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