2fasta
+ LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) \
+- xobjwrite xobjread $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \
++ xobjwrite variation_utils $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr
xobjutil valerr xregexp \
+ ncbi_xdbapi_ftds dbapi $(ncbi_xreader_pubseqos2) $(FTDS_LIB) \
+ entrez2cli entrez2 tables $(OBJMGR_LIBS) $(PCRE_LIB)
+
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 72f3ad016..761058824 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -113,7 +113,11 @@ src_prepare() {
"${FILESDIR}"/${P}-configure.patch
"${FILESDIR}"/${P}-fix-install.patch
"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
+ "${FILESDIR}"/${P}-fix-annotwriter-linking.patch
+ "${FILESDIR}"/${P}-fix-undefined-xobjread.patch
+ "${FILESDIR}"/${P}-fix-apps-blast-linking.patch
)
+ #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
# make sure this one is the last one and contains the actual patches
applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
