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sci-biology/ncbi-tools++

NCBI C++ Toolkit, including NCBI BLAST+

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  • ncbi-tools++-12.0.0
    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 sqlite3 tiff xerces xalan xml xpm xslt X

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    Overlay: science (layman)

ChangeLog

# ChangeLog for sci-biology/ncbi-tools++
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $

16 Sep 2014; Christoph Junghans <ottxor@gentoo.org>
-files/ncbi-tools++-12.0.0-as-needed.patch,
-files/ncbi-tools++-9.0.0-as-needed.patch,
-files/ncbi-tools++-9.0.0-conf-opts.patch,
-files/ncbi-tools++-9.0.0-disable_test_compress.patch,
-files/ncbi-tools++-9.0.0-fix-creaders-linking.patch,
-files/ncbi-tools++-9.0.0-fix-order-of-libs.patch,
-files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch, -files/ncbi-tools++-9.0.
0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch,
-files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch,
-ncbi-tools++-9.0.0-r1.ebuild, -ncbi-tools++-9.0.0.ebuild, metadata.xml,
ncbi-tools++-12.0.0.ebuild:
major clean, drop old version and unused patches

23 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog:
add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed),
patches from upstream:
http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62745
http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62750
http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62760

14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-9.0.0-r1.ebuild:
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.

14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-9.0.0-r1.ebuild,
+files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch:
Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with
line
offset changes.

13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild,
+files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch,
+files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch:
Fix URL to point to a public SVN repository (an upstream patch from email
list):

Date: Sun, 28 Jul 2013 22:05:34 -0400
CC: <cpp@ncbi.nlm.nih.gov>
Subject: Re: [C++] new project startup example needed

13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-12.0.0.ebuild,
files/ncbi-tools++-9.0.0-fix-creaders-linking.patch,
+files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch,
files/ncbi-tools++-12.0.0-fix-creaders-linking.patch:
Added an upstream patch from:

Date: Wed, 28 Aug 2013 10:50:29 -0400
List cpp <cpp@ncbi.nlm.nih.gov>
Subject: Re: [C++] error building ncbi toolkit v.12.0.0

Fixed line offsets in the ncbi-tools++-12.0.0-fix-creaders-linking.patch
file.

Fixed file path in ncbi-tools++-9.0.0-fix-creaders-linking.patch header.

The patches copied blindly from ncbi-tools++-9.0.0-r1 under 12.0.0 need to be
adjusted still to have correct line numbers. They do NOT apply cleanly at the
moment.

13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild,
files/ncbi-tools++-9.0.0-as-needed.patch,
+files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.
patch, files/ncbi-tools++-12.0.0-as-needed.patch:
files/ncbi-tools++-12.0.0-as-needed.patch
files/ncbi-tools++-9.0.0-as-needed.patch

Remove redundant connect per message from Aaron Ucko <ucko@ncbi.nlm.nih.gov>:

> +DLL_LIB = xncbi xutil seqset connect xconnect xnetblast
Then simply remove connect, which is redundant with xconnect. (connect
consists of code shared with NCBI's C Toolkit; xconnect adds a C++
layer.)


13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-12.0.0.ebuild,
+files/ncbi-tools++-12.0.0-fix-creaders-linking.patch:
No, the fix-creaders-linking is needed for 12.0.0 as well.

*ncbi-tools++-12.0.0 (13 Sep 2013)

13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ncbi-tools++-12.0.0.ebuild, +files/ncbi-tools++-12.0.0-as-needed.patch,
+files/ncbi-tools++-12.0.0-conf-opts.patch:
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.

13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
ncbi-tools++-9.0.0-r1.ebuild,
+files/ncbi-tools++-9.0.0-fix-creaders-linking.patch:
add glew to dependencies inferrred via mesa
fix lib/libxobjread.so: undefined reference to 'AlignmentFileFree' message by
upstream patch

12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
Drop empty line

12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
Drop autotools.eclass

01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
Some Prefix love

01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
Some Prefix love


03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
Document USE

03 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0.ebuild,
ncbi-tools++-9.0.0-r1.ebuild:
Clean whitespace errors

03 Mar 2013; Justin Lecher <jlec@gentoo.org> +metadata.xml:
Add metadata.xml