From: Justin Lecher Date: Sun, 29 Mar 2015 09:35:54 +0000 (+0000) Subject: Drop old X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=dcf28ed20c05ba14d18d996a0cb84a822be97606;p=gentoo.git 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 569dca4c6a60..4d9275a04df8 100644 --- 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 -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 biopython-1.65.ebuild: Stable for ppc, wrt bug #544544 diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 86096395e5c1..b7e71cfff198 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,33 +1,27 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 -AUX SffIO_broken_padding.patch 1294 SHA256 2dece94f54f58a46ec87108d39ecfee4d0da7c0453108c795e27716865d205b6 SHA512 d8876201d354241305b8e7cc687f9b2bcaaf880163f4e249ea2c59659f7cd0aa7fff42dd3894b6edaab9b2c4d1f7be588b7dadbb5b321b9f9260cf6ef7233ed9 WHIRLPOOL a8cee103e83e30116dce0cd823366af863cc9f694287251591761373a8024556992e8baf71baf3186f873dd14d98e40b94cbbceb20f70f8c7831f9cacccc6c70 -AUX SffIO_error_in_check_eof.patch 511 SHA256 49492906fcab2a7694c9adc12fdb5f636cda49d181027a1e43956209f0093864 SHA512 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-# 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 index 09e531bc734d..000000000000 --- 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 index a009c58cbd04..000000000000 --- 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 index 9059604f6faa..000000000000 --- 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 index afd509444c68..000000000000 --- 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 index 7f2208ef63c4..000000000000 --- 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 6ec2a510fc9f..63ffdea51c0f 100644 --- 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 -cutg-151.ebuild, + -cutg-160.ebuild: + Drop old 28 Mar 2015; Agostino Sarubbo cutg-160-r1.ebuild: Stable for ppc, wrt bug #542246 diff --git 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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 index 7008d60b98fc..000000000000 --- 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 -}