diff options
101 files changed, 537 insertions, 112 deletions
diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml index 513e8631c..6c001f352 100644 --- a/dev-java/htsjdk/metadata.xml +++ b/dev-java/htsjdk/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">picard</remote-id> + <remote-id type="github">samtools/htsjdk</remote-id> </upstream> </pkgmetadata> diff --git a/dev-libs/opencl-clhpp/metadata.xml b/dev-libs/opencl-clhpp/metadata.xml index 222c1e307..5ef422065 100644 --- a/dev-libs/opencl-clhpp/metadata.xml +++ b/dev-libs/opencl-clhpp/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> -</pkgmetadata>
\ No newline at end of file + <upstream> + <remote-id type="github">KhronosGroup/OpenCL-CLHPP</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/PeakUtils/metadata.xml b/dev-python/PeakUtils/metadata.xml index c39ab9b4e..a4c17d458 100644 --- a/dev-python/PeakUtils/metadata.xml +++ b/dev-python/PeakUtils/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -14,5 +14,6 @@ </longdescription> <upstream> <remote-id type="pypi">PeakUtils</remote-id> + <remote-id type="bitbucket">lucashnegri/peakutils</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/busfactor/metadata.xml b/dev-python/busfactor/metadata.xml index ec9fa9d47..edbc63649 100644 --- a/dev-python/busfactor/metadata.xml +++ b/dev-python/busfactor/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">SOM-Research/busfactor</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ffnet/metadata.xml b/dev-python/ffnet/metadata.xml index e40054cae..81dcc789e 100644 --- a/dev-python/ffnet/metadata.xml +++ b/dev-python/ffnet/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -8,11 +8,13 @@ <longdescription lang="en"> ffnet is a fast and easy-to-use feed-forward neural network training library for python. -</longdescription> + </longdescription> <use> <flag name="matplotlib">Use matplotlib for drawing</flag> </use> <upstream> <remote-id type="github">mrkwjc/ffnet</remote-id> + <remote-id type="pypi">ffnet</remote-id> + <remote-id type="sourceforge">ffnet</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/ffnetui/metadata.xml b/dev-python/ffnetui/metadata.xml index 6e1e5f91c..50cd8d0c5 100644 --- a/dev-python/ffnetui/metadata.xml +++ b/dev-python/ffnetui/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -7,8 +7,10 @@ </maintainer> <longdescription lang="en"> GUI for ffnet - feed forward neural network for python -</longdescription> + </longdescription> <upstream> <remote-id type="github">mrkwjc/ffnetui</remote-id> + <remote-id type="pypi">ffnetui</remote-id> + <remote-id type="sourceforge">ffnet</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/gitana/metadata.xml b/dev-python/gitana/metadata.xml index ec9fa9d47..221a98348 100644 --- a/dev-python/gitana/metadata.xml +++ b/dev-python/gitana/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">SOM-Research/gitana</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/matplotlib-venn/metadata.xml b/dev-python/matplotlib-venn/metadata.xml index 01447d81f..8401ce8b5 100644 --- a/dev-python/matplotlib-venn/metadata.xml +++ b/dev-python/matplotlib-venn/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="github">matplotlib-venn</remote-id> + <remote-id type="pypi">matplotlib-venn</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/py2bit/metadata.xml b/dev-python/py2bit/metadata.xml index f68a1b6fa..71d7d5a6a 100644 --- a/dev-python/py2bit/metadata.xml +++ b/dev-python/py2bit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">dpryan79/py2bit</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml index f68a1b6fa..764884a58 100644 --- a/dev-python/pyBigWig/metadata.xml +++ b/dev-python/pyBigWig/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">dpryan79/pyBigWig</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/shove/metadata.xml b/dev-python/shove/metadata.xml index f68a1b6fa..a5faa4b26 100644 --- a/dev-python/shove/metadata.xml +++ b/dev-python/shove/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lcrees/shove</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml index 63e701edd..9fb8f07d6 100644 --- a/dev-python/snakemake/metadata.xml +++ b/dev-python/snakemake/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,7 @@ </maintainer> <upstream> <remote-id type="github">dev-python/snakemake</remote-id> + <remote-id type="bitbucket">johanneskoester/snakemake</remote-id> + <remote-id type="pypi">snakemake</remote-id> </upstream> </pkgmetadata> diff --git a/dev-util/emscripten-fastcomp/metadata.xml b/dev-util/emscripten-fastcomp/metadata.xml index d9e70962e..ee38ab80a 100644 --- a/dev-util/emscripten-fastcomp/metadata.xml +++ b/dev-util/emscripten-fastcomp/metadata.xml @@ -1,8 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>harald.weiner@jku.at</email> <name>Harald Weiner</name> </maintainer> + <upstream> + <remote-id type="github">kripken/emscripten-fastcomp-clang</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-util/emscripten/metadata.xml b/dev-util/emscripten/metadata.xml index d9e70962e..bbd406949 100644 --- a/dev-util/emscripten/metadata.xml +++ b/dev-util/emscripten/metadata.xml @@ -1,8 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>harald.weiner@jku.at</email> <name>Harald Weiner</name> </maintainer> + <upstream> + <remote-id type="github">kripken/emscripten</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-util/mad-numdiff/metadata.xml b/dev-util/mad-numdiff/metadata.xml index 7ec6883d7..729575510 100644 --- a/dev-util/mad-numdiff/metadata.xml +++ b/dev-util/mad-numdiff/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-physics@gentoo.org</email> <name>Gentoo Physics Project</name> </maintainer> + <upstream> + <remote-id type="github">quinoacomputing/ndiff</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Fastaq/metadata.xml b/sci-biology/Fastaq/metadata.xml index f68a1b6fa..04b6bd54b 100644 --- a/sci-biology/Fastaq/metadata.xml +++ b/sci-biology/Fastaq/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">sanger-pathogens/Fastaq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml index f68a1b6fa..cfa9e50ee 100644 --- a/sci-biology/MolBioLib/metadata.xml +++ b/sci-biology/MolBioLib/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">molbiolib</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Rcorrector/metadata.xml b/sci-biology/Rcorrector/metadata.xml index 1699e58b2..7cca6fb36 100644 --- a/sci-biology/Rcorrector/metadata.xml +++ b/sci-biology/Rcorrector/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">mourisl/Rcorrector</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Scaffolder-evaluation/metadata.xml b/sci-biology/Scaffolder-evaluation/metadata.xml index f68a1b6fa..ede9259b5 100644 --- a/sci-biology/Scaffolder-evaluation/metadata.xml +++ b/sci-biology/Scaffolder-evaluation/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">martinghunt/Scaffolder-evaluation</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml index f68a1b6fa..c7accda31 100644 --- a/sci-biology/SnpEff/metadata.xml +++ b/sci-biology/SnpEff/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">snpeff</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/VarScan-bin/metadata.xml b/sci-biology/VarScan-bin/metadata.xml index fae01f1fa..e27dba2e9 100644 --- a/sci-biology/VarScan-bin/metadata.xml +++ b/sci-biology/VarScan-bin/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">varscan</remote-id> + <remote-id type="github">dkoboldt/varscan</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/VarScan/metadata.xml b/sci-biology/VarScan/metadata.xml index fae01f1fa..e27dba2e9 100644 --- a/sci-biology/VarScan/metadata.xml +++ b/sci-biology/VarScan/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">varscan</remote-id> + <remote-id type="github">dkoboldt/varscan</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/assembly-stats/metadata.xml b/sci-biology/assembly-stats/metadata.xml index f68a1b6fa..e528fb05f 100644 --- a/sci-biology/assembly-stats/metadata.xml +++ b/sci-biology/assembly-stats/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">martinghunt/assembly-stats</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bam-readcount/metadata.xml b/sci-biology/bam-readcount/metadata.xml index f68a1b6fa..2f50f6cb0 100644 --- a/sci-biology/bam-readcount/metadata.xml +++ b/sci-biology/bam-readcount/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">genome/bam-readcount</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bedops/Manifest b/sci-biology/bedops/Manifest new file mode 100644 index 000000000..54a156cc2 --- /dev/null +++ b/sci-biology/bedops/Manifest @@ -0,0 +1 @@ +DIST bedops-2.4.26.tar.gz 27057360 SHA256 9b8ff43beec7b6e327179477b800a9c7ce98a010bbf59ba41fc2d7da9869586d SHA512 6c43ff4f42168da8e181e5d50e8d41a1c0a8c24bde3ca6ab81f9b2324d47b4f7d265e3031adf39ea7ad0e65773462d13ed59580774f5a0906b205b27648a8eaa WHIRLPOOL ad25d562dee5a51f10ee66d5a74984071b6aaddb1cde139b8fa2b420a2b6b10860c389eaf59f74c5fabc09851629f366747e7330432c0aa9c9d174606a3ffbfb diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild new file mode 100644 index 000000000..d281fbede --- /dev/null +++ b/sci-biology/bedops/bedops-2.4.26.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs eutils + +DESCRIPTION="Manipulate BED file (alternative to bedtools)" +HOMEPAGE="http://bedops.readthedocs.io + https://github.com/bedops/bedops" +SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + default + local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch) + epatch ${PATCHES[@]} +} diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch new file mode 100644 index 000000000..16ac4e2b0 --- /dev/null +++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch @@ -0,0 +1,138 @@ +--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200 +@@ -28,7 +28,7 @@ + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} + STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ +-BLDFLAGS = -O3 ${STDFLAGS} ++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} + + + FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} +--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200 +@@ -24,7 +24,7 @@ + INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} +-BLDFLAGS = -Wall -pedantic -O3 -std=c++11 ++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 + SFLAGS = -static + + dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding +@@ -64,4 +64,4 @@ + rm -rf $(OBJDIR) + rm -f $(BINDIR)/$(PROG) + rm -f $(BINDIR)/*.$(PROG) +- rm -rf $(BINDIR) +\ No newline at end of file ++ rm -rf $(BINDIR) +--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200 +@@ -28,7 +28,7 @@ + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} + STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ +-BLDFLAGS = -O3 ${STDFLAGS} ++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} + + FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} + +--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200 +@@ -23,7 +23,7 @@ + INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} +-BLDFLAGS = -Wall -pedantic -O3 -std=c++11 ++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 + SFLAGS = -static + + dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding +--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200 +@@ -1,7 +1,7 @@ + MIN_OSX_VERSION = 10.7 + BLDFLAGS = -Wall -Wextra -pedantic -std=c99 + COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 +-CFLAGS = -O3 ++CFLAGS = ${CXXFLAGS:--O3} + CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline + CPFLAGS = -pg + LIBS = -lpthread +--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200 +@@ -1,6 +1,6 @@ + BLDFLAGS = -Wall -Wextra -pedantic -std=c99 + COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 +-CFLAGS = -O3 ++CFLAGS = ${CXXFLAGS:--O3} + CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline + CPFLAGS = -pg + LIBS = -lpthread +--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200 +@@ -27,7 +27,7 @@ + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} + STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ +-BLDFLAGS = -O3 ${STDFLAGS} ++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} + + FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} + +--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200 +@@ -25,7 +25,7 @@ + INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} +-BLDFLAGS = -Wall -pedantic -O3 -std=c++11 ++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 + SFLAGS = -static + + dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding +--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200 +@@ -28,7 +28,7 @@ + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} + STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ +-BLDFLAGS = -O3 ${STDFLAGS} ++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} + + FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} + +--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200 +@@ -23,7 +23,7 @@ + INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} + LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} + LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} +-BLDFLAGS = -Wall -pedantic -O3 -std=c++11 ++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 + SFLAGS = -static + + dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding +--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200 +@@ -7,7 +7,7 @@ + PROG = sort-bed + DIST_DIR = ../bin + OBJ_DIR = objects_${ARCH} +-OPTIMIZE = -O3 -std=c++11 -stdlib=libc++ ++OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++ + WARNINGS = -Wall + MAIN = ../../../.. + HEAD = ${MAIN}/interfaces/general-headers +--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200 +@@ -29,7 +29,7 @@ + BINDIR = ../bin + OBJDIR = objects + WARNINGS = -Wall -Wextra -pedantic +-BLDFLAGS = ${WARNINGS} -O3 -std=c++11 ++BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11 + SFLAGS = -static + + dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/bedops/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml index f68a1b6fa..45f337087 100644 --- a/sci-biology/bfast/metadata.xml +++ b/sci-biology/bfast/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">bfast</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bio-cd-hit-report/metadata.xml b/sci-biology/bio-cd-hit-report/metadata.xml index f68a1b6fa..ed211409a 100644 --- a/sci-biology/bio-cd-hit-report/metadata.xml +++ b/sci-biology/bio-cd-hit-report/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="rubygems">bio-cd-hit-report</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml index 2880d6633..1f3b07521 100644 --- a/sci-biology/cd-hit/metadata.xml +++ b/sci-biology/cd-hit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -19,8 +19,9 @@ datasets and identifies the sequences in db2 that are similar to db1 above a threshold. CD-HIT-454 is a program to identify natural and artificial duplicates from pyrosequencing reads. The usage of other programs and scripts can be found in CD-HIT user's guide. -</longdescription> + </longdescription> <upstream> <remote-id type="google-code">cdhit</remote-id> + <remote-id type="github">weizhongli/cdhit</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml index f68a1b6fa..8d38b0b1a 100644 --- a/sci-biology/conrad/metadata.xml +++ b/sci-biology/conrad/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">conradcrf</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml index f68a1b6fa..0a1821f4a 100644 --- a/sci-biology/cramtools/metadata.xml +++ b/sci-biology/cramtools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">enasequence/cramtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/cross_genome/metadata.xml b/sci-biology/cross_genome/metadata.xml index f68a1b6fa..18786886b 100644 --- a/sci-biology/cross_genome/metadata.xml +++ b/sci-biology/cross_genome/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">phusion2</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml index dde730ca4..d432ff9a4 100644 --- a/sci-biology/cutadapt/metadata.xml +++ b/sci-biology/cutadapt/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">cutadapt</remote-id> + <remote-id type="github">marcelm/cutadapt</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/deeptools/metadata.xml b/sci-biology/deeptools/metadata.xml index f68a1b6fa..ae7de7d62 100644 --- a/sci-biology/deeptools/metadata.xml +++ b/sci-biology/deeptools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">fidelram/deepTools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml index f68a1b6fa..2457da65b 100644 --- a/sci-biology/ensembl-tools/metadata.xml +++ b/sci-biology/ensembl-tools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">Ensembl/ensembl-tools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fgap-bin/metadata.xml b/sci-biology/fgap-bin/metadata.xml index f68a1b6fa..59e8a4413 100644 --- a/sci-biology/fgap-bin/metadata.xml +++ b/sci-biology/fgap-bin/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">fgap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fgap/metadata.xml b/sci-biology/fgap/metadata.xml index f68a1b6fa..59e8a4413 100644 --- a/sci-biology/fgap/metadata.xml +++ b/sci-biology/fgap/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">fgap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/flexbar/metadata.xml b/sci-biology/flexbar/metadata.xml index ce8e58909..6bf81a0d4 100644 --- a/sci-biology/flexbar/metadata.xml +++ b/sci-biology/flexbar/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">flexbar</remote-id> + <remote-id type="github">seqan/flexbar</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml index f68a1b6fa..745bce5e5 100644 --- a/sci-biology/gemini/metadata.xml +++ b/sci-biology/gemini/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">arq5x/gemini</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/grabix/metadata.xml b/sci-biology/grabix/metadata.xml index f68a1b6fa..5ad9ab32c 100644 --- a/sci-biology/grabix/metadata.xml +++ b/sci-biology/grabix/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">arq5x/grabix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml index 1699e58b2..8563b702d 100644 --- a/sci-biology/grass/metadata.xml +++ b/sci-biology/grass/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">AlexeyG/GRASS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml index f68a1b6fa..b28711aa3 100644 --- a/sci-biology/hisat2/metadata.xml +++ b/sci-biology/hisat2/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">infphilo/hisat2</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/hts-python/metadata.xml b/sci-biology/hts-python/metadata.xml index f68a1b6fa..39221baa1 100644 --- a/sci-biology/hts-python/metadata.xml +++ b/sci-biology/hts-python/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">brentp/hts-python</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jannovar-bin/metadata.xml b/sci-biology/jannovar-bin/metadata.xml index 1699e58b2..faceb6e46 100644 --- a/sci-biology/jannovar-bin/metadata.xml +++ b/sci-biology/jannovar-bin/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">charite/jannovar</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jannovar/metadata.xml b/sci-biology/jannovar/metadata.xml index f68a1b6fa..faceb6e46 100644 --- a/sci-biology/jannovar/metadata.xml +++ b/sci-biology/jannovar/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">charite/jannovar</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jtreeview-bin/metadata.xml b/sci-biology/jtreeview-bin/metadata.xml index f68a1b6fa..40552f721 100644 --- a/sci-biology/jtreeview-bin/metadata.xml +++ b/sci-biology/jtreeview-bin/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">jtreeview</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml index 3b98c8e27..a7083bff9 100644 --- a/sci-biology/jtreeview/metadata.xml +++ b/sci-biology/jtreeview/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">jtreeview</remote-id> + <remote-id type="bitbucket">TreeView3Dev/treeview3</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/karect/metadata.xml b/sci-biology/karect/metadata.xml index f68a1b6fa..0ac12d618 100644 --- a/sci-biology/karect/metadata.xml +++ b/sci-biology/karect/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">aminallam/karect</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml index f68a1b6fa..5561548a6 100644 --- a/sci-biology/kat/metadata.xml +++ b/sci-biology/kat/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">TGAC/KAT</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/libBigWig/metadata.xml b/sci-biology/libBigWig/metadata.xml index f68a1b6fa..dafe9d1fd 100644 --- a/sci-biology/libBigWig/metadata.xml +++ b/sci-biology/libBigWig/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">dpryan79/libBigWig</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/lumpy-sv/metadata.xml b/sci-biology/lumpy-sv/metadata.xml index f68a1b6fa..27a0e1f28 100644 --- a/sci-biology/lumpy-sv/metadata.xml +++ b/sci-biology/lumpy-sv/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">arq5x/lumpy-sv</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/megahit/metadata.xml b/sci-biology/megahit/metadata.xml index f68a1b6fa..deaf720d8 100644 --- a/sci-biology/megahit/metadata.xml +++ b/sci-biology/megahit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">voutcn/megahit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml index 959160fe4..9afdf8282 100644 --- a/sci-biology/mothur/metadata.xml +++ b/sci-biology/mothur/metadata.xml @@ -1,8 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">mothur/mothur</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest index b9f25caf1..c0683d041 100644 --- a/sci-biology/ncbi-blast+/Manifest +++ b/sci-biology/ncbi-blast+/Manifest @@ -1,3 +1,3 @@ DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 SHA256 26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40 SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17 WHIRLPOOL 64f63fdf1502f3d069ffa645b378fb50469d689b70eefbbc85e04bbe4ae896d1e4dfc860a81e2d7c27bc9484eb6a9651ac02ee1d712b9a511d33a9be241154e9 DIST ncbi-blast-2.2.31+-src.tar.gz 18971327 SHA256 f0960e8af2a6021fde6f2513381493641f687453a804239a7e598649b432f8a5 SHA512 2681a4394cc250d1ee545cd85dc962d73b1dbbdd987790a029bf51a58e74cbb08b5c8cf4a02b9b7c95916e3fb0d1613e2ed8631bb7ad683156759421081bb4ca WHIRLPOOL 65e93f87d4c48d8c44cf90c672bdb2035ddb960a388d46f6438c113972392ac23ec0b859a4ecf9c3493c4ee7739dc1f54e545f2758aa889c61d0d95ef9f0a173 -DIST ncbi-blast-2.3.0+-src.tar.gz 19233464 SHA256 7ce8dc62f58141b6cdcd56b55ea3c17bea7a672e6256dfd725e6ef94825e94e9 SHA512 de1002eecf062f3cae61eaec5561a7d8a6118dbcaf243899421a49ebd98f1f7aa54b86d7478445ff6109b0b09645d4969a6ce947a968093d92c41c335ec1c600 WHIRLPOOL 6cec5490251701d8e1e5200144eaa22bfaaa110499b143c832d8f86daf34d214f9871566e65767a44e66fef0b95c01f43a6ab02b985e5b6c3bf25dc3d4a7d3ae +DIST ncbi-blast-2.6.0+-src.tar.gz 20025526 SHA256 0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996 SHA512 ea6444892a0b10459193d33d243b5960ad206b702e01e94a554a5ebda0291ff45e1ce43479713c23a96eba676b40bb8c57a7ef9dd2118729feef6b2cd98560c6 WHIRLPOOL 1283f8b6eb04e910245963bc2931d2de88bc21128266c28c16ed65b8365e0b12909d3395035c0cf7a19ee7924cea4facc1dd3246175f10dd5e64dcb12a1061a3 diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild index 7791cf3e5..6adbefad3 100644 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild +++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -239,7 +239,9 @@ src_configure() { $(use_with mesa mesa "${EPREFIX}/usr") $(use_with opengl glut "${EPREFIX}/usr") $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) + # + # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 + # $(use_with opengl glew-mx) $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") $(use_with wxwidgets wxwidgets-ucs) $(use_with freetype freetype "${EPREFIX}/usr") @@ -264,6 +266,8 @@ src_configure() { $(use_with curl curl "${EPREFIX}/usr") # $(use_with X x "${EPREFIX}/usr") # $(use_with X x) # there is no --with-x option + # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution + --without-vdb ) # http://www.ncbi.nlm.nih.gov/books/NBK7167/ diff --git a/sci-biology/nilearn/metadata.xml b/sci-biology/nilearn/metadata.xml index 7fee88bbe..3954d1f57 100644 --- a/sci-biology/nilearn/metadata.xml +++ b/sci-biology/nilearn/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -19,5 +19,6 @@ </use> <upstream> <remote-id type="pypi">nilearn</remote-id> + <remote-id type="github">nilearn/nilearn</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/nwalign/metadata.xml b/sci-biology/nwalign/metadata.xml index 1699e58b2..d5c7b72f2 100644 --- a/sci-biology/nwalign/metadata.xml +++ b/sci-biology/nwalign/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="pypi">nwalign</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/nxtrim/metadata.xml b/sci-biology/nxtrim/metadata.xml index f68a1b6fa..b4b118dab 100644 --- a/sci-biology/nxtrim/metadata.xml +++ b/sci-biology/nxtrim/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">sequencing/NxTrim</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/oncotator/metadata.xml b/sci-biology/oncotator/metadata.xml index f68a1b6fa..4f2a2f45a 100644 --- a/sci-biology/oncotator/metadata.xml +++ b/sci-biology/oncotator/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">broadinstitute/oncotator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/perga/metadata.xml b/sci-biology/perga/metadata.xml index f68a1b6fa..be641f1a0 100644 --- a/sci-biology/perga/metadata.xml +++ b/sci-biology/perga/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">hitbio/PERGA</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml index 1699e58b2..d0f646374 100644 --- a/sci-biology/phusion2/metadata.xml +++ b/sci-biology/phusion2/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">downloads</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml index 513e8631c..4ec209225 100644 --- a/sci-biology/picard/metadata.xml +++ b/sci-biology/picard/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">picard</remote-id> + <remote-id type="github">broadinstitute/picard</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/prinseq-lite/metadata.xml b/sci-biology/prinseq-lite/metadata.xml index f68a1b6fa..d5c8298fe 100644 --- a/sci-biology/prinseq-lite/metadata.xml +++ b/sci-biology/prinseq-lite/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">prinseq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/psychopy/metadata.xml b/sci-biology/psychopy/metadata.xml index c74323f81..e5d49f5cb 100644 --- a/sci-biology/psychopy/metadata.xml +++ b/sci-biology/psychopy/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">psychpy</remote-id> + <remote-id type="github">psychopy/psychopy</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/pybrain/metadata.xml b/sci-biology/pybrain/metadata.xml index 8425c0d53..0ac4c31dd 100644 --- a/sci-biology/pybrain/metadata.xml +++ b/sci-biology/pybrain/metadata.xml @@ -1,8 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">pybrain/pybrain</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml index f68a1b6fa..1bd906efe 100644 --- a/sci-biology/pysamstats/metadata.xml +++ b/sci-biology/pysamstats/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,8 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">alimanfoo/pysamstats</remote-id> + <remote-id type="pypi">pysamstats</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ruffus/metadata.xml b/sci-biology/ruffus/metadata.xml index 1699e58b2..5541360c7 100644 --- a/sci-biology/ruffus/metadata.xml +++ b/sci-biology/ruffus/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="pypi">ruffus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml index f68a1b6fa..ab03f4219 100644 --- a/sci-biology/sambamba/metadata.xml +++ b/sci-biology/sambamba/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lomereiter/sambamba</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_blast/metadata.xml b/sci-biology/scbi_blast/metadata.xml index 5c826014b..dd1623955 100644 --- a/sci-biology/scbi_blast/metadata.xml +++ b/sci-biology/scbi_blast/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + <remote-id type="rubygems">scbi_blast</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_fasta/metadata.xml b/sci-biology/scbi_fasta/metadata.xml index 5c826014b..f8f3e47a2 100644 --- a/sci-biology/scbi_fasta/metadata.xml +++ b/sci-biology/scbi_fasta/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + <remote-id type="rubygems">scbi_fasta</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_fastq/metadata.xml b/sci-biology/scbi_fastq/metadata.xml index f68a1b6fa..69f445f42 100644 --- a/sci-biology/scbi_fastq/metadata.xml +++ b/sci-biology/scbi_fastq/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="rubygems">scbi_fastq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_mapreduce/metadata.xml b/sci-biology/scbi_mapreduce/metadata.xml index 5c826014b..a39eed183 100644 --- a/sci-biology/scbi_mapreduce/metadata.xml +++ b/sci-biology/scbi_mapreduce/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + <remote-id type="rubygems">scbi_mapreduce</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_plot/metadata.xml b/sci-biology/scbi_plot/metadata.xml index 5c826014b..5e2713549 100644 --- a/sci-biology/scbi_plot/metadata.xml +++ b/sci-biology/scbi_plot/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + <remote-id type="rubygems">scbi_plot</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/scbi_zcat/metadata.xml b/sci-biology/scbi_zcat/metadata.xml index f68a1b6fa..a55e8612a 100644 --- a/sci-biology/scbi_zcat/metadata.xml +++ b/sci-biology/scbi_zcat/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="rubygems">scbi_zcat</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/smalt/metadata.xml b/sci-biology/smalt/metadata.xml index 1699e58b2..4b2ca765e 100644 --- a/sci-biology/smalt/metadata.xml +++ b/sci-biology/smalt/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">smalt</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/snpomatic/metadata.xml b/sci-biology/snpomatic/metadata.xml index f68a1b6fa..47ff2f6ab 100644 --- a/sci-biology/snpomatic/metadata.xml +++ b/sci-biology/snpomatic/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">magnusmanske/snpomatic</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml index f68a1b6fa..d931eaf33 100644 --- a/sci-biology/somatic-sniper/metadata.xml +++ b/sci-biology/somatic-sniper/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">genome/somatic-sniper</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml index f68a1b6fa..73d16b005 100644 --- a/sci-biology/staden_doc/metadata.xml +++ b/sci-biology/staden_doc/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">staden</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/stringtie/metadata.xml b/sci-biology/stringtie/metadata.xml index f68a1b6fa..b909ea058 100644 --- a/sci-biology/stringtie/metadata.xml +++ b/sci-biology/stringtie/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gpertea/stringtie</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/vcflib/metadata.xml b/sci-biology/vcflib/metadata.xml index f68a1b6fa..ce295b942 100644 --- a/sci-biology/vcflib/metadata.xml +++ b/sci-biology/vcflib/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">vcflib/vcflib</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml index 77f6f92e0..6c22d1920 100644 --- a/sci-biology/vcftools/metadata.xml +++ b/sci-biology/vcftools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="sourceforge">vcftools</remote-id> + <remote-id type="github">vcftools/vcftools</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/verifyBamID/metadata.xml b/sci-biology/verifyBamID/metadata.xml index f68a1b6fa..41b69bc9c 100644 --- a/sci-biology/verifyBamID/metadata.xml +++ b/sci-biology/verifyBamID/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">statgen/libStatGen</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/vt/metadata.xml b/sci-biology/vt/metadata.xml index f68a1b6fa..ab18754bf 100644 --- a/sci-biology/vt/metadata.xml +++ b/sci-biology/vt/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">atks/vt</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/yaha/metadata.xml b/sci-biology/yaha/metadata.xml index f68a1b6fa..4d610cc7e 100644 --- a/sci-biology/yaha/metadata.xml +++ b/sci-biology/yaha/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">GregoryFaust/yaha</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml index 19df98469..fa784e844 100644 --- a/sci-chemistry/wxmacmolplt/metadata.xml +++ b/sci-chemistry/wxmacmolplt/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -17,4 +17,7 @@ Add support for flash movie generation using <pkg>media-libs/ming</pkg> </flag> </use> + <upstream> + <remote-id type="github">brettbode/wxmacmolplt</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/arrayfire/metadata.xml b/sci-libs/arrayfire/metadata.xml index 9903267a4..994d7bb3d 100644 --- a/sci-libs/arrayfire/metadata.xml +++ b/sci-libs/arrayfire/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -36,4 +36,7 @@ Build Backend-Independent API. </flag> </use> + <upstream> + <remote-id type="github">google/googletest</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/bloom/metadata.xml b/sci-libs/bloom/metadata.xml index 1699e58b2..ea4817fa3 100644 --- a/sci-libs/bloom/metadata.xml +++ b/sci-libs/bloom/metadata.xml @@ -1,12 +1,15 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">arashpartow/bloom</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/dtk/metadata.xml b/sci-libs/dtk/metadata.xml index ec9fa9d47..92ff8e86b 100644 --- a/sci-libs/dtk/metadata.xml +++ b/sci-libs/dtk/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">d-tk/dtk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/lib2bit/metadata.xml b/sci-libs/lib2bit/metadata.xml index f68a1b6fa..1f37ac0f9 100644 --- a/sci-libs/lib2bit/metadata.xml +++ b/sci-libs/lib2bit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">dpryan79/lib2bit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libStatGen/metadata.xml b/sci-libs/libStatGen/metadata.xml index f68a1b6fa..41b69bc9c 100644 --- a/sci-libs/libStatGen/metadata.xml +++ b/sci-libs/libStatGen/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">statgen/libStatGen</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/lmfit/metadata.xml b/sci-libs/lmfit/metadata.xml index 8425c0d53..a4573ac05 100644 --- a/sci-libs/lmfit/metadata.xml +++ b/sci-libs/lmfit/metadata.xml @@ -1,8 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="sourceforge">lmfit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/nexus/metadata.xml b/sci-libs/nexus/metadata.xml index 4ef50910d..901161d45 100644 --- a/sci-libs/nexus/metadata.xml +++ b/sci-libs/nexus/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -23,4 +23,7 @@ <flag name="java">Build the Java bindings</flag> <flag name="utils">Build optional utility applications</flag> </use> + <upstream> + <remote-id type="github">nexusformat/code</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/nipype/metadata.xml b/sci-libs/nipype/metadata.xml index c9064b1ae..8e5a54081 100644 --- a/sci-libs/nipype/metadata.xml +++ b/sci-libs/nipype/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -23,5 +23,6 @@ </longdescription> <upstream> <remote-id type="sourceforge">nipy</remote-id> + <remote-id type="github">nipy/nipype</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/pmx/metadata.xml b/sci-libs/pmx/metadata.xml index 988041704..cb2e5209a 100644 --- a/sci-libs/pmx/metadata.xml +++ b/sci-libs/pmx/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -13,4 +13,7 @@ functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations. </longdescription> + <upstream> + <remote-id type="github">dseeliger/pmx</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/shtools/metadata.xml b/sci-libs/shtools/metadata.xml index bacae8d93..518b8e2dd 100644 --- a/sci-libs/shtools/metadata.xml +++ b/sci-libs/shtools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -15,4 +15,7 @@ reconstructions, rotations of data expressed in spherical harmonics, and multitaper spectral analyses on the sphere. </longdescription> + <upstream> + <remote-id type="github">SHTOOLS/SHTOOLS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/dolfin/metadata.xml b/sci-mathematics/dolfin/metadata.xml index 70a8a021f..c45db3d3e 100644 --- a/sci-mathematics/dolfin/metadata.xml +++ b/sci-mathematics/dolfin/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -7,19 +7,20 @@ </maintainer> <longdescription lang="en"> DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations. -</longdescription> + </longdescription> <use> <flag name="cgal">Adds support for geometric algorithms with <pkg>sci-mathematics/cgal</pkg></flag> <flag name="cholmod">Adds support for sparse Cholesky factorization with <pkg>sci-libs/cholmod</pkg></flag> - <flag name="hdf5">Adds support for <pkg>sci-libs/hdf5</pkg></flag> + <flag name="hdf5">Adds support for <pkg>sci-libs/hdf5</pkg></flag> <flag name="parmetis">Adds support for parallel graph partitioning with <pkg>sci-libs/parmetis</pkg></flag> - <flag name="petsc">Adds support for numerical linear algebra toolkit <pkg>sci-mathematics/petsc</pkg></flag> + <flag name="petsc">Adds support for numerical linear algebra toolkit <pkg>sci-mathematics/petsc</pkg></flag> <flag name="scotch">Adds support for graph partitioning with <pkg>sci-libs/scotch</pkg></flag> - <flag name="trilinos">Adds support for numerical linear algebra toolkit <pkg>sci-libs/trilinos</pkg></flag> + <flag name="trilinos">Adds support for numerical linear algebra toolkit <pkg>sci-libs/trilinos</pkg></flag> <flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag> <flag name="vtk">Adds support for the visualization toolkit <pkg>sci-libs/vtk</pkg></flag> </use> <upstream> <remote-id type="launchpad">dolfin</remote-id> + <remote-id type="bitbucket">fenics-project/dolfin</remote-id> </upstream> </pkgmetadata> diff --git a/sci-mathematics/mathics/metadata.xml b/sci-mathematics/mathics/metadata.xml index 9cb351fa7..d2e5a63b0 100644 --- a/sci-mathematics/mathics/metadata.xml +++ b/sci-mathematics/mathics/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> @@ -18,4 +18,7 @@ However, Mathics is in no way affiliated or supported by Wolfram. Mathics will probably never have the power to compete with Mathematica® in industrial applications; yet, it might be an interesting alternative for educational purposes. </longdescription> + <upstream> + <remote-id type="github">mathics/Mathics</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml index 3be7b5248..04bcf9b8c 100644 --- a/sci-mathematics/tisean/metadata.xml +++ b/sci-mathematics/tisean/metadata.xml @@ -1,8 +1,11 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>jlec@gentoo.org</email> <name>Justin Lecher (jlec)</name> </maintainer> + <upstream> + <remote-id type="github">heggus/Tisean</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/mitlm/metadata.xml b/sci-misc/mitlm/metadata.xml index 5e38f5236..05123bc6e 100644 --- a/sci-misc/mitlm/metadata.xml +++ b/sci-misc/mitlm/metadata.xml @@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,6 +9,9 @@ designed for the efficient estimation of statistical n-gram language models involving iterative parameter estimation. It achieves much of its efficiency through the use of a compact - vector representation of n-grams. + vector representation of n-grams. </longdescription> + <upstream> + <remote-id type="github">mitlm/mitlm</remote-id> + </upstream> </pkgmetadata> |