[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 903f1a13a0c2953d5f556ccdd996d72120188c56
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Apr 5 15:24:06 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 5 15:26:16 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=903f1a13
sci-biology/ncbi-tools++: set -rpath-link to temp build location
Add more regexps specifying which parts of the test suite should
not be compiled at all.
We have so far problems with say ncbi-tools++-18.0.0 libs installed
in ${EPREFIX}/usr/lib64/ncbi-tools++/ which get picked during linking
of a currently emerged package, like ncbi-tools++-22.0.0. That happens
due to LDPATH being set through
```
echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
doenvd "${S}/99${PN}"
```
which results in
```
$ cat /etc/env.d/99ncbi-tools++
LDPATH=/usr/lib64/ncbi-tools++
$
```
and later used during linking of a future version. Some symbols will be
resolved by ${EPREFIX}/usr/lib64/ncbi-tools++/ from older version,
some probably not. It is confusing to debug the errors popping up
during compilation/linking.
Aaron Ucko from NCBI proposed:
To avoid interference from old installations, please try passing
`LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib` to configure, no patches
(likely) needed.
@kiwifb François Bissey commented with:
LDPATH is used to generate the ld.so.conf.d files. So it is important
to have it to be able to find the libraries that are not in a standard
path. LDPATH is a Gentoo special. You need to regenerate the cache with
ldconfig after installing such a library and such a path.
...
$ /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -Wl,--verbose
-Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0
-Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-O1
-Wl,--as-needed -g speedtest.o
-L/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
ncbi_cxx--22_0_0_build/lib
-lprosplign -lxalgoalignutil -ltaxon1 -lxalgoseq -lxcleanup
-lxobjedit -ltaxon3 -lvalid -lvalerr -lproteinkmer -lxblast
-lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask
-lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr
-lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli
-lxnetblast -lblastdb -lscoremat -ltables -lxqueryparse -lxregexp
-lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2
-lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect
-lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit
-lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline
-lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -lz -lbz2
-llzo2 -lz -lnsl -ldl -lpcre -llmdb -lpthread -ldw -ldl -lm
-lpthread -o speedtest
It cannot find libmlacli.so. Note that there isn’t a `-lmlacli`
anywhere in the above line. It is searched for because you are
compiling an executable and executable cannot have unresolved
symbols. It must in the table of needed libraries for libxobjedit.so
libmlacli.so needed by /scratch/var/tmp/portage/sci-biology/\
ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib/libxobjedit.so
Because there is no path or possibly a final path in libxobjedit.so
that library cannot be found.
Two solutions here:
1) add -lmlacli in the compilation line above
2) Precede the whole line with
LD_LIBRARY_PATH=/scratch/var/tmp/portage/sci-biology/\
ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib
The LDPATH setting probably enabled you to find a previously
installed version of the library.
François
PS: You can pass that analysis upstream because -lmlacli should
probably be added by right.
Later François also wrote:
rpath are usually the preferred solution but it is not the end all
solution. Looking for LDPATH in your /etc/env.d/ may shock you.
In the case of ncbi, adding path is only one of the solution I
would consider. I don’t see why they need to install in
/usr/lib{,64}/ncbi-tools++ rather than just /usr/lib{,64} in
the first place. It is not even versioned to allow several versions
installed in parallel. It is not plugins or “modules” or other
special kinds of shared objects.
Possibly it is some language runtime - at best. Does it use names
that could collide easily with something else? May be some of them
should be prefixed then.
make[3]: Entering directory '/scratch/var/tmp/portage/sci-biology/\
ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/app/speedtest'
Updating dependency information for /scratch/var/tmp/portage/sci-biology/\
ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp.
/usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -c -Wall -Wno-format-y2k
-pthread -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -fPIC
-g -D_DEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-D_MT -D_REENTRANT -D_THREAD_SAFE
-I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
ncbi_cxx--22_0_0_build/inc
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 339162f1f266f025acebcffc1225961c3a50a24b
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Mar 27 00:44:01 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 27 00:44:01 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=339162f1
sci-biology/ncbi-tools++: and more
Package-Manager: Portage-2.3.5, Repoman-2.3.1
.../ncbi-tools++-18.0.0-fix-app-tls-linking.patch | 11 +++
...cbi-tools++-18.0.0-fix-app-vecscreen-linking.patch | 19 +++
sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 ++
3 files changed, 32 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
new file mode 100644
index 0..541dc2514
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori 2017-03-27
02:33:36.312151540 +0200
ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app 2017-03-27
02:34:19.372151184 +0200
+@@ -10,7 +10,7 @@
+ SRC = tls
+
+ LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \
+- xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
++ xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS)
+
+ LIBS = $(PCRE_LIBS) \
+$(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
new file mode 100644
index 0..9f33392d3
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
@@ -0,0 +1,19 @@
+--- ncbi_cxx--18_0_0/src/app/vecscreen/Makefile.vecscreen.app.ori
2017-03-27 02:34:44.242150979 +0200
ncbi_cxx--18_0_0/src/app/vecscreen/Makefile.vecscreen.app 2017-03-27
02:36:22.752150165 +0200
+@@ -4,7 +4,7 @@
+
+ APP = vecscreen
+ SRC = vecscreen_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+ # FIXME: do we need blast_app_util
+ #LIB = blast_app_util $(LIB_:%=%$(STATIC))
+@@ -15,6 +15,6 @@
+ LDFLAGS = $(FAST_LDFLAGS:ppc=i386)
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 40db6cfa3..5d0547875 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -130,6 +130,8 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
"${FILESDIR}"/${P}-remove-old-symlinks.patch
"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
+ "${FILESDIR}"/${P}-fix-app-tls-linking.patch
+ "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
)
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: b0f5d1f1974db03f189da3df7aa6d64532f4949d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Mar 26 22:48:16 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Mar 26 22:48:16 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0f5d1f1
sci-biology/ncbi-tools++: fix table2asn linking
Package-Manager: Portage-2.3.5, Repoman-2.3.1
.../ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch | 13 +
sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 1 +
2 files changed, 14 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
new file mode 100644
index 0..222cb2c06
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch
@@ -0,0 +1,13 @@
+--- ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app.ori
2017-03-27 00:41:58.742206850 +0200
ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app 2017-03-27
00:43:13.142206236 +0200
+@@ -12,8 +12,8 @@
+
+ LIB = xdiscrepancy xalgophytree fastme prosplign xalgoalignutil xalgoseq
xmlwrapp \
+xvalidate xobjwrite xobjreadex valerr biotree macro \
+- $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) id2cli \
+- xregexp $(PCRE_LIB) $(SRAREAD_LIBS) $(DATA_LOADERS_UTIL_LIB)
$(OBJMGR_LIBS)
++ $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) taxon1 id2cli \
++ xregexp $(PCRE_LIB) xqueryparse $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS)
+
+ LIBS = $(LIBXSLT_LIBS) $(DATA_LOADERS_UTIL_LIBS) $(LIBXML_LIBS) $(CMPRS_LIBS)
$(PCRE_LIBS) \
+$(SRA_SDK_SYSLIBS) \
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 02426ab42..40db6cfa3 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -129,6 +129,7 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-srcchk-linking.patch
"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
"${FILESDIR}"/${P}-remove-old-symlinks.patch
+ "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
)
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 74d160e9dc55ef771da05ac064bfbe3f2ccd2cfb
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Mar 26 20:37:15 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Mar 26 20:37:15 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=74d160e9
sci-biology/ncbi-tools++: more fixes
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch | 11 +++
.../files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch| 7 +--
.../files/ncbi-tools++-18.0.0-remove-old-symlinks.patch | 10 ++
sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 ++
4 files changed, 28 insertions(+), 2 deletions(-)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
new file mode 100644
index 0..fce7263b2
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori
2017-03-26 18:49:50.431994978 +0200
ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app2017-03-26
18:50:11.222552131 +0200
+@@ -2,7 +2,7 @@
+
+ APP = rmblastn
+ SRC = rmblastn_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util $(LIB_:%=%$(STATIC))
+
+ # De-universalize Mac builds to work around a PPC toolchain limitation
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
index 0724fa2cf..2568662f5 100644
---
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
@@ -7,7 +7,10 @@
-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 $(OBJMGR_LIBS)
++ 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) $(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-remove-old-symlinks.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
new file mode 100644
index 0..098a9ad1e
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
@@ -0,0 +1,10 @@
+--- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old
2017-03-26 19:01:58.101495278 +0200
ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in
2017-03-26 19:02:16.581990522 +0200
+@@ -13,6 +13,7 @@
+-a ! -d $(libdir)/64 ]; then \
+ cd $(libdir) && $(LN_S) . 64; \
+ fi
++ $(RM) $(LINK)
+ cd $(libdir) && $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK)
+
+ clean:;
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index f3bf993b0..02426ab42 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -127,6 +127,8 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-speedtest-linking.patch
"${FILESDIR}"/${P}-fix-splign-linking.patch
"${FILESDIR}"/${P}-fix-srcchk-linking.patch
+ "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
+ "${FILESDIR}"/${P}-remove-old-symlinks.patch
)
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 77145c77d44bccc7054c1395e0ce21213746f290 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Mar 23 21:28:40 2017 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Mar 23 21:28:40 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=77145c77 sci-biology/ncbi-tools++: continuing with linking patches Package-Manager: Portage-2.3.3, Repoman-2.3.1 ...bi-tools++-18.0.0-fix-app-hfilter-linking.patch | 15 ...bi-tools++-18.0.0-fix-app-igblast-linking.patch | 42 ++ .../ncbi-tools++-18.0.0-fix-ncfetch-linking.patch | 11 ++ ...++-18.0.0-fix-netcache_cgi_sample-linking.patch | 11 ++ ...-tools++-18.0.0-fix-netstorage_gc-linking.patch | 11 ++ ...ncbi-tools++-18.0.0-fix-speedtest-linking.patch | 11 ++ .../ncbi-tools++-18.0.0-fix-splign-linking.patch | 11 ++ .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild| 7 8 files changed, 119 insertions(+) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch new file mode 100644 index 0..77b1ba05e --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch @@ -0,0 +1,15 @@ +--- ncbi_cxx--18_0_0/src/app/hfilter/Makefile.hfilter.app.ori 2017-03-23 19:47:10.204018194 +0100 ncbi_cxx--18_0_0/src/app/hfilter/Makefile.hfilter.app 2017-03-23 19:51:51.601108063 +0100 +@@ -5,9 +5,10 @@ + APP = hfilter + SRC = hitfilter_app + +-LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) ++LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ ++ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) + +-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch new file mode 100644 index 0..8610c7fd3 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch @@ -0,0 +1,42 @@ +--- ncbi_cxx--18_0_0/src/app/igblast/Makefile.igblastn.app.ori 2017-03-23 20:30:35.667921836 +0100 ncbi_cxx--18_0_0/src/app/igblast/Makefile.igblastn.app 2017-03-23 20:32:04.553561820 +0100 +@@ -2,7 +2,8 @@ + + APP = igblastn + SRC = igblastn_app +-LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) ++LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ ++ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) + LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) + + # De-universalize Mac builds to work around a PPC toolchain limitation +@@ -10,7 +11,7 @@ + CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386) + LDFLAGS = $(FAST_LDFLAGS:ppc=i386) + +-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/igblast/Makefile.igblastp.app.ori 2017-03-23 20:33:03.215124531 +0100 ncbi_cxx--18_0_0/src/app/igblast/Makefile.igblastp.app 2017-03-23 20:34:22.817243181 +0100 +@@ -2,7 +2,8 @@ + + APP = igblastp + SRC = igblastp_app +-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) ++LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ ++ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) + LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) + + # De-universalize Mac builds to work around a PPC toolchain limitation +@@ -10,7 +11,7 @@ + CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386) + LDFLAGS = $(FAST_LDFLAGS:ppc=i386) + +-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-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch new file mode 100644 index 0..aacb20a6c --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch @@ -0,0 +1,11 @@ +--- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori 2017-03-23 21:12:52.028724998 +0100 ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app2017-03-23 21:13:30.079737366 +0100 +@@ -5,7 +5,7 @@ + APP = ncfetch.cgi + SRC = ncfetch + +-LIB = xcgi xconnserv xconnect xutil xncbi ++LIB = xcgi xconnserv xthrserv xconnect xutil xncbi + LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + WATCHERS = sadyrovr diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch new file mode
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 0ece3b3803a4d4be8aeeb140f51b3b46dee6ee6f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Mar 23 18:28:08 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Mar 23 18:28:08 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0ece3b38
sci-biology/ncbi-tools++: yet another linking fix
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch | 11 +++
sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 1 +
2 files changed, 12 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
new file mode 100644
index 0..e495c9645
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app.ori
2017-03-23 19:24:31.534280319 +0100
ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app
2017-03-23 19:25:14.395360214 +0100
+@@ -2,7 +2,7 @@
+
+ APP = convert_seq
+ SRC = convert_seq
+-LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite \
++LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite variation_utils \
+ $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil tables xregexp \
+ $(PCRE_LIB) $(OBJMGR_LIBS)
+
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 7a70e8f5e..ce5b4ddb8 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -118,6 +118,7 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
+ "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
)
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 69763b2b7798dac7b061b881c2b76e6ec7fa005b
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Mar 23 17:17:40 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Mar 23 17:17:40 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=69763b2b
sci-biology/ncbi-tools++: more patches
Package-Manager: Portage-2.3.3, Repoman-2.3.1
...i-tools++-18.0.0-fix-app-compartp-linking.patch | 31 ++
...tools++-18.0.0-fix-sample-app-cgi-linking.patch | 11
.../ncbi-tools++/ncbi-tools++-18.0.0.ebuild| 2 ++
3 files changed, 44 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
new file mode 100644
index 0..0b4b76e4f
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch
@@ -0,0 +1,31 @@
+--- ncbi_cxx--18_0_0/src/app/compart/Makefile.compart.app.ori 2017-03-23
14:49:24.915182566 +0100
ncbi_cxx--18_0_0/src/app/compart/Makefile.compart.app 2017-03-23
14:50:32.926896138 +0100
+@@ -5,11 +5,11 @@
+ APP = compart
+ SRC = compart
+
+-LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \
+- $(BLAST_LIBS:%=%$(STATIC)) \
++LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1
xqueryparse \
++ $(BLAST_LIBS:%=%$(STATIC)) xregexp $(REGEXP_LIB) \
+$(OBJMGR_LIBS:%=%$(STATIC))
+
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(REGEXP_LIBS) $(ORIG_LIBS)
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+--- ncbi_cxx--18_0_0/src/app/compart/Makefile.compartp.app.ori 2017-03-23
18:05:44.135172346 +0100
ncbi_cxx--18_0_0/src/app/compart/Makefile.compartp.app 2017-03-23
18:09:00.990132154 +0100
+@@ -5,9 +5,9 @@
+ APP = compartp
+ SRC = compartp
+
+-LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS)
++LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse
xregexp $(REGEXP_LIB) $(OBJMGR_LIBS)
+
+-LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(REGEXP_LIBS)
$(ORIG_LIBS)
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
new file mode 100644
index 0..c45d4ad96
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori
2017-03-22 23:52:58.984696074 +0100
ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app
2017-03-22 23:53:54.746258126 +0100
+@@ -11,7 +11,7 @@
+ # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
+
+ ### BEGIN COPIED SETTINGS
+-LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
++LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
+
+ LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 761058824..7a70e8f5e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -116,6 +116,8 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
+ "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
+ "${FILESDIR}"/${P}-fix-app-compartp-linking.patch
)
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 505486cbc011b906cb37e3af2376dc4deeba06d6 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Mar 22 22:35:40 2017 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Mar 22 22:35:40 2017 + 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 0..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 18:14:10.98851 +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 0..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)
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: ef30e8a1e8ba6e56b365f8dbaddd1b4812306392
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Dec 2 23:27:56 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Dec 2 23:27:56 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ef30e8a1
sci-biology/ncbi-tools++: fix bug #579248#c by disabling more tests
This will likely also fix the #579248 bug in rmblast (untested).
Our $FILESDIR/disable-testsuite-compilation.txt only excludes test
applications from usingboost, not the support library. Hence the above
bug.
We could either add --without-boost to the configuration command line
to disable the bosost-related code in support library or, which is the
path we take in this commit, we disable building of the yet escaping
unit_tests which needed boost.
Upstream further said:
The C++ Toolkit makes very little use of Boost outside of unit tests,
but that's a fair question. The simplest fix preserving other uses of
Boost would be to edit .../src/corelib/Makefile.in and remove test_boost
from LIB_PROJ. (You'll still also need to exclude building the tests by
adding '-.*/unit_tests' to the $FILESDIR/disable-testsuite-compilation.txt
file.)
Package-Manager: portage-2.3.2
.../ncbi-tools++/files/disable-testsuite-compilation.txt | 1 +
.../files/ncbi-tools++-12.0.0-never_build_test_boost.patch| 11 +++
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
3 files changed, 13 insertions(+)
diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
index aeaf75e..8df346f 100644
--- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
+++ b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
@@ -1,3 +1,4 @@
.*
-.*/test
-.*/unit_test
+-.*/unit_tests
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
new file mode 100644
index 000..68baea0
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01
20:28:33.239758102 +0100
ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659
+0100
+@@ -7,7 +7,7 @@
+ #
+
+ USR_PROJ = precompile
+-LIB_PROJ = corelib test_mt test_boost
++LIB_PROJ = corelib test_mt
+ SUB_PROJ = test
+ PROJ_TAG = core
+
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index c9f6911..1236c13 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -120,6 +120,7 @@ src_prepare() {
"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
"${FILESDIR}"/${P}-fix-install.patch
"${FILESDIR}"/${P}-bdb6.patch
+ "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
)
# "${FILESDIR}"/${P}-as-needed.patch
# "${FILESDIR}"/${P}-fix-creaders-linking.patch
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: d9e17bf2b88b99ee5a31c5406f39cf91964dde10
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Thu Jun 26 20:41:58 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Thu Jun 26 20:41:58 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d9e17bf2
sci-biology/ncbi-tools++: fix 'make install if USE=pch
---
.../ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch | 11 +++
sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
2 files changed, 12 insertions(+)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
new file mode 100644
index 000..8d53ebe
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori (revision 439078)
ncbi_cxx--12_0_0/src/build-system/Makefile.in.top (working copy)
+@@ -48,7 +48,7 @@
+for x in *.a; do ln -s $$x `basename \$$x\ .a`-static.a; done
+cd $(includedir0) find * -name CVS -prune -o -print |\
+ cpio -pd $(pincludedir)
+- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
++ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+
+ install-gbench:
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 23ff5d8..3429e05 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -114,6 +114,7 @@ src_prepare() {
${FILESDIR}/${P}-linkage-tuneups-addons.patch
${FILESDIR}/${P}-configure.patch
${FILESDIR}/${P}-drop-STATIC-from-LIB.patch
+ ${FILESDIR}/${P}-fix-install.patch
)
# ${FILESDIR}/${P}-as-needed.patch
# ${FILESDIR}/${P}-fix-creaders-linking.patch
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: 1aca3e5aae88192ca717e47c5a947ef806b69b2e Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Wed Jun 25 20:58:36 2014 + Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz CommitDate: Wed Jun 25 20:58:36 2014 + URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1aca3e5a sci-biology/ncbi-tools++-12.0.0: first compile-able ebuild, wow, huge thanks to Aaron Ucko from NCBI developers on the cpp@ mailing list --- .../files/ncbi-tools++-12.0.0-as-needed.patch | 2 +- ...cbi-tools++-12.0.0-linkage-tuneups-addons.patch | 13 + .../ncbi-tools++-12.0.0-linkage-tuneups.patch | 421 + .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild| 14 +- 4 files changed, 444 insertions(+), 6 deletions(-) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch index e97c77f..a9d166e 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch @@ -344,7 +344,7 @@ index 872b92e..78261eb 100644 CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp ++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb blast xregexp diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib index c7e2778..51ebe9d 100644 --- a/src/algo/phy_tree/Makefile.xalgophytree.lib diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch new file mode 100644 index 000..553e41d --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch @@ -0,0 +1,13 @@ +--- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori (revision 439078) ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app (working copy) +@@ -7,8 +7,8 @@ + SRC = agpconvert + + LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ +-ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) +-LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++ tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) ++LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch new file mode 100644 index 000..86e96b8 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch @@ -0,0 +1,421 @@ +Index: src/algo/blast/format/Makefile.xblastformat.lib +=== +--- src/algo/blast/format/Makefile.xblastformat.lib(revision 439078) src/algo/blast/format/Makefile.xblastformat.lib(working copy) +@@ -7,6 +7,6 @@ + + CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) + +-DLL_LIB = align_format blastxml xhtml xcgi ++DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi + + WATCHERS = jianye zaretska madden camacho fongah2 +Index: src/app/compart/Makefile.compart.app +=== +--- src/app/compart/Makefile.compart.app (revision 439078) src/app/compart/Makefile.compart.app (working copy) +@@ -5,11 +5,11 @@ + APP = compart + SRC = compart + +-LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ +- $(BLAST_LIBS:%=%$(STATIC)) \ +- $(OBJMGR_LIBS:%=%$(STATIC)) ++LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ ++ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ ++ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) + +-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ++LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) +Index: src/app/compart/Makefile.compartp.app +=== +--- src/app/compart/Makefile.compartp.app (revision 439078) src/app/compart/Makefile.compartp.app (working copy) +@@ -5,7 +5,8 @@ + APP = compartp + SRC = compartp + +-LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) ++LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ ++ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) + + LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) + +Index: src/app/grid/util/Makefile.ncfetch.app +=== +--- src/app/grid/util/Makefile.ncfetch.app (revision
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
commit: f88f1a0e9b529e9ca95ecec39f080675a4ae20de
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Jun 25 23:24:16 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Jun 25 23:24:16 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f88f1a0e
sci-biology/ncbi-tools++-12.0.0: dropped unneeded patches, added direct
dependency on glew because the dependency on virtual/opengl does not work
---
.../files/ncbi-tools++-12.0.0-linking.patch| 52 --
.../files/ncbi-tools++-12.0.0-linking2.patch | 10 -
.../ncbi-tools++/ncbi-tools++-12.0.0.ebuild| 7 +--
3 files changed, 2 insertions(+), 67 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
deleted file mode 100644
index 196f3a4..000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
+++ /dev/null
@@ -1,52 +0,0 @@
ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib.ori
(revision 400707)
-+++
ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
(working copy)
-@@ -10,6 +10,6 @@
- LIB_OR_DLL = both
-
- # Dependencies for shared library
--DLL_LIB = ncbi_xreader$(DLL)
-+DLL_LIB = $(GENBANK_LDEP)
-
- WATCHERS = vasilche
ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app.ori (revision
400707)
-+++ ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app (working copy)
-@@ -5,7 +5,7 @@
- APP = ncfetch.cgi
- SRC = ncfetch
-
--LIB = xcgi xconnserv xconnect xutil xncbi
-+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
-
- WATCHERS = kazimird
ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori
(revision 400707)
-+++ ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app
(working copy)
-@@ -4,7 +4,7 @@
- SRC = netcache_cgi_sample
-
- ### BEGIN COPIED SETTINGS
--LIB = xconnserv xconnect xcgi xhtml xutil xncbi
-+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
-
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
- ### END COPIED SETTINGS
ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib.ori
2014-06-24 21:42:11.0 +0200
-+++ ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib2014-06-24
21:42:29.0 +0200
-@@ -10,4 +10,4 @@
-
- WATCHERS = vakatov
-
--DLL_LIB = xncbi xcgi xconnserv xhtml
-+DLL_LIB = xhtml xcgi xconnserv
ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib.ori 2014-06-24
22:54:55.0 +0200
-+++ ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib 2014-06-24
22:55:05.0 +0200
-@@ -8,6 +8,7 @@
- CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \
-$(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE
$(ORIG_CPPFLAGS)
-
--DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
-+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) krypto$(DLL) \
-+ kfg$(DLL) kfs$(DLL) klib$(DLL)
-
- LIB_OR_DLL = both
-
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
deleted file mode 100644
index 5507b84..000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
+++ /dev/null
@@ -1,10 +0,0 @@
ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori
2014-06-24 21:50:43.0 +0200
-+++ ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app
2014-06-24 21:50:48.0 +0200
-@@ -11,7 +11,7 @@
- # the lines reading ### BEGIN/END COPIED SETTINGS in any way.
-
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
-
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 746a3fe..d8b7d97 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -42,7 +42,7 @@ DEPEND=
mysql? ( virtual/mysql )
ssl? ( dev-libs/openssl )
fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl )
+ opengl? ( virtual/opengl media-libs/glew )
mesa? ( media-libs/mesa
media-libs/glew
)
@@ -72,7 +72,7 @@ DEPEND=
# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC
OEChem sge
-# seems muParser is required, also glew is required. configure exits otherwise
+# seems muParser is required, also glew is required. configure exits otherwise
if these are explicitly passed to it (due to USE flag enabled)
RDEPEND=${DEPEND}
@@ -117,9
