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sci-biology/ncbi-tools++

NCBI C++ Toolkit, including NCBI BLAST+

Screenshots

  • ncbi-tools++-22.0.0
    ~amd64 ~x86 ~amd64-linux ~x86-linux
    debug static-libs static threads pch test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite tiff xerces xalan xml xpm xslt X python_targets_python2_7

    View      Download      Browse     License: public-domain   
    Overlay: science (layman)
  • ncbi-tools++-18.0.0
    ~amd64 ~x86 ~amd64-linux ~x86-linux
    debug static-libs static threads pch test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite tiff xerces xalan xml xpm xslt X python_targets_python2_7

    View      Download      Browse     License: public-domain   
    Overlay: science (layman)
  • ncbi-tools++-12.0.0
    ~amd64
    debug static-libs static threads pch test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite tiff xerces xalan xml xpm xslt X python_targets_python2_7

    View      Download      Browse     License: public-domain   
    Overlay: science (layman)

ChangeLog

commit 903f1a13a0c2953d5f556ccdd996d72120188c56
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Apr 5 17:24:06 2019 +0200

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 $/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=$/usr/$(get_libdir)/$" > $/99$
doenvd "$/99$"
```

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 $/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,"$"_build/lib` to configure, no patches
(likely) needed.

@kiwifb François Bissey commented with:

<quote>
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.
</quote>

Later François also wrote:

<quote>
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/ncbi-tools++ rather than just /usr/lib 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.
</quote>

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
-I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
ncbi_cxx--22_0_0/include
/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp
-o speedtest.o
/usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11
-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
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/\
bin/ld: warning: 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, not found (try using -rpath or -rpath-link)

The problem here is that the rpath would have to be provided when
you link libxobjedit.so. I checked the log and it wasn’t done.
And you definitely don’t want to do that unless you re-link without
the rpath (or the correct final rpath) at install time. For information
cmake does exactly that.
But in the end adding a path in this case is no substitute to providing
the libraries you need. When building stuff with libtool, libtool produces
test scripts that set LD_LIBRARY_PATH properly for running the tests before
install. So the test executables don’t have to be linked with rpath to
the build folder. Or the objects that you want to ship either.
</quote>

This change will ensure `LDFLAGS=-Wl,-rpath-link,"$"_build/lib` is
passed to `bash ./src/build-system/configure` in `src_configure()`
and at least helps to get symbols resolved during linking although it
is probably still far from ideal.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Mar 30 07:42:42 2019 +0100

sci-biology/ncbi-tools++: document possible issue with builds

I have the following defined due to ncbi-tools++-18.0.0 installed
on my system:

/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0:
/usr/lib/llvm/7/lib32:
/usr/lib/llvm/7/lib64:
/usr/lib64/itcl4.1.1:
/usr/lib64/itk4.1.0:
/lib64:
/usr/lib64:
/usr/local/lib64:
/lib32:
/usr/lib32:
/usr/lib64/rust-1.29.2:
/usr/lib64/R/lib:
/usr/lib64/fltk:
/usr/lib64/ncbi-tools++:
/usr/lib64/staden:

grep: /etc: No such file or directory
grep: /etc/env.d: No such file or directory
/etc/env.d/99ncbi-tools++:LDPATH=/usr/lib64/ncbi-tools++
...

That in turn makes linker pick "$"/ncbi_cxx--22_0_0_build/lib/*
files but later overrides some of them with /usr/lib64/ncbi-tools++/*,
depending on the ordering of -lXXXXXX arguments.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit 220946d413cfcfa399e3609f2b215eabdc8df3a8
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Sat Mar 30 01:13:51 2019 +0100

sci-biology/ncbi-tools++: version bump

It does not link if older version is installed because linker
picks up older version of libraries and obviously does not find
newly added functions.

Upstream says:
Please try either supplying an LD_RUN_PATH environment setting
or a -Wl,-rpath-link,... flag pointing at your build tree's lib
directory. Also, please bear in mind that adding the old
installation's library directory to the central search path largely
defeats the purpose of making it a separate directory.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

commit 3072d10e6c4f21185d53e4728d0fa0fad58537e7
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Dec 10 22:20:38 2017 +0000

Update Manifests to new hashes

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit bce61aa3e4fe85fe411df858eb30ebe72a3a8f88
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Nov 18 20:39:44 2017 +0000

Consistently ident with tabs

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 0eb19cf5891c22bab171539902ba6dac381a8ba2
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Jul 28 22:50:56 2017 +0200

sci-biology/ncbi-tools++: re-adding the patch with PCRE_LIBS added

Package-Manager: Portage-2.3.6, Repoman-2.3.3

commit 6ad973f70eefbffeebb8ff400d57572d5059cf37
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Jul 28 22:19:40 2017 +0200

sci-biology/ncbi-tools++: resolving my 'stash pop' with an empty change

Sorry for noise.

Package-Manager: Portage-2.3.6, Repoman-2.3.3

commit 6317bbf43e4179c733694df8ba540f9cfc251fbf
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue May 23 23:26:04 2017 +0200

sci-biology/ncbi-tools++: do not add $(PCRE_LIBS) unless necessary (from Aaron Ucko)

Package-Manager: Portage-2.3.5, Repoman-2.3.2

commit ad511c8fb80754d29a9fa8e2b10e87be87d073ad
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Apr 11 10:41:28 2017 +0200

sci-biology/ncbi-tools++: add note on idfetch collision by upstream

Package-Manager: Portage-2.3.5, Repoman-2.3.2

commit eb01dd274c938f4b647546b9ec2924d2ee3f5876
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Mar 27 07:35:10 2017 +0200

sci-biology/ncbi-tools++: avoid file collision, KEYWORDS added back

Package-Manager: Portage-2.3.5, Repoman-2.3.1

commit 20b211f3ab9ace0a1ae4bd0a09831ad71ec691da
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Mar 27 03:08:12 2017 +0200

sci-biology/ncbi-tools++: compiles via 'make -j1' now

Package-Manager: Portage-2.3.5, Repoman-2.3.1

commit 339162f1f266f025acebcffc1225961c3a50a24b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Mar 27 02:44:01 2017 +0200

sci-biology/ncbi-tools++: and more

Package-Manager: Portage-2.3.5, Repoman-2.3.1

commit b0f5d1f1974db03f189da3df7aa6d64532f4949d
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Mar 27 00:48:16 2017 +0200

sci-biology/ncbi-tools++: fix table2asn linking

Package-Manager: Portage-2.3.5, Repoman-2.3.1

commit 74d160e9dc55ef771da05ac064bfbe3f2ccd2cfb
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun Mar 26 22:37:15 2017 +0200

sci-biology/ncbi-tools++: more fixes

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit 8a773e1d1d08a4fed7fdbf65003f7a9b6f67abb4
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 24 23:49:31 2017 +0100

sci-biology/ncbi-tools++: add another patch (with an incomplete fix)

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit 77145c77d44bccc7054c1395e0ce21213746f290
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Mar 23 22:28:40 2017 +0100

sci-biology/ncbi-tools++: continuing with linking patches

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit 0ece3b3803a4d4be8aeeb140f51b3b46dee6ee6f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Mar 23 19:28:08 2017 +0100

sci-biology/ncbi-tools++: yet another linking fix

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit 69763b2b7798dac7b061b881c2b76e6ec7fa005b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Mar 23 18:17:40 2017 +0100

sci-biology/ncbi-tools++: more patches

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit 505486cbc011b906cb37e3af2376dc4deeba06d6
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Mar 22 23:35:40 2017 +0100

sci-biology/ncbi-tools++: fix plenty linking issues, still far from completeness

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit a38e0d15267bbbe41f2e36f421c71b320d1c8326
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Mar 17 19:27:57 2017 +0100

sci-biology/ncbi-tools++: version bump, does not link yet

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit a83e16235eb2a5fcadacac3570df72f70e0d21fd
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Mar 15 00:07:53 2017 +0100

sci-biology/ncbi-tools++-12.0.0: do not force --without-downloaded-vdb

This configure flag appeared only in more recent versions.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

commit db6617fcd21401115d88ef59b233ae5430650d18
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sun Feb 26 23:13:52 2017 +0100

sci-biology/gbench and sci-biology/ncbi-tools++: do not download ncbi-vdb

Do not download sources from github during configure phase. This disables
the feature completely. Somehow it does not find vdb binaries provided
by our sci-biology/ncbi-tools++ package?

commit f69e73182fc7cdc6c600a72fceb88ae1626db25d
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Feb 25 16:50:59 2017 +0000

Drop leftover from CVS in HEADER

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit e0bb430dd8c078ea0aa22268eba26a47febe7b31
Author: Justin Lecher <jlec@gentoo.org>
Date: Fri Feb 3 16:55:14 2017 +0000

Drop all trailing whitespaces

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 0d1b801349367e3210c3feb0247936d51efdcdc5
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Dec 3 12:33:53 2016 +0100

sci-biology/ncbi-tools++: add a comment about >=gcc-5.3.0 incompatibility

Package-Manager: portage-2.3.2

commit ef30e8a1e8ba6e56b365f8dbaddd1b4812306392
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Dec 3 00:27:56 2016 +0100

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

commit 9d6cc9b456888a65bad46444f380e7e0cc59dae3
Author: Justin Lecher <jlec@gentoo.org>
Date: Tue Aug 23 20:16:51 2016 +0000

sci-biology/ncbi-tools++: Fix SLOT operators

Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit d54c7320a32ad973252bc1cbcb8cb3d7a32aed62
Author: Justin Lecher <jlec@gentoo.org>
Date: Tue Aug 23 20:15:13 2016 +0000

sci-biology/ncbi-tools++: Drop obsolete dep

Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit d1b1268845627553e3b15302a1d35e4bee8333ea
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Mar 6 20:54:08 2016 +0000

Fix invalid metadata.xml syntax

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 057a98c5e6346d6696fcc7b0ec8fefc9e826245f
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:53:09 2016 +0100

metadata.xml: Set type

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit b9d823e1ea1018d1356a0c18a083eab4d5ea6d8d
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Jan 25 09:50:12 2016 +0100

metadata.xml: convert hard -> proj

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 2ef24e800910be3786e23a31a0217ba0f38659f8
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Jan 7 15:10:39 2016 +0100

Drop ChangeLogs in favour of commit messages

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit b9a147bbcb472ff957ec8552b6893351e062cba2
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Jan 6 09:48:53 2016 +0100

sci-biology/ncbi-tools++: Drop sqlite-2 support

Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 6271f0c55cbb6af7fe88ae1ec9d7dbdedd562565
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Aug 17 08:53:12 2015 +0200

Convert all $Header$ to $Id$ tags as it has be done in gentoo.git

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 635c7ada0349d113b3e112a4cd0d41a27c7c51e6
Author: Andrew Savchenko <bircoph@gmail.com>
Date: Fri Jul 17 03:39:45 2015 +0300

Fix repoman fatal error (invalid USE description)

commit 879ae552d91f82bacace60a97757f862a461ee83
Author: Horea Christian <h.chr@mail.ru>
Date: Tue Jun 23 17:20:25 2015 +0200

added dep needed at build-time

Package-Manager: portage-2.2.20

commit a891336052fb27fd9f3f82e33c30f0984f50ea54
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:25:27 2015 +0200

Revert "Gentoo does https by default now"

This reverts commit 98718494343af4990facdefb0033471686e975a6.

commit 98718494343af4990facdefb0033471686e975a6
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Jun 21 12:14:25 2015 +0200

Gentoo does https by default now

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit d92148d58c196ab5e1fb22e51e0bc7d2407d277b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 11 19:50:27 2015 +0200

sci-biology/ncbi-tools++: added upstream patch to compile against sys-libs/db-6.0.30

Package-Manager: portage-2.2.18

commit 3b861411b3276f99250fa28b5615513590a38270
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Apr 17 23:34:52 2015 +0200

sci-biology/ncbi-tools++: re-added KEYWORDS

Package-Manager: portage-2.2.18

commit abea2757044d9b4ee86ceea1a0f6afe974c03f62
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Feb 18 14:29:11 2015 +0100

sci-biology/ncbi-tools++: fix SLOT operators; correct python deps

Package-Manager: portage-2.2.17

commit 5b06e2557cb96c8fb6f7aae9cc43662175579b17
Author: mschubert <mschu.dev@gmail.com>
Date: Thu Oct 9 22:32:01 2014 +0100

ncbi-tools++: fix prefix libdir, muparser/hdf5 use flags

commit 963a1fab8ea050e44077f03bc5783decff5f8ac8
Author: Christoph Junghans <ottxor@gentoo.org>
Date: Mon Sep 15 21:32:57 2014 -0600

major clean, drop old version and unused patches

Package-Manager: portage-2.2.8-r1

commit e5e343c4a4dd2e5df08f92798c800e2ecaf5f4f7
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 23:25:35 2014 +0200

sci-biology/ncbi-tools++-12.0.0: improved comment text

commit 7d0dda709757bcc413823ffd963152c024551303
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 23:05:51 2014 +0200

sci-biology/ncbi-tools++: so require media-libs/mesa[osmesa] for USE=mesa

commit 5bdca751bc342372b06bcaa65796885de3a1d513
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 22:52:38 2014 +0200

sci-biology/ncbi-tools++: reworked patch

commit 0fc3dc7cd2dabc62b52e5fdba7acc838263e07f4
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 22:44:53 2014 +0200

sci-biology/ncbi-tools++: bring back USE=mesa although it is about OSMesa

commit d9e17bf2b88b99ee5a31c5406f39cf91964dde10
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 22:41:58 2014 +0200

sci-biology/ncbi-tools++: fix 'make install if USE=pch

commit 2513d463dc99aaf7b5f70f2689f97af7de3c4483
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 21:48:49 2014 +0200

sci-biology/ncbi-tools++: dropped USE=ftds as it is useless and recommended by upstream to be disabled altogether

commit 19b0ba203ab340ea1b4f4ea9f950b3024905127f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 21:04:06 2014 +0200

sci-biology/ncbi-tools++-12.0.0: drop forgotten IUSE=ssl

commit f18aa6a66c0e20b32d49289548aff679a8092be9
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 19:31:01 2014 +0200

sci-biology/ncbi-tools++-12.0.0: added a blocker with sci-biology/sra_sdk

commit a28e615a1579b782b069ac9f6224c1d24b986788
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 18:56:12 2014 +0200

sci-biology/ncbi-tools++-12.0.0: more places where to drop ':%=%'

commit a9c97c981e04e280b2d1b21a54d178f680f0dba4
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 17:52:27 2014 +0200

sci-biology/ncbi-tools++-12.0.0: more entries to ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch

commit c9cc902bf22b5154a8dcc82a937da0fd7ebae446
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 17:10:53 2014 +0200

sci-biology/ncbi-tools++-12.0.0: added the patch istelf dropping :%=% from LIB settings

commit 47da4cc7e724f425a41f532ce56155fff072657b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 17:09:03 2014 +0200

sci-biology/ncbi-tools++-12.0.0: dropping :%=% from LIB settings

commit 4093a5178b56aba0459005460bf7dd5f3d2beba0
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 16:38:00 2014 +0200

sci-biology/ncbi-tools++-9.0.0*: dropped altogether openssl-related USE flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings); dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version; however, --with-lzo is still advantageous for http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html

commit a2f461519e3a62831c5d05b9ef0016e9eaf61adc
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 16:31:53 2014 +0200

sci-biology/ncbi-tools++-12.0.0: dropped altogether openssl-related USE flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings); dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version; however, --with-lzo is still advantageous for http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html

commit 29634acbbe011256ad517af5f0d946c876e7ba12
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 15:29:31 2014 +0200

sci-biology/ncbi-tools++-12.0.0: cleanup comments and shutdown a false alarm message from mv

commit 88e4dd4274fab0bd7e7a26ad618d34de95489656
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 01:24:59 2014 +0200

sci-biology/ncbi-tools++-12.0.0: dropped unneeded patch

commit f88f1a0e9b529e9ca95ecec39f080675a4ae20de
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Thu Jun 26 01:24:16 2014 +0200

sci-biology/ncbi-tools++-12.0.0: dropped unneeded patches, added direct dependency on glew because the dependency on virtual/opengl does not work

commit b5afb3e918e1e43fcc80466e3dafa96550761a12
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Jun 25 23:56:38 2014 +0200

sci-biology/ncbi-tools++-12.0.0: re-added update patch to configure so that we can avoid eautoconf until there is autoconf-2.59 system-wide

commit 3f54d211a74334d29b3c624edc1c96743aa8785b
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Jun 25 23:02:00 2014 +0200

sci-biology/ncbi-tools++-12.0.0: install colliding files under a name suffixed by a plus sign

commit 1aca3e5aae88192ca717e47c5a947ef806b69b2e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Jun 25 22:58:36 2014 +0200

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

commit 10e04f5023b0d6d66f63f277104707e2aea0fda7
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed Jun 25 17:00:13 2014 +0200

more changes to get ncbi-tools++-12.0.0 compiled

commit cb7af5375a7fbfdfaeddf149fed723aa81e1827e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jun 23 22:38:29 2014 +0200

dropped the duplicate part from the patch

commit 8e4a566fecc849dd4e007fc85b6ebfd423d637ae
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jun 23 22:34:11 2014 +0200

add an extra patch for configure until we find a way to ensure user has autoconf-2.59 or for ncbi-tools++-12.0.0 may have autoconf-2.60

commit 41e720e3552ebd75742dba2126eeffed95ce6769
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jun 23 18:17:38 2014 +0200

updating the ChangeLog to note where the ncbi-tools++-12.0.0-support-autoconf-2.60.patch comes from

commit 8d30af0e3afd031e00f5d69fce3683233a23b487
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jun 23 18:10:25 2014 +0200

add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed)

commit cb2f6200cc1de77fcdb6b3ac1b5b1d835ab4225f
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jun 2 14:06:58 2014 +0200

sci-biology/ncbi-tools++: added a note about a taxonomy database add-on not yet installed by Gentoo

commit 3a46fa5d7e08ae791daad0e9455c739a03e6ff97
Author: Justin Lecher <jlec@gentoo.org>
Date: Tue May 6 09:10:48 2014 +0200

Configure works

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 44ffc4b87ef68b5dc623060f5335ba44339abb19
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue Mar 25 11:48:44 2014 +0100

sci-biology/ncbi-tools++: add deps on jpeg-turbo

commit 1b9a1a664fe4a1e2515c3eedc842f0231dc0fcec
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Jan 30 09:10:53 2014 +0100

Sanitize ebuild header

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 77dbaf65a12dfd3b782f4c6e18c31acb308a16ee
Author: Justin Lecher <jlec@gentoo.org>
Date: Sat Jan 25 14:39:33 2014 +0100

Start to work on it again

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 5c30b638891d5120f4a6757229945f6103dffa43
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Sep 14 10:46:29 2013 +0200

Support at least when user passes USE='gnutls -ssl -openssl' but what we really want is to prefer gnutls over openssl if both are available on the system.

commit 2159e8e3583f47d97226803cd59fa3e715979c01
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Sep 14 10:18:58 2013 +0200

Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with line offset changes.

commit 51dbd486d1fb08026b4f366e33c2a1395f49b16e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Sep 14 00:18:50 2013 +0200

Fix URL to point to a public SVN repository

commit db3890c80a85542d3c14254c20a03bf72a2caae0
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Sat Sep 14 00:06:41 2013 +0200

more 12.0.0 cleanup, still not working

commit a42ec1c56c4d2691ac3adbff76c5d9ec4f686aa6
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 23:28:39 2013 +0200

add ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch; get around a bug in the C++ Toolkit's handling of --without-runpath with certain linker versions by running configure with -Wl,-rpath-link,_build/lib in LDFLAGS (assuming _build is an absolute path; otherwise, prepend /home/mmokrejs/proj/sci/sci-biology/ncbi-tools++/) [from Aaron Ucko].

commit cbacda12d70dc97ab35fe390abf09d44502b1c3d
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 22:24:36 2013 +0200

fix version number in the ebuild

commit a7ae3afe2de608896ea47fa540b1d61e9f5cb6a1
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 22:23:27 2013 +0200

Remove redundant connect from DLL_LIB lines.

commit 16bbfdefcf0e1b35ba1502f6c8948d6d60c9e5ed
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 22:23:24 2013 +0200

Remove redundant connect from DLL_LIB lines.

commit fc2c3ad28c32659d2b55076c7f7d4d2f0da0aa00
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 22:14:16 2013 +0200

Remove redundant connect from DLL_LIB lines.

commit 58b3cd84dbafc6fb04a305a29889b3332d9890e5
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 18:53:33 2013 +0200

No, the fix-creaders-linking is needed for 12.0.0 as well.

commit 1f50f92899961b2c6522f8a071184138ff5aa94e
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 18:46:50 2013 +0200

Latest release which needs so far only the two Gentoo patches. Would be better to drop from their filename to avoid their duplication I think.

commit 2936a6fec14426e76f9e3f095b82e25eddcc1072
Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Fri Sep 13 18:09:46 2013 +0200

add glew to dependencies inferrred via mesa; fix lib/libxobjread.so: undefined reference to 'AlignmentFileFree' message by upstream patch

commit bc92c82534cb0dae36a4001b184e11fd719e8d86
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Jun 12 22:06:37 2013 +0200

sci-biology/ncbi-tools++: Drop empty line

Package-Manager: portage-2.2.0_alpha179
RepoMan-Options: --force

commit 5b52557e87bd23e7b860e6c8bfc195c653d4536d
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Jun 12 20:57:31 2013 +0200

sci-biology/ncbi-tools++: Drop autotools.eclass

Package-Manager: portage-2.2.0_alpha179
RepoMan-Options: --force

commit 2b64eb561a6fb14fd4af81a272d17ac9590f0a23
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Apr 1 15:26:22 2013 +0200

sci-biology/ncbi-tools++: Some Prefix love

Package-Manager: portage-2.2.0_alpha170
RepoMan-Options: --force

commit 6814d886acb1a78640b5e8f85926c9b62a0b432e
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Mar 3 18:37:26 2013 +0100

sci-biology/ncbi-tools++: Document USE

Package-Manager: portage-2.2.0_alpha164
RepoMan-Options: --force

commit 49b25fad765eaac9aed591426a7554281ca070db
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Mar 3 17:32:10 2013 +0100

sci-biology/ncbi-tools++: Clean whitespace errors

Package-Manager: portage-2.2.0_alpha164
RepoMan-Options: --force

commit fd8d6862c4e55fd4a7d487f08449c7a819181209
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Mar 3 16:58:16 2013 +0100

sci-biology/ncbi-tools++: Add metadata.xml

Package-Manager: portage-2.2.0_alpha164
RepoMan-Options: --force

commit ae3e6180c230a13dc94e8d8599316d55ceab3d39
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Feb 21 23:56:39 2013 +0100

First working patch

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit de7706fa8dab9c1d4868d1a4202d5f9188e6cad3
Author: Justin Lecher <jlec@gentoo.org>
Date: Mon Feb 4 18:19:16 2013 +0100

Next couple of fixes

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 5ea1a4083bccc5fba615a8172113f0fee0381df6
Author: Justin Lecher <jlec@gentoo.org>
Date: Sun Feb 3 20:12:45 2013 +0100

And another step forward

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 575b7bf60f71c08b611ee74eb25ca2b8c25d0ee4
Author: Justin Lecher <jlec@gentoo.org>
Date: Thu Jan 31 17:18:57 2013 +0100

Some more patching

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 18c9916513894240043fe47a76012e9a58342605
Author: Justin Lecher <jlec@gentoo.org>
Date: Wed Jan 30 18:07:57 2013 +0100

More work on as-needed problems

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 22fd8327e252d7cf356f2337cafed02bef31a42d
Author: Justin Lecher <jlec@gentoo.org>
Date: Tue Jan 29 22:23:35 2013 +0100

my version

Signed-off-by: Justin Lecher <jlec@gentoo.org>

commit 5ff468a609fca01339602640f7cc34531a459fb3
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Tue Jan 8 00:00:20 2013 +0100

reverting to --no-as-needed LDFLAG

commit 4ef26689d731fc16766d88682ec2fc8903fcfcde
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jan 7 23:59:45 2013 +0100

reverting to --no-as-needed LDFLAG

commit c98c3577380e98c53079ded665754cb13da1be43
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jan 7 23:11:42 2013 +0100

put back in the --as-needed LDFLAG to yield hopefully smaller executables; recreating the patch so that it applies automatically

commit cd1e9304f788b93e10e6efe79580395d9cc04160
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Mon Jan 7 18:07:51 2013 +0100

sci-biology/ncbi-tools++-9.0.0: although masked a not passing repoman checks this ebuild works for me, finally. All patches from upstream.

commit 5a943c6e03b67dc35df1700cb8354ec20630bf25
Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Fri Dec 28 20:18:59 2012 +0100

sci-biology/ncbi-tools++-9.0.0: a sketch of an updated ebuild, bug #279606, does not pass repoman checks due to IUSE items

commit b03e11c822689d4775a2f0b3bec046f30c5f29ed
Author: Andrey Kislyuk <kislyuk@onyx.(none)>
Date: Sun Jul 26 20:27:22 2009 -0400

In main tree

commit f14b61ecafd4b6f03ace0c5a9ba9a68f682533f7
Author: Andrey Kislyuk <kislyuk@onyx.(none)>
Date: Sat Jul 25 12:48:33 2009 -0400

Version bump

commit 2fc1f7a6b322bd69d239906dbcaae5edb0ec54d8
Author: Justin Lecher (jlec) <jlec@j-schmitz.net>
Date: Wed Apr 29 19:55:29 2009 +0200

sci-biology/ncbi-tools++ fixed libdir
(Portage version: 2.2_rc31/git/Linux i686)
(Unsigned Manifest commit)

commit eadcc8beb665d22a9de2dd414bfc4d69bbcc0934
Author: Andrey Kislyuk <weaver@gentoo.org>
Date: Tue Apr 28 10:40:18 2009 -0400

New package