Drop old

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 569dca4c6a608c8df559dbdeccdcf0b2cf8c596e..4d9275a04df8a439cb7ff2e90486ef4ddec2fe6a 100644 (file)
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/biopython
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.83 2015/03/28 21:39:49 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.84 2015/03/29 09:35:53 jlec Exp $
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> -biopython-1.57.ebuild,
+  -biopython-1.64.ebuild, -files/SffIO_broken_padding.patch,
+  -files/SffIO_error_in_check_eof.patch, -files/biopython-1.51-flex.patch,
+  -files/biopython-1.62-SffIO.patch:
+  Drop old
 
   28 Mar 2015; Agostino Sarubbo <ago@gentoo.org> biopython-1.65.ebuild:
   Stable for ppc, wrt bug #544544

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 86096395e5c13dea7cbb35628414a428334fe68e..b7e71cfff198760c3304d7f6b175bcf080f45061 100644 (file)
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,33 +1,27 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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 AUX biopython-1.65-test-fix-backport.patch 2070 SHA256 e232b49f97f417255f62ff4cd4be70a43b7b958840d4be411e62d503e463a9aa SHA512 c5b2ed12361727bde109c98d5e2733fe7b826e6accb25279eb8c0190dcd89dc3b5e9b7328a3ace2d57ce91f0668617518c2eeb21e80f6eb97ff9010e4004f53b WHIRLPOOL dff88a361a6564732a665fb5142155f81ae10e108eac230b199fd2adaea0f0ee45e8c02b94696c968af0473481caa5d36ddd88c7438db361f8d24fd5bb773a97
-DIST biopython-1.57.tar.gz 6945024 SHA256 07c16a86127770c8d5b653a6e82fee0999159f7284a3a01c98cf66ed2f0ec4a0
-DIST biopython-1.64.tar.gz 11671170 SHA256 f79c4f4a7abc6a73b546f2177f041e5d27f68610be8685065b7180d21ec78916 SHA512 f744eee08e4eaa63836ff8fbc56be4d70659d1e36b52c5eed517001bd9d5e64b1d5f3f1c9879c1e82318ff981b3bd6b8d50942415c40b0e855df5aec41ab3dc6 WHIRLPOOL 1f2c4478109d90f73fdc7325c1d298d9f2508f6257ecaf5d3bd8a38bf51019ff596da57665fc2d480eb006b628ee123934c661a1da1746fd8ba27e9e6001dcaa
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diff --git a/sci-biology/biopython/biopython-1.57.ebuild b/sci-biology/biopython/biopython-1.57.ebuild
deleted file mode 100644 (file)
index 630ae3b..0000000
--- a/sci-biology/biopython/biopython-1.57.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.57.ebuild,v 1.6 2012/12/14 10:00:10 ulm Exp $
-
-EAPI=3
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.* *-jython"
-
-inherit distutils eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="amd64 ppc x86"
-IUSE="mysql postgres"
-
-RDEPEND="
-       dev-python/numpy
-       dev-python/reportlab
-       mysql? ( dev-python/mysql-python )
-       postgres? ( dev-python/psycopg )"
-DEPEND="${RDEPEND}
-       sys-devel/flex"
-
-PYTHON_CFLAGS=("2.* + -fno-strict-aliasing")
-
-DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES="1"
-DOCS="CONTRIB DEPRECATED NEWS README"
-PYTHON_MODNAME="Bio BioSQL"
-
-src_prepare() {
-       distutils_src_prepare
-       epatch "${FILESDIR}/${PN}-1.51-flex.patch"
-}
-
-src_test() {
-       testing() {
-               cd Tests
-               PYTHONPATH="$(ls -d ../build/lib.*)" "$(PYTHON)" run_tests.py
-       }
-       python_execute_function --nonfatal -s testing
-}
-
-src_install() {
-       distutils_src_install
-
-       insinto /usr/share/doc/${PF}
-       doins -r Doc/* || die "Installation of documentation failed"
-       insinto /usr/share/${PN}
-       cp -r --preserve=mode Scripts Tests "${ED}usr/share/${PN}" || die "Installation of shared files failed"
-}

diff --git a/sci-biology/biopython/biopython-1.64.ebuild b/sci-biology/biopython/biopython-1.64.ebuild
deleted file mode 100644 (file)
index 09e531b..0000000
--- a/sci-biology/biopython/biopython-1.64.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.64.ebuild,v 1.2 2015/03/03 16:03:42 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="mysql postgres"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-       dev-python/matplotlib[${PYTHON_USEDEP}]
-       dev-python/networkx[${PYTHON_USEDEP}]
-       dev-python/numpy[${PYTHON_USEDEP}]
-       dev-python/rdflib[${PYTHON_USEDEP}]
-       dev-python/pygraphviz[${PYTHON_USEDEP}]
-       dev-python/reportlab[${PYTHON_USEDEP}]
-       media-gfx/pydot[${PYTHON_USEDEP}]
-       mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
-       postgres? ( dev-python/psycopg:2[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-       sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-python_test() {
-       cd Tests || die
-       ${PYTHON} run_tests.py || die
-}
-
-python_install_all() {
-       distutils-r1_python_install_all
-
-       dodir /usr/share/${PN}
-       cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}

diff --git a/sci-biology/biopython/files/SffIO_broken_padding.patch b/sci-biology/biopython/files/SffIO_broken_padding.patch
deleted file mode 100644 (file)
index a009c58..0000000
--- a/sci-biology/biopython/files/SffIO_broken_padding.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 735d55b..b89cf41 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -933,12 +933,20 @@ def _check_eof(handle, index_offset, index_length):
-                          "null padding region ended '.sff' which could "
-                          "be the start of a concatenated SFF file? "
-                          "See offset %i" % (padding, offset))
-+    if padding and not extra:
-+        #TODO - Is this error harmless enough to just ignore?
-+        import warnings
-+        from Bio import BiopythonParserWarning
-+        warnings.warn("Your SFF file is technically invalid as it is missing "
-+                      "a terminal %i byte null padding region." % padding,
-+                      BiopythonParserWarning)
-+        return
-     if extra.count(_null) != padding:
-         import warnings
-         from Bio import BiopythonParserWarning
-         warnings.warn("Your SFF file is invalid, post index %i byte "
--                      "null padding region contained data." % padding,
--                      BiopythonParserWarning)
-+                      "null padding region contained data: %r"
-+                      % (padding, extra), BiopythonParserWarning)
- 
-     offset = handle.tell()
-     assert offset % 8 == 0, \

diff --git a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
deleted file mode 100644 (file)
index 9059604..0000000
--- a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 2bb0dac..735d55b 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -941,7 +941,8 @@ def _check_eof(handle, index_offset, index_length):
-                       BiopythonParserWarning)
- 
-     offset = handle.tell()
--    assert offset % 8 == 0
-+    assert offset % 8 == 0, \
-+        "Wanted offset %i %% 8 = %i to be zero" % (offset, offset % 8)
-     # Should now be at the end of the file...
-     extra = handle.read(4)
-     if extra == _sff:

diff --git a/sci-biology/biopython/files/biopython-1.51-flex.patch b/sci-biology/biopython/files/biopython-1.51-flex.patch
deleted file mode 100644 (file)
index afd5094..0000000
--- a/sci-biology/biopython/files/biopython-1.51-flex.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- setup.py.old       2008-11-25 18:03:16.000000000 +0100
-+++ setup.py   2008-11-25 18:04:14.000000000 +0100
-@@ -341,12 +341,12 @@
-               include_dirs=["Bio"]
-               ),
- #Commented out due to the build dependency on flex, see Bug 2619
--#   Extension('Bio.PDB.mmCIF.MMCIFlex',
--#              ['Bio/PDB/mmCIF/lex.yy.c',
--#               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
--#              include_dirs=["Bio"],
--#              libraries=["fl"]
--#              ),
-+    Extension('Bio.PDB.mmCIF.MMCIFlex',
-+              ['Bio/PDB/mmCIF/lex.yy.c',
-+               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
-+              include_dirs=["Bio"],
-+              libraries=["fl"]
-+              ),
-     Extension('Bio.Nexus.cnexus',
-               ['Bio/Nexus/cnexus.c']
-               ),

diff --git a/sci-biology/biopython/files/biopython-1.62-SffIO.patch b/sci-biology/biopython/files/biopython-1.62-SffIO.patch
deleted file mode 100644 (file)
index 7f2208e..0000000
--- a/sci-biology/biopython/files/biopython-1.62-SffIO.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- Bio/SeqIO/SffIO.py.ori     2013-09-25 13:28:51.000000000 +0200
-+++ Bio/SeqIO/SffIO.py 2013-09-25 13:37:44.000000000 +0200
-@@ -383,7 +383,14 @@
-         if padding:
-             padding = 8 - padding
-             if handle.read(padding).count(_null) != padding:
--                raise ValueError("Post quality %i byte padding region contained data"
-+                import warnings
-+                from Bio import BiopythonParserWarning
-+                warnings.warn("Your SFF file is valid but post quality %i byte "
-+                              "padding region contains UNUSED data. Was the "
-+                              "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
-+                              "It did not clear some internal buffer while writing "
-+                              "out new data so that previous values remained in the"
-+                              "output unless overwritten by new real values."
-                                  % padding)
-         #print read, name, record_offset
-         yield name, record_offset
---- Bio/SeqIO/SffIO.py.ori     2013-09-25 14:07:14.000000000 +0200
-+++ Bio/SeqIO/SffIO.py 2013-09-25 14:08:59.000000000 +0200
-@@ -596,7 +596,14 @@
-     if padding:
-         padding = 8 - padding
-         if handle.read(padding).count(_null) != padding:
--            raise ValueError("Post quality %i byte padding region contained data"
-+            import warnings
-+            from Bio import BiopythonParserWarning
-+            warnings.warn("Your SFF file is valid but post quality %i byte "
-+                          "padding region contains UNUSED data. Was the "
-+                          "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
-+                          "It did not clear some internal buffer while writing "
-+                          "out new data so that previous values remained in the"
-+                          "output unless overwritten by new real values."
-                              % padding)
-     #Follow Roche and apply most aggressive of qual and adapter clipping.
-     #Note Roche seems to ignore adapter clip fields when writing SFF,

diff --git a/sci-biology/cutg/ChangeLog b/sci-biology/cutg/ChangeLog
index 6ec2a510fc9fe6e1d78dc56aa3941e43ddd92c21..63ffdea51c0f68b8ee6f26a8fa79828cfa85d6ac 100644 (file)
--- a/sci-biology/cutg/ChangeLog
+++ b/sci-biology/cutg/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/cutg
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.61 2015/03/28 21:39:28 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.62 2015/03/29 09:35:00 jlec Exp $
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> -cutg-151.ebuild,
+  -cutg-160.ebuild:
+  Drop old
 
   28 Mar 2015; Agostino Sarubbo <ago@gentoo.org> cutg-160-r1.ebuild:
   Stable for ppc, wrt bug #542246

diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
index 444b3adcc1e6f859a72a59b6fc18ea62600fc529..abdb3fe154c706176f331abe9822ca76484b36d9 100644 (file)
--- a/sci-biology/cutg/Manifest
+++ b/sci-biology/cutg/Manifest
@@ -1,28 +1,26 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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-DIST cutg-160.tar.bz2 204801251 SHA256 8d5139a5f1441535296f2d5625b90863be0c26fabe703a01c290b1d91bae936f SHA512 3f52e39b8ab97289d6d7b401046f75f8a93b3e54d97ad6f3e11faa2bbb6591608693ac57ecbda901b6586c1d6a1d833cfbe23777b45873b3fb20c46af65a8e65 WHIRLPOOL ce62b45d042c48ec27e86d764c9cd081752b2806ec57ad7e773aaa5a3016e65996c920db4ed04872da74a76d1f09e48a791f046f988567599690dde210a4a209
 DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93
-EBUILD cutg-151.ebuild 1336 SHA256 ea1ee12ccb126955e9121a86886a65aa956a00ccb1afee4a5c174e9aa7507da3 SHA512 12173f73920d39b92c3e9614c77e0c185de63430f09b2b9be34a43296559000dc88403c7c6355fc3b0c26acc23a692300238e705e9299c468330d26524557afc WHIRLPOOL ad9363efffc338754a048e1e49d07e60b05aaeb3887c24b1ba8d9e8bd9ad45bd239a84432da1fefa21ab94e62567df64123c47ef66f7defa2672673e15bc1805
 EBUILD cutg-160-r1.ebuild 1384 SHA256 2c5121c373b0ef7b69a4491a15f9cda0cd3d1315464e32038dbd7661b16072a4 SHA512 0b13652c70e4fbb21d0133f085f9ccbf7dde96b6bffb9684cd5918c7f56be7d234e83ed1045760c7f3b92cb13b708b1ae56ec8acc3063a2585a0ad09fac6b695 WHIRLPOOL e1bc9f5cb8e56dd9bcc55634115d979b32542dcc51f66b56a185fffd7a75c25295630af4c3c623e87639b79d7db0ac2c3fbddde1d20893a0f888ffe44e6a4dd0
-EBUILD cutg-160.ebuild 1414 SHA256 bfe2694fef33b8f7568d487e6491259e51e4b4fc8855e4c186ec2be49f622ce1 SHA512 9b8ed300839a2798da0204d78f62aefabbc0c6e394375d8e17a80902690e6968808f6fdcf0e3821114073063c9b0295fac1d248302892847a758916a7b67a8d1 WHIRLPOOL 76559a63ed6ed406d1f36a93478a5acf7f43f6397af2174fd665b90dc2167fca34f751d27fd55460f97e50b2b617bdbaf0e4792b3844ff1ba7393ac7b08aaf60
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 MISC metadata.xml 507 SHA256 70c2bfb0dece5d434c19995ad254bd05045717b30c84c806d9d8253209154c22 SHA512 beca673e58112943bd3e84b5962a1c732fe539f83fb3b4a3a5e3bd8129b4a557d3d3dae29589c8468487b3f04622c6d99aa52379d164561e00bbfaf749a14a24 WHIRLPOOL acc2121d7036206d0868ed607aed32d248517427112ce265eb85e7660f43490f9a00a5224e3d281e65b0ac6b7938328d87c5290f88dcfef7b9da0780645ef82a
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diff --git a/sci-biology/cutg/cutg-151.ebuild b/sci-biology/cutg/cutg-151.ebuild
deleted file mode 100644 (file)
index 80c86e6..0000000
--- a/sci-biology/cutg/cutg-151.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-151.ebuild,v 1.11 2011/08/09 15:36:16 xarthisius Exp $
-
-DESCRIPTION="Codon usage tables calculated from GenBank"
-HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="ftp://ftp.kazusa.or.jp/pub/codon/current/compressed/CUTG.${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="public-domain"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-IUSE="emboss minimal"
-KEYWORDS="amd64 ppc x86"
-
-DEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-RESTRICT="binchecks strip"
-
-src_compile() {
-       if use emboss; then
-               mkdir CODONS
-               echo
-               einfo "Indexing CUTG for usage with EMBOSS."
-               EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
-                       "Indexing CUTG failed."
-               echo
-       fi
-}
-
-src_install() {
-       if ! use minimal; then
-               mkdir -p "${D}"usr/share/${PN}
-               mv *.codon *.spsum "${D}"/usr/share/${PN} || die \
-                       "Installing raw CUTG database failed."
-       fi
-       dodoc README
-       if use emboss; then
-               mkdir -p "${D}"/usr/share/EMBOSS/data/CODONS
-               cd CODONS
-               for file in *; do
-                       mv ${file} "${D}"/usr/share/EMBOSS/data/CODONS || die \
-                               "Installing the EMBOSS-indexed database failed."
-               done
-       fi
-}

diff --git a/sci-biology/cutg/cutg-160.ebuild b/sci-biology/cutg/cutg-160.ebuild
deleted file mode 100644 (file)
index 7008d60..0000000
--- a/sci-biology/cutg/cutg-160.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-160.ebuild,v 1.6 2011/08/09 15:36:16 xarthisius Exp $
-
-EAPI="3"
-
-DESCRIPTION="Codon usage tables calculated from GenBank"
-HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-SLOT="0"
-LICENSE="public-domain"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-IUSE="emboss minimal"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-
-DEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${DEPEND}"
-
-RESTRICT="binchecks strip"
-
-src_compile() {
-       if use emboss; then
-               mkdir CODONS
-               echo
-               einfo "Indexing CUTG for usage with EMBOSS."
-               EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
-                       "Indexing CUTG failed."
-               echo
-       fi
-}
-
-src_install() {
-       if ! use minimal; then
-               mkdir -p "${ED}"usr/share/${PN}
-               mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \
-                       "Installing raw CUTG database failed."
-       fi
-       dodoc README CODON_LABEL SPSUM_LABEL || die \
-                       "Failed to install documentation."
-       if use emboss; then
-               mkdir -p "${ED}"/usr/share/EMBOSS/data/CODONS
-               cd CODONS
-               for file in *; do
-                       mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS || die \
-                               "Installing the EMBOSS-indexed database failed."
-               done
-       fi
-}