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commit: 47244d4397c75f700e48a7b60ba59cc3053d3750 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sat Sep 24 19:01:30 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sat Sep 24 19:02:11 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=47244d43 |
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|
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sci-biology/amos: Allow for compiling with GCC 6 |
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|
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Gentoo-bug: 594928 |
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* EAPI=6 |
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* [QA] fix implicit declarations |
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|
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Package-Manager: portage-2.3.1 |
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|
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sci-biology/amos/Manifest | 1 + |
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sci-biology/amos/amos-3.1.0-r1.ebuild | 37 ------ |
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sci-biology/amos/amos-3.1.0-r2.ebuild | 48 ++++++++ |
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sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch | 136 +++++++++++++++++++++ |
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4 files changed, 185 insertions(+), 37 deletions(-) |
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|
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diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest |
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index 27ad50f..3628b48 100644 |
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--- a/sci-biology/amos/Manifest |
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+++ b/sci-biology/amos/Manifest |
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@@ -1 +1,2 @@ |
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+DIST amos-3.1.0-fix-c++14.patch.bz2 8033 SHA256 23b853959147466e7d766b1fe54e0afabfe3a89b84c89f788f2b8e749344efd6 SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 WHIRLPOOL d4530a5b3ff2a90419a1368a0e652bad367d2fb7601765ca42e8110ade87e8360f90070c0021aa25f5a6421815794a83491581e16fa9cb26be23bcb187840ff3 |
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DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 |
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|
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diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild |
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deleted file mode 100644 |
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index a4c860b..00000000 |
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--- a/sci-biology/amos/amos-3.1.0-r1.ebuild |
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+++ /dev/null |
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@@ -1,37 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-PYTHON_COMPAT=( python2_7 ) |
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- |
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-inherit eutils python-r1 |
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- |
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-DESCRIPTION="A Modular, Open-Source whole genome assembler" |
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-HOMEPAGE="http://amos.sourceforge.net/" |
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-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" |
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- |
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-LICENSE="Artistic" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86" |
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-IUSE="qt4" |
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- |
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-DEPEND="qt4? ( dev-qt/qtcore:4 )" |
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-RDEPEND="${DEPEND} |
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- dev-perl/DBI |
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- dev-perl/Statistics-Descriptive |
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- sci-biology/mummer" |
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- |
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-MAKEOPTS+=" -j1" |
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- |
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-src_prepare() { |
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- epatch \ |
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- "${FILESDIR}"/${P}-gcc-4.7.patch \ |
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- "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch |
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-} |
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- |
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-src_install() { |
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- default |
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- python_replicate_script "${ED}"/usr/bin/goBambus2 |
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-} |
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|
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diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild |
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new file mode 100644 |
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index 00000000..91c1f69 |
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--- /dev/null |
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+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild |
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@@ -0,0 +1,48 @@ |
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+# Copyright 1999-2016 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=6 |
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+ |
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+PYTHON_COMPAT=( python2_7 ) |
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+ |
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+inherit flag-o-matic python-r1 |
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+ |
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+DESCRIPTION="A Modular, Open-Source whole genome assembler" |
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+HOMEPAGE="http://amos.sourceforge.net/" |
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+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz |
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+ https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" |
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+ |
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+LICENSE="Artistic" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="qt4" |
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+ |
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+DEPEND="qt4? ( dev-qt/qtcore:4 )" |
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+RDEPEND="${DEPEND} |
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+ dev-perl/DBI |
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+ dev-perl/Statistics-Descriptive |
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+ sci-biology/mummer" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}"/${P}-gcc-4.7.patch |
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+ "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch |
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+ "${WORKDIR}"/${P}-fix-c++14.patch |
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+ "${FILESDIR}"/${P}-qa-Wformat.patch |
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+) |
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+ |
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+src_configure() { |
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+ # prevent GCC 6 log pollution due to hash_map deprecation in C++11 |
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+ append-cxxflags -Wno-cpp |
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+ |
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+ default |
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+} |
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+ |
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+src_compile() { |
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+ emake -j1 |
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+} |
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+ |
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+src_install() { |
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+ default |
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+ python_replicate_script "${ED%/}/usr/bin/goBambus2" |
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+} |
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|
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diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch |
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new file mode 100644 |
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index 00000000..13f4eeb |
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--- /dev/null |
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+++ b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch |
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@@ -0,0 +1,136 @@ |
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+Fix QA warnings, due to using incorrect format specifiers in printf: |
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+* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’, |
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+* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=] |
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+* fprintf (stderr, "%u b contigs\n", b . size ()); |
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+ |
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+--- a/src/Align/align.cc |
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++++ b/src/Align/align.cc |
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+@@ -1936,7 +1936,7 @@ |
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+ n = align . size (); |
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+ con = consensus . c_str (); |
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+ |
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+- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); |
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++ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); |
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+ |
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+ for (i = 0; i < n; i ++) |
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+ { |
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+@@ -3936,7 +3936,7 @@ |
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+ } |
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+ |
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+ // Array of sum of quality scores in the slice for A,C,G,T,- resp. |
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+- for (j = 0; j < 6; j ++) |
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++ for (j = 0; j < 5; j ++) |
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+ qvsum [j] = 0; |
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+ |
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+ int nof_ambiguities = 0; |
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+--- a/src/Align/align_poly.cc |
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++++ b/src/Align/align_poly.cc |
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+@@ -1761,7 +1761,7 @@ |
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+ n = align . size (); |
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+ con = consensus . c_str (); |
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+ |
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+- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); |
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++ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); |
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+ for (i = 0; i < n; i ++) |
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+ { |
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+ fprintf (fp, "\nString #%d:\n", i); |
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+--- a/src/Align/count-qmers.cc |
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++++ b/src/Align/count-qmers.cc |
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+@@ -191,8 +191,8 @@ |
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+ |
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+ PrintMers(mer_table, min_count); |
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+ |
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+- fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT); |
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+- fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n", LEN); |
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++ fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT); |
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++ fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n", LEN); |
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+ } |
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+ catch (Exception_t & e) |
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+ { |
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+--- a/src/Align/kmer-cov.cc |
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++++ b/src/Align/kmer-cov.cc |
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+@@ -485,7 +485,7 @@ |
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+ Kmer_Len = s . length (); |
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+ else if (Kmer_Len != int (s . length ())) |
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+ { |
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+- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", |
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++ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", |
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+ s . c_str (), s . length (), Kmer_Len); |
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+ Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); |
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+ } |
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+--- a/src/Align/kmer-cov-plot.cc |
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++++ b/src/Align/kmer-cov-plot.cc |
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+@@ -316,7 +316,7 @@ |
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+ } |
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+ else if (Kmer_Len != int (s . length ())) |
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+ { |
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+- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", |
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++ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", |
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+ s . c_str (), s . length (), Kmer_Len); |
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+ Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); |
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+ } |
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+--- a/src/Align/make-consensus.cc |
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++++ b/src/Align/make-consensus.cc |
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+@@ -303,7 +303,7 @@ |
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+ break; |
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+ } |
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+ |
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+- sprintf (sid, "%ld", ++layout_id); |
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++ sprintf (sid, "%u", ++layout_id); |
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+ cid = string (sid); |
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+ ID_t lid = layout.getIID (); |
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+ if (lid == 0) |
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+--- a/src/Align/make-consensus_poly.cc |
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++++ b/src/Align/make-consensus_poly.cc |
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+@@ -279,7 +279,7 @@ |
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+ break; |
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+ } |
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+ |
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+- sprintf(sid, "%ld", ++layout_id); |
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++ sprintf(sid, "%u", ++layout_id); |
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+ cid = string(sid); |
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+ ID_t lid = layout.getIID(); |
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+ if (lid == 0) { |
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+--- a/src/Align/simple-overlap.cc |
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++++ b/src/Align/simple-overlap.cc |
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+@@ -422,7 +422,7 @@ |
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+ "Options:\n" |
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+ " -a Also show alignments of overlaps \n" |
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+ " -E <x> Maximum error rate for overlaps is <x>\n" |
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+- " e.g., -E 0.06 for 6% error rate\n" |
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++ " e.g., -E 0.06 for 6%% error rate\n" |
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+ " -F Input is a fasta file\n" |
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+ " -h Print this usage message\n" |
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+ " -o <n> Set minimum overlap length to <n>\n" |
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+--- a/src/Compare/contig-cmp.cc |
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++++ b/src/Compare/contig-cmp.cc |
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+@@ -145,7 +145,7 @@ |
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+ |
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+ fclose (fp); |
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+ |
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+- fprintf (stderr, "%u a contigs\n", a . size ()); |
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++ fprintf (stderr, "%zu a contigs\n", a . size ()); |
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+ vector <Unitig_t> a_contig (max_id + 1); |
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+ n = a . size (); |
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+ for (i = 0; i < n; i ++) |
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+@@ -234,7 +234,7 @@ |
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+ |
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+ fclose (fp); |
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+ |
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+- fprintf (stderr, "%u b contigs\n", b . size ()); |
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++ fprintf (stderr, "%zu b contigs\n", b . size ()); |
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+ vector <Unitig_t> b_contig (max_id + 1); |
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+ n = b . size (); |
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+ for (i = 0; i < n; i ++) |
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+--- a/src/Staden/progs/trace_convert.c |
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++++ b/src/Staden/progs/trace_convert.c |
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+@@ -6,6 +6,9 @@ |
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+ #include "traceType.h" |
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+ #include "seqIOABI.h" |
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+ |
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++#include <fcntl.h> |
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++#include <unistd.h> |
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++ |
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+ static char fileIdentifier[] = "$Id$"; |
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+ |
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+ struct opts { |