* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2014-12-02 8:19 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2014-12-02 8:19 UTC (permalink / raw
To: gentoo-commits
commit: 1747e93926b4fc0e704589b65ce0f4701941e673
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Sat Nov 29 16:04:36 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 1 15:24:41 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1747e939
Add discrover ebuilds
---
sci-biology/discrover/discrover-1.1.2.ebuild | 74 ++++++++++++++++++++++++++++
sci-biology/discrover/discrover-9999.ebuild | 74 ++++++++++++++++++++++++++++
sci-biology/discrover/metadata.xml | 22 +++++++++
3 files changed, 170 insertions(+)
diff --git a/sci-biology/discrover/discrover-1.1.2.ebuild b/sci-biology/discrover/discrover-1.1.2.ebuild
new file mode 100644
index 0000000..f1cac2a
--- /dev/null
+++ b/sci-biology/discrover/discrover-1.1.2.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+inherit cmake-utils
+
+DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
+HOMEPAGE="https://github.com/maaskola/discrover"
+SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc"
+
+RDEPEND="
+ dev-libs/boost
+ dreme? ( sci-biology/meme )
+ logo? (
+ dev-lang/ruby
+ dev-texlive/texlive-latex
+ dev-tex/pgf
+ dev-tex/xcolor
+ media-gfx/imagemagick
+ )
+ misc_scripts? ( dev-lang/ruby )
+ rmathlib? ( dev-lang/R )
+ tcmalloc? ( dev-util/google-perftools )
+"
+DEPEND="${RDEPEND}
+ doc? (
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ dev-texlive/texlive-latexrecommended
+ media-gfx/imagemagick
+ )
+"
+src_configure() {
+ local mycmakeargs=(
+ $(cmake-utils_use_with dreme DREME)
+ $(cmake-utils_use_with doc DOC)
+ $(cmake-utils_use_with logo LOGO)
+ $(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
+ $(cmake-utils_use_with rmathlib RMATHLIB)
+ $(cmake-utils_use_with tcmalloc TCMALLOC)
+ )
+
+ unset R_HOME
+
+ if use rmathlib ; then
+ elog
+ elog "Using statistical routines from standalone Rmathlib."
+ elog
+ fi
+ if use dreme ; then
+ elog
+ elog "Linking to DREME from the MEME suite."
+ elog
+ else
+ elog
+ elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
+ elog "You will not be able to use DREME to find seeds."
+ elog
+ fi
+
+ if use doc ; then
+ elog
+ elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
+ elog
+ fi
+
+ cmake-utils_src_configure
+}
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
new file mode 100644
index 0000000..1d0ac53
--- /dev/null
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+inherit cmake-utils git-2
+
+DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
+HOMEPAGE="https://github.com/maaskola/discrover"
+EGIT_REPO_URI="https://github.com/maaskola/${PN}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc"
+
+RDEPEND="
+ dev-libs/boost
+ dreme? ( sci-biology/meme )
+ logo? (
+ dev-lang/ruby
+ dev-texlive/texlive-latex
+ dev-tex/pgf
+ dev-tex/xcolor
+ media-gfx/imagemagick
+ )
+ misc_scripts? ( dev-lang/ruby )
+ rmathlib? ( dev-lang/R )
+ tcmalloc? ( dev-util/google-perftools )
+"
+DEPEND="${RDEPEND}
+ doc? (
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ dev-texlive/texlive-latexrecommended
+ media-gfx/imagemagick
+ )
+"
+src_configure() {
+ local mycmakeargs=(
+ $(cmake-utils_use_with dreme DREME)
+ $(cmake-utils_use_with doc DOC)
+ $(cmake-utils_use_with logo LOGO)
+ $(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
+ $(cmake-utils_use_with rmathlib RMATHLIB)
+ $(cmake-utils_use_with tcmalloc TCMALLOC)
+ )
+
+ unset R_HOME
+
+ if use rmathlib ; then
+ elog
+ elog "Using statistical routines from standalone Rmathlib."
+ elog
+ fi
+ if use dreme ; then
+ elog
+ elog "Linking to DREME from the MEME suite."
+ elog
+ else
+ elog
+ elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
+ elog "You will not be able to use DREME to find seeds."
+ elog
+ fi
+
+ if use doc ; then
+ elog
+ elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
+ elog
+ fi
+
+ cmake-utils_src_configure
+}
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
new file mode 100644
index 0000000..cda9ddd
--- /dev/null
+++ b/sci-biology/discrover/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>jonas@maaskola.de</email>
+ <name>Jonas Maaskola</name>
+ </maintainer>
+ <use>
+ <flag name="dreme">
+ Allow to use DREME from the MEME package for seeding
+ </flag>
+ <flag name="logo">
+ Enable LaTeX/TikZ based ruby script for sequence logo drawing
+ </flag>
+ <flag name="misc_scripts">
+ Install miscellaneous scripts, e.g. for sequence length statistics
+ </flag>
+ <flag name="rmathlib">
+ Link to the standalone Rmathlib for statistical routines
+ </flag>
+ </use>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2014-12-16 23:01 Christoph Junghans
0 siblings, 0 replies; 9+ messages in thread
From: Christoph Junghans @ 2014-12-16 23:01 UTC (permalink / raw
To: gentoo-commits
commit: 9625aabce6e38948b057246b4b994d1710d1dc26
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Mon Dec 15 14:32:08 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Dec 15 14:32:08 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9625aabc
sci-biology/discrover: version bump; add to RDEPEND
Bump ebuild for new release.
When the USE flag "logo" is used, we also need to depend on texlive-latexextra for the standalone package.
Package-Manager: portage-2.2.14
---
sci-biology/discrover/ChangeLog | 11 +++++++++++
.../{discrover-1.1.2.ebuild => discrover-1.3.1.ebuild} | 1 +
sci-biology/discrover/discrover-9999.ebuild | 1 +
3 files changed, 13 insertions(+)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
new file mode 100644
index 0000000..8994dda
--- /dev/null
+++ b/sci-biology/discrover/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/discrover
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*discrover-1.3.1 (15 Dec 2014)
+
+ 15 Dec 2014; Jonas Maaskola <jonas@maaskola.de> +discrover-1.3.1.ebuild,
+ -discrover-1.1.2.ebuild, discrover-9999.ebuild:
+ sci-biology/discrover: version bump; add to RDEPEND Bump ebuild for new
+ release. When the USE flag "logo" is used, we also need to depend on texlive-
+ latexextra for the standalone package.
diff --git a/sci-biology/discrover/discrover-1.1.2.ebuild b/sci-biology/discrover/discrover-1.3.1.ebuild
similarity index 98%
rename from sci-biology/discrover/discrover-1.1.2.ebuild
rename to sci-biology/discrover/discrover-1.3.1.ebuild
index f1cac2a..c892c73 100644
--- a/sci-biology/discrover/discrover-1.1.2.ebuild
+++ b/sci-biology/discrover/discrover-1.3.1.ebuild
@@ -20,6 +20,7 @@ RDEPEND="
logo? (
dev-lang/ruby
dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
dev-tex/pgf
dev-tex/xcolor
media-gfx/imagemagick
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index 1d0ac53..d01dfdc 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -20,6 +20,7 @@ RDEPEND="
logo? (
dev-lang/ruby
dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
dev-tex/pgf
dev-tex/xcolor
media-gfx/imagemagick
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2015-01-06 0:19 Christoph Junghans
0 siblings, 0 replies; 9+ messages in thread
From: Christoph Junghans @ 2015-01-06 0:19 UTC (permalink / raw
To: gentoo-commits
commit: d7354e6cfc75c9d524af453e34cf21d6829b920c
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Sun Jan 4 20:14:11 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 5 04:54:49 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7354e6c
Bump minor version to 1.4.0.
Introduces a new USE flag: 'cairo'.
x11-libs/cairo is used to generate sequence logos.
The USE flag 'logo' has been renamed to 'tikzlogo'.
The tikzlogo Ruby script served the purpose that is now fulfilled by the
Cairo-based code. tikzlogo requires Ruby, ImageMagick, and a full TeX Live
installation (including the large dev-texlive/texlive-latexextra).
Compared to that, the new Cairo-based code has much reduced dependencies,
and is hence the preferred way to generate sequence logos.
Package-Manager: portage-2.2.14
---
sci-biology/discrover/ChangeLog | 14 +++++++++++++-
.../{discrover-1.3.1.ebuild => discrover-1.4.0.ebuild} | 10 ++++++----
sci-biology/discrover/discrover-9999.ebuild | 10 ++++++----
sci-biology/discrover/metadata.xml | 5 ++++-
4 files changed, 29 insertions(+), 10 deletions(-)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index 8994dda..c2c5253 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -1,7 +1,19 @@
# ChangeLog for sci-biology/discrover
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*discrover-1.4.0 (04 Jan 2015)
+
+ 04 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.0.ebuild,
+ -discrover-1.3.1.ebuild, discrover-9999.ebuild, metadata.xml:
+ Bump minor version to 1.4.0. Introduces a new USE flag: 'cairo'.
+ x11-libs/cairo is used to generate sequence logos. The USE flag 'logo' has
+ been renamed to 'tikzlogo'. The tikzlogo Ruby script served the purpose that
+ is now fulfilled by the Cairo-based code. tikzlogo requires Ruby, ImageMagick,
+ and a full TeX Live installation (including the large dev-texlive/texlive-
+ latexextra). Compared to that, the new Cairo-based code has much reduced
+ dependencies, and is hence the preferred way to generate sequence logos.
+
*discrover-1.3.1 (15 Dec 2014)
15 Dec 2014; Jonas Maaskola <jonas@maaskola.de> +discrover-1.3.1.ebuild,
diff --git a/sci-biology/discrover/discrover-1.3.1.ebuild b/sci-biology/discrover/discrover-1.4.0.ebuild
similarity index 87%
rename from sci-biology/discrover/discrover-1.3.1.ebuild
rename to sci-biology/discrover/discrover-1.4.0.ebuild
index c892c73..5ae256f 100644
--- a/sci-biology/discrover/discrover-1.3.1.ebuild
+++ b/sci-biology/discrover/discrover-1.4.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -12,12 +12,13 @@ SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc tikzlogo misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
+ cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
- logo? (
+ tikzlogo? (
dev-lang/ruby
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
@@ -39,9 +40,10 @@ DEPEND="${RDEPEND}
"
src_configure() {
local mycmakeargs=(
+ $(cmake-utils_use_with cairo CAIRO)
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
- $(cmake-utils_use_with logo LOGO)
+ $(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index d01dfdc..5d3cf63 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -12,12 +12,13 @@ EGIT_REPO_URI="https://github.com/maaskola/${PN}"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc tikzlogo misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
+ cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
- logo? (
+ tikzlogo? (
dev-lang/ruby
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
@@ -39,9 +40,10 @@ DEPEND="${RDEPEND}
"
src_configure() {
local mycmakeargs=(
+ $(cmake-utils_use_with cairo CAIRO)
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
- $(cmake-utils_use_with logo LOGO)
+ $(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
index cda9ddd..24958c9 100644
--- a/sci-biology/discrover/metadata.xml
+++ b/sci-biology/discrover/metadata.xml
@@ -6,10 +6,13 @@
<name>Jonas Maaskola</name>
</maintainer>
<use>
+ <flag name="cairo">
+ Use Cairo for sequence logo plotting capabilities
+ </flag>
<flag name="dreme">
Allow to use DREME from the MEME package for seeding
</flag>
- <flag name="logo">
+ <flag name="tikzlogo">
Enable LaTeX/TikZ based ruby script for sequence logo drawing
</flag>
<flag name="misc_scripts">
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2015-01-06 0:19 Christoph Junghans
0 siblings, 0 replies; 9+ messages in thread
From: Christoph Junghans @ 2015-01-06 0:19 UTC (permalink / raw
To: gentoo-commits
commit: 318ec2fd461c24cecc8a1d91abc836f0ab21264e
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Mon Jan 5 04:42:10 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 5 04:54:49 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=318ec2fd
Bump patch version
Package-Manager: portage-2.2.14
---
sci-biology/discrover/ChangeLog | 6 ++++++
.../discrover/{discrover-1.4.0.ebuild => discrover-1.4.1.ebuild} | 0
2 files changed, 6 insertions(+)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index c2c5253..d81ca8c 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*discrover-1.4.1 (05 Jan 2015)
+
+ 05 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.1.ebuild,
+ -discrover-1.4.0.ebuild:
+ Bump patch version
+
*discrover-1.4.0 (04 Jan 2015)
04 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.0.ebuild,
diff --git a/sci-biology/discrover/discrover-1.4.0.ebuild b/sci-biology/discrover/discrover-1.4.1.ebuild
similarity index 100%
rename from sci-biology/discrover/discrover-1.4.0.ebuild
rename to sci-biology/discrover/discrover-1.4.1.ebuild
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2015-01-31 20:19 Christoph Junghans
0 siblings, 0 replies; 9+ messages in thread
From: Christoph Junghans @ 2015-01-31 20:19 UTC (permalink / raw
To: gentoo-commits
commit: 06b18fa7ff04d5abcc2f8d216d0162a068255a7b
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Tue Jan 27 22:40:43 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jan 27 22:40:43 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=06b18fa7
sci-biology/discrover: bump package version, add USE flag for link-time optimization, install doc to /usr/share/doc/${PF}
Package-Manager: portage-2.2.14
---
sci-biology/discrover/ChangeLog | 7 +++++++
.../{discrover-1.4.1.ebuild => discrover-1.5.2.ebuild} | 14 +++++++++++++-
sci-biology/discrover/discrover-9999.ebuild | 16 ++++++++++++++--
sci-biology/discrover/metadata.xml | 5 ++++-
4 files changed, 38 insertions(+), 4 deletions(-)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index d81ca8c..fd6eb45 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*discrover-1.5.2 (27 Jan 2015)
+
+ 27 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.5.2.ebuild,
+ -discrover-1.4.1.ebuild, discrover-9999.ebuild, metadata.xml:
+ sci-biology/discrover: bump package version, add USE flag for link-time
+ optimization, install doc to /usr/share/doc/${PF}
+
*discrover-1.4.1 (05 Jan 2015)
05 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.1.ebuild,
diff --git a/sci-biology/discrover/discrover-1.4.1.ebuild b/sci-biology/discrover/discrover-1.5.2.ebuild
similarity index 74%
rename from sci-biology/discrover/discrover-1.4.1.ebuild
rename to sci-biology/discrover/discrover-1.5.2.ebuild
index 5ae256f..b17687e 100644
--- a/sci-biology/discrover/discrover-1.4.1.ebuild
+++ b/sci-biology/discrover/discrover-1.5.2.ebuild
@@ -12,7 +12,7 @@ SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc tikzlogo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
@@ -37,16 +37,28 @@ DEPEND="${RDEPEND}
dev-texlive/texlive-latexrecommended
media-gfx/imagemagick
)
+ lto? ( >=sys-devel/gcc-4.8 )
"
+pkg_pretend() {
+ if use lto; then
+ if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
+ eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
+ eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
+ die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
+ fi
+ fi
+}
src_configure() {
local mycmakeargs=(
$(cmake-utils_use_with cairo CAIRO)
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
+ $(cmake-utils_use_with lto LTO)
$(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
+ -DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
)
unset R_HOME
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index 5d3cf63..34ce8c0 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -3,7 +3,7 @@
# $Header: $
EAPI=5
-inherit cmake-utils git-2
+inherit cmake-utils git-r3
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
@@ -12,7 +12,7 @@ EGIT_REPO_URI="https://github.com/maaskola/${PN}"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc tikzlogo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
@@ -37,16 +37,28 @@ DEPEND="${RDEPEND}
dev-texlive/texlive-latexrecommended
media-gfx/imagemagick
)
+ lto? ( >=sys-devel/gcc-4.8 )
"
+pkg_pretend() {
+ if use lto; then
+ if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
+ eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
+ eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
+ die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
+ fi
+ fi
+}
src_configure() {
local mycmakeargs=(
$(cmake-utils_use_with cairo CAIRO)
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
+ $(cmake-utils_use_with lto LTO)
$(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
+ -DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
)
unset R_HOME
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
index 24958c9..0862889 100644
--- a/sci-biology/discrover/metadata.xml
+++ b/sci-biology/discrover/metadata.xml
@@ -10,7 +10,10 @@
Use Cairo for sequence logo plotting capabilities
</flag>
<flag name="dreme">
- Allow to use DREME from the MEME package for seeding
+ Enable usage of DREME from the MEME package for seeding
+ </flag>
+ <flag name="lto">
+ Compile with link-time optimization (LTO)
</flag>
<flag name="tikzlogo">
Enable LaTeX/TikZ based ruby script for sequence logo drawing
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: f2888f2e2f6610f9876bb14d112f8fdcb696248a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:21:25 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:21:25 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f2888f2e
sci-biology/discrover: fix SLOT operators; correct ruby deps
Package-Manager: portage-2.2.17
---
sci-biology/discrover/ChangeLog | 4 ++++
sci-biology/discrover/discrover-1.5.2.ebuild | 28 +++++++++++++++------------
sci-biology/discrover/discrover-9999.ebuild | 29 ++++++++++++++++------------
sci-biology/discrover/metadata.xml | 24 +++++++++++------------
4 files changed, 49 insertions(+), 36 deletions(-)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index fd6eb45..aba75b4 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> discrover-1.5.2.ebuild,
+ discrover-9999.ebuild, metadata.xml:
+ sci-biology/discrover: fix SLOT operators; correct ruby deps
+
*discrover-1.5.2 (27 Jan 2015)
27 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.5.2.ebuild,
diff --git a/sci-biology/discrover/discrover-1.5.2.ebuild b/sci-biology/discrover/discrover-1.5.2.ebuild
index b17687e..f0992e2 100644
--- a/sci-biology/discrover/discrover-1.5.2.ebuild
+++ b/sci-biology/discrover/discrover-1.5.2.ebuild
@@ -3,7 +3,11 @@
# $Header: $
EAPI=5
-inherit cmake-utils
+
+USE_RUBY="ruby19"
+RUBY_OPTIONAL=yes
+
+inherit cmake-utils ruby-fakegem
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
@@ -19,14 +23,14 @@ RDEPEND="
cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
tikzlogo? (
- dev-lang/ruby
+ $(ruby_implementations_depend)
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
dev-tex/pgf
dev-tex/xcolor
media-gfx/imagemagick
)
- misc_scripts? ( dev-lang/ruby )
+ misc_scripts? ( $(ruby_implementations_depend) )
rmathlib? ( dev-lang/R )
tcmalloc? ( dev-util/google-perftools )
"
@@ -37,7 +41,7 @@ DEPEND="${RDEPEND}
dev-texlive/texlive-latexrecommended
media-gfx/imagemagick
)
- lto? ( >=sys-devel/gcc-4.8 )
+ lto? ( >=sys-devel/gcc-4.8:* )
"
pkg_pretend() {
if use lto; then
@@ -64,25 +68,25 @@ src_configure() {
unset R_HOME
if use rmathlib ; then
- elog
+ echo
elog "Using statistical routines from standalone Rmathlib."
- elog
+ echo
fi
if use dreme ; then
- elog
+ echo
elog "Linking to DREME from the MEME suite."
- elog
+ echo
else
- elog
+ echo
elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
elog "You will not be able to use DREME to find seeds."
- elog
+ echo
fi
if use doc ; then
- elog
+ echo
elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
- elog
+ echo
fi
cmake-utils_src_configure
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index 34ce8c0..8131e9b 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -3,10 +3,15 @@
# $Header: $
EAPI=5
-inherit cmake-utils git-r3
+
+USE_RUBY="ruby19"
+RUBY_OPTIONAL=yes
+
+inherit cmake-utils git-r3 ruby-fakegem
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
+SRC_URI=""
EGIT_REPO_URI="https://github.com/maaskola/${PN}"
LICENSE="GPL-3+"
@@ -19,14 +24,14 @@ RDEPEND="
cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
tikzlogo? (
- dev-lang/ruby
+ $(ruby_implementations_depend)
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
dev-tex/pgf
dev-tex/xcolor
media-gfx/imagemagick
)
- misc_scripts? ( dev-lang/ruby )
+ misc_scripts? ( $(ruby_implementations_depend) )
rmathlib? ( dev-lang/R )
tcmalloc? ( dev-util/google-perftools )
"
@@ -37,7 +42,7 @@ DEPEND="${RDEPEND}
dev-texlive/texlive-latexrecommended
media-gfx/imagemagick
)
- lto? ( >=sys-devel/gcc-4.8 )
+ lto? ( >=sys-devel/gcc-4.8:* )
"
pkg_pretend() {
if use lto; then
@@ -64,25 +69,25 @@ src_configure() {
unset R_HOME
if use rmathlib ; then
- elog
+ echo
elog "Using statistical routines from standalone Rmathlib."
- elog
+ echo
fi
if use dreme ; then
- elog
+ echo
elog "Linking to DREME from the MEME suite."
- elog
+ echo
else
- elog
+ echo
elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
elog "You will not be able to use DREME to find seeds."
- elog
+ echo
fi
if use doc ; then
- elog
+ echo
elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
- elog
+ echo
fi
cmake-utils_src_configure
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
index 0862889..6bfaf6c 100644
--- a/sci-biology/discrover/metadata.xml
+++ b/sci-biology/discrover/metadata.xml
@@ -1,28 +1,28 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>jonas@maaskola.de</email>
- <name>Jonas Maaskola</name>
- </maintainer>
- <use>
- <flag name="cairo">
+ <maintainer>
+ <email>jonas@maaskola.de</email>
+ <name>Jonas Maaskola</name>
+ </maintainer>
+ <use>
+ <flag name="cairo">
Use Cairo for sequence logo plotting capabilities
</flag>
- <flag name="dreme">
+ <flag name="dreme">
Enable usage of DREME from the MEME package for seeding
</flag>
- <flag name="lto">
+ <flag name="lto">
Compile with link-time optimization (LTO)
</flag>
- <flag name="tikzlogo">
+ <flag name="tikzlogo">
Enable LaTeX/TikZ based ruby script for sequence logo drawing
</flag>
- <flag name="misc_scripts">
+ <flag name="misc_scripts">
Install miscellaneous scripts, e.g. for sequence length statistics
</flag>
- <flag name="rmathlib">
+ <flag name="rmathlib">
Link to the standalone Rmathlib for statistical routines
</flag>
- </use>
+ </use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2015-03-18 7:23 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2015-03-18 7:23 UTC (permalink / raw
To: gentoo-commits
commit: 4146556d83260726494e66ebb05ec89c76ba11d5
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Wed Mar 18 00:09:04 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 18 00:13:06 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4146556d
sci-biology/discrover: version bump; drop USE flag
Package-Manager: portage-2.2.14
sci-biology/discrover/ChangeLog | 6 ++++++
...scrover-1.5.2.ebuild => discrover-1.6.0.ebuild} | 18 ++---------------
sci-biology/discrover/discrover-9999.ebuild | 18 ++---------------
sci-biology/discrover/metadata.xml | 23 ++++++++++------------
4 files changed, 20 insertions(+), 45 deletions(-)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index aba75b4..f4e2dcd 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*discrover-1.6.0 (18 Mar 2015)
+
+ 18 Mar 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.6.0.ebuild,
+ -discrover-1.5.2.ebuild, discrover-9999.ebuild, metadata.xml:
+ sci-biology/discrover: version bump; drop USE flag
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> discrover-1.5.2.ebuild,
discrover-9999.ebuild, metadata.xml:
sci-biology/discrover: fix SLOT operators; correct ruby deps
diff --git a/sci-biology/discrover/discrover-1.5.2.ebuild b/sci-biology/discrover/discrover-1.6.0.ebuild
similarity index 83%
rename from sci-biology/discrover/discrover-1.5.2.ebuild
rename to sci-biology/discrover/discrover-1.6.0.ebuild
index f0992e2..5f1281c 100644
--- a/sci-biology/discrover/discrover-1.5.2.ebuild
+++ b/sci-biology/discrover/discrover-1.6.0.ebuild
@@ -3,11 +3,7 @@
# $Header: $
EAPI=5
-
-USE_RUBY="ruby19"
-RUBY_OPTIONAL=yes
-
-inherit cmake-utils ruby-fakegem
+inherit cmake-utils
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
@@ -16,21 +12,12 @@ SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
- tikzlogo? (
- $(ruby_implementations_depend)
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- dev-tex/pgf
- dev-tex/xcolor
- media-gfx/imagemagick
- )
- misc_scripts? ( $(ruby_implementations_depend) )
rmathlib? ( dev-lang/R )
tcmalloc? ( dev-util/google-perftools )
"
@@ -58,7 +45,6 @@ src_configure() {
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
$(cmake-utils_use_with lto LTO)
- $(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index 8131e9b..6958803 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -3,11 +3,7 @@
# $Header: $
EAPI=5
-
-USE_RUBY="ruby19"
-RUBY_OPTIONAL=yes
-
-inherit cmake-utils git-r3 ruby-fakegem
+inherit cmake-utils git-r3
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
@@ -17,21 +13,12 @@ EGIT_REPO_URI="https://github.com/maaskola/${PN}"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
- tikzlogo? (
- $(ruby_implementations_depend)
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- dev-tex/pgf
- dev-tex/xcolor
- media-gfx/imagemagick
- )
- misc_scripts? ( $(ruby_implementations_depend) )
rmathlib? ( dev-lang/R )
tcmalloc? ( dev-util/google-perftools )
"
@@ -59,7 +46,6 @@ src_configure() {
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
$(cmake-utils_use_with lto LTO)
- $(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
index 6bfaf6c..fb652d7 100644
--- a/sci-biology/discrover/metadata.xml
+++ b/sci-biology/discrover/metadata.xml
@@ -7,22 +7,19 @@
</maintainer>
<use>
<flag name="cairo">
- Use Cairo for sequence logo plotting capabilities
- </flag>
+ Use Cairo for sequence logo plotting capabilities
+ </flag>
<flag name="dreme">
- Enable usage of DREME from the MEME package for seeding
- </flag>
+ Enable usage of DREME from the MEME package for seeding
+ </flag>
<flag name="lto">
- Compile with link-time optimization (LTO)
- </flag>
- <flag name="tikzlogo">
- Enable LaTeX/TikZ based ruby script for sequence logo drawing
- </flag>
+ Compile with link-time optimization (LTO)
+ </flag>
<flag name="misc_scripts">
- Install miscellaneous scripts, e.g. for sequence length statistics
- </flag>
+ Install miscellaneous scripts
+ </flag>
<flag name="rmathlib">
- Link to the standalone Rmathlib for statistical routines
- </flag>
+ Link to the standalone Rmathlib for statistical routines
+ </flag>
</use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2015-03-18 7:23 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2015-03-18 7:23 UTC (permalink / raw
To: gentoo-commits
commit: ba80f4042addbeb24766f8763c60e1322f4ac5bc
Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de>
AuthorDate: Wed Mar 18 00:09:04 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 18 07:23:22 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ba80f404
sci-biology/discrover: version bump; drop USE flag
Package-Manager: portage-2.2.14
sci-biology/discrover/ChangeLog | 6 ++++++
...scrover-1.5.2.ebuild => discrover-1.6.0.ebuild} | 18 ++---------------
sci-biology/discrover/discrover-9999.ebuild | 18 ++---------------
sci-biology/discrover/metadata.xml | 23 ++++++++++------------
4 files changed, 20 insertions(+), 45 deletions(-)
diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index aba75b4..f4e2dcd 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*discrover-1.6.0 (18 Mar 2015)
+
+ 18 Mar 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.6.0.ebuild,
+ -discrover-1.5.2.ebuild, discrover-9999.ebuild, metadata.xml:
+ sci-biology/discrover: version bump; drop USE flag
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> discrover-1.5.2.ebuild,
discrover-9999.ebuild, metadata.xml:
sci-biology/discrover: fix SLOT operators; correct ruby deps
diff --git a/sci-biology/discrover/discrover-1.5.2.ebuild b/sci-biology/discrover/discrover-1.6.0.ebuild
similarity index 83%
rename from sci-biology/discrover/discrover-1.5.2.ebuild
rename to sci-biology/discrover/discrover-1.6.0.ebuild
index f0992e2..5f1281c 100644
--- a/sci-biology/discrover/discrover-1.5.2.ebuild
+++ b/sci-biology/discrover/discrover-1.6.0.ebuild
@@ -3,11 +3,7 @@
# $Header: $
EAPI=5
-
-USE_RUBY="ruby19"
-RUBY_OPTIONAL=yes
-
-inherit cmake-utils ruby-fakegem
+inherit cmake-utils
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
@@ -16,21 +12,12 @@ SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
- tikzlogo? (
- $(ruby_implementations_depend)
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- dev-tex/pgf
- dev-tex/xcolor
- media-gfx/imagemagick
- )
- misc_scripts? ( $(ruby_implementations_depend) )
rmathlib? ( dev-lang/R )
tcmalloc? ( dev-util/google-perftools )
"
@@ -58,7 +45,6 @@ src_configure() {
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
$(cmake-utils_use_with lto LTO)
- $(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index 8131e9b..6958803 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -3,11 +3,7 @@
# $Header: $
EAPI=5
-
-USE_RUBY="ruby19"
-RUBY_OPTIONAL=yes
-
-inherit cmake-utils git-r3 ruby-fakegem
+inherit cmake-utils git-r3
DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
HOMEPAGE="https://github.com/maaskola/discrover"
@@ -17,21 +13,12 @@ EGIT_REPO_URI="https://github.com/maaskola/${PN}"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
RDEPEND="
dev-libs/boost
cairo? ( x11-libs/cairo )
dreme? ( sci-biology/meme )
- tikzlogo? (
- $(ruby_implementations_depend)
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- dev-tex/pgf
- dev-tex/xcolor
- media-gfx/imagemagick
- )
- misc_scripts? ( $(ruby_implementations_depend) )
rmathlib? ( dev-lang/R )
tcmalloc? ( dev-util/google-perftools )
"
@@ -59,7 +46,6 @@ src_configure() {
$(cmake-utils_use_with dreme DREME)
$(cmake-utils_use_with doc DOC)
$(cmake-utils_use_with lto LTO)
- $(cmake-utils_use_with tikzlogo TIKZLOGO)
$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
$(cmake-utils_use_with rmathlib RMATHLIB)
$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
index 6bfaf6c..fb652d7 100644
--- a/sci-biology/discrover/metadata.xml
+++ b/sci-biology/discrover/metadata.xml
@@ -7,22 +7,19 @@
</maintainer>
<use>
<flag name="cairo">
- Use Cairo for sequence logo plotting capabilities
- </flag>
+ Use Cairo for sequence logo plotting capabilities
+ </flag>
<flag name="dreme">
- Enable usage of DREME from the MEME package for seeding
- </flag>
+ Enable usage of DREME from the MEME package for seeding
+ </flag>
<flag name="lto">
- Compile with link-time optimization (LTO)
- </flag>
- <flag name="tikzlogo">
- Enable LaTeX/TikZ based ruby script for sequence logo drawing
- </flag>
+ Compile with link-time optimization (LTO)
+ </flag>
<flag name="misc_scripts">
- Install miscellaneous scripts, e.g. for sequence length statistics
- </flag>
+ Install miscellaneous scripts
+ </flag>
<flag name="rmathlib">
- Link to the standalone Rmathlib for statistical routines
- </flag>
+ Link to the standalone Rmathlib for statistical routines
+ </flag>
</use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/
@ 2020-09-27 4:32 Horea Christian
0 siblings, 0 replies; 9+ messages in thread
From: Horea Christian @ 2020-09-27 4:32 UTC (permalink / raw
To: gentoo-commits
commit: 0a98a3bfa820bf8ffd6d9258daa3a3469f15427a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 04:31:16 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 04:31:16 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a98a3bf
sci-biology/discrover: removed deprecated package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/discrover/discrover-1.6.0.ebuild | 78 ---------------------------
sci-biology/discrover/discrover-9999.ebuild | 79 ----------------------------
sci-biology/discrover/metadata.xml | 28 ----------
3 files changed, 185 deletions(-)
diff --git a/sci-biology/discrover/discrover-1.6.0.ebuild b/sci-biology/discrover/discrover-1.6.0.ebuild
deleted file mode 100644
index 5840283fd..000000000
--- a/sci-biology/discrover/discrover-1.6.0.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils
-
-DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
-HOMEPAGE="https://github.com/maaskola/discrover"
-SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
-
-RDEPEND="
- dev-libs/boost
- cairo? ( x11-libs/cairo )
- dreme? ( sci-biology/meme )
- rmathlib? ( dev-lang/R )
- tcmalloc? ( dev-util/google-perftools )
-"
-DEPEND="${RDEPEND}
- doc? (
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- dev-texlive/texlive-latexrecommended
- media-gfx/imagemagick
- )
- lto? ( >=sys-devel/gcc-4.8:* )
-"
-pkg_pretend() {
- if use lto; then
- if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
- eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
- eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
- die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
- fi
- fi
-}
-src_configure() {
- local mycmakeargs=(
- $(cmake-utils_use_with cairo CAIRO)
- $(cmake-utils_use_with dreme DREME)
- $(cmake-utils_use_with doc DOC)
- $(cmake-utils_use_with lto LTO)
- $(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
- $(cmake-utils_use_with rmathlib RMATHLIB)
- $(cmake-utils_use_with tcmalloc TCMALLOC)
- -DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
- )
-
- unset R_HOME
-
- if use rmathlib ; then
- echo
- elog "Using statistical routines from standalone Rmathlib."
- echo
- fi
- if use dreme ; then
- echo
- elog "Linking to DREME from the MEME suite."
- echo
- else
- echo
- elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
- elog "You will not be able to use DREME to find seeds."
- echo
- fi
-
- if use doc ; then
- echo
- elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
- echo
- fi
-
- cmake-utils_src_configure
-}
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
deleted file mode 100644
index 627f32059..000000000
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils git-r3
-
-DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
-HOMEPAGE="https://github.com/maaskola/discrover"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/maaskola/${PN}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
-
-RDEPEND="
- dev-libs/boost
- cairo? ( x11-libs/cairo )
- dreme? ( sci-biology/meme )
- rmathlib? ( dev-lang/R )
- tcmalloc? ( dev-util/google-perftools )
-"
-DEPEND="${RDEPEND}
- doc? (
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- dev-texlive/texlive-latexrecommended
- media-gfx/imagemagick
- )
- lto? ( >=sys-devel/gcc-4.8:* )
-"
-pkg_pretend() {
- if use lto; then
- if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
- eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
- eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
- die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
- fi
- fi
-}
-src_configure() {
- local mycmakeargs=(
- $(cmake-utils_use_with cairo CAIRO)
- $(cmake-utils_use_with dreme DREME)
- $(cmake-utils_use_with doc DOC)
- $(cmake-utils_use_with lto LTO)
- $(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
- $(cmake-utils_use_with rmathlib RMATHLIB)
- $(cmake-utils_use_with tcmalloc TCMALLOC)
- -DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
- )
-
- unset R_HOME
-
- if use rmathlib ; then
- echo
- elog "Using statistical routines from standalone Rmathlib."
- echo
- fi
- if use dreme ; then
- echo
- elog "Linking to DREME from the MEME suite."
- echo
- else
- echo
- elog "Not linking to DREME from the MEME suite (sci-biology/meme)."
- elog "You will not be able to use DREME to find seeds."
- echo
- fi
-
- if use doc ; then
- echo
- elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
- echo
- fi
-
- cmake-utils_src_configure
-}
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
deleted file mode 100644
index 6f5916ea8..000000000
--- a/sci-biology/discrover/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>jonas@maaskola.de</email>
- <name>Jonas Maaskola</name>
- </maintainer>
- <use>
- <flag name="cairo">
-Use Cairo for sequence logo plotting capabilities
-</flag>
- <flag name="dreme">
-Enable usage of DREME from the MEME package for seeding
-</flag>
- <flag name="lto">
-Compile with link-time optimization (LTO)
-</flag>
- <flag name="misc_scripts">
-Install miscellaneous scripts
-</flag>
- <flag name="rmathlib">
-Link to the standalone Rmathlib for statistical routines
-</flag>
- </use>
- <upstream>
- <remote-id type="github">maaskola/discrover</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
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