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* [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/
@ 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
* [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/
@ 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/
@ 2015-01-31 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/
@ 2015-01-06  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/
@ 2015-01-06  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/
@ 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/
@ 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
end of thread, other threads:[~2020-09-27  4:32 UTC | newest]

Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
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2015-03-18  7:23 Justin Lecher
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2015-01-31 20:19 Christoph Junghans
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