biology/trowel/trowel-0.1.4.1.ebuild sci-chemistry/pesto/pesto-9999.ebuild sci-libs/fdlibm/fdlibm-5.3.ebuild sci-libs/geom/geom-5.1.2.7.ebuild sci-libs/libmatheval/libmatheval-1.1.10.ebuild sci-libs/modglue/modglue-1.19.ebuild sci-libs/pytorch/pytorch-1.4.0_p0-r1.ebuild sci-libs/zarja/zarja-1.1.1.ebuild sci-mathematics/cipi/cipi-1.0.ebuild sci-mathematics/lie/lie-2.2.2.ebuild sci-mathematics/netgen/netgen-4.9.13.ebuild sci-mathematics/netgen/netgen-5.0.0.ebuild sci-mathematics/netgen/netgen-5.3.1.ebuild sci-mathematics/scilab/scilab-5.5.2-r1.ebuild sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild sci-misc/elmer-meta/elmer-meta-9999.ebuild sci-physics/genfit/genfit-02.00.00.ebuild sci-physics/genfit/genfit-9999.ebuild X-VCS-Directories: sci-biology/OBO-Edit/ sci-biology/staden_doc/ sci-biology/NGSEPcore/ sci-biology/SnpEff/ dev-java/jogl/ sci-biology/glean/ sci-biology/IMAGE/ sci-biology/skewer-bin/ sci-biology/manatee-igs/ sci-mathematics/scilab/ sci-biology/subread/ sci-biology/bambus/ sci-biology/FLASH/ sci-misc/elmer-meta/ sci-biology/parafly/ sci-biology/jtreeview/ sci-biology/quast/ sci-biology/jtreeview-bin/ sci-biology/kraken/ sci-mathematics/netgen/ app-doc/blacs-docs/ sci-biology/BBmap/ sci-biology/estscan/ sci-biology/staden/ sci-biology/trowel/ dev-lang/icc/ sci-biology/SolexaQA/ sci-biology/conrad/ sci-biology/InterMine/ sci-biology/lucy/ sci-biology/screed/ sci-libs/modglue/ sci-chemistry/pesto/ sci-mathematics/lie/ sci-biology/smalt/ sci-biology/clview/ sci-libs/libmatheval/ sci-biology/autoeditor/ sci-biology/tigr-foundation-libs/ sci-physics/genfit/ sci-libs/geom/ sci-biology/cortex_var/ sci-libs/zarja/ sci-libs/fdlibm/ sci-biology/NGSEPcore/files/ dev-java/hdf-java/ sci-mathemati cs/cipi/ sci-biology/samstat/ sci-biology/scaffold_builder/ sci-libs/pytorch/ X-VCS-Committer: epsilon-0 X-VCS-Committer-Name: Aisha Tammy X-VCS-Revision: a04795846141641b7608b245d7ae06d33d721985 X-VCS-Branch: master Date: Tue, 29 Dec 2020 19:45:30 +0000 (UTC)
commit: a04795846141641b7608b245d7ae06d33d721985 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Dec 29 14:15:11 2020 +0000 Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc> CommitDate: Tue Dec 29 19:45:21 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0479584 */* misc fixes to make repoman happier - http to https where possible - remove some blank lines - quote unqouted variables - fdo-mime to xdg-utils - clean up profiles/ - clean up licenses Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> Closes: https://github.com/gentoo/sci/pull/999 Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc> app-doc/blacs-docs/blacs-docs-1.1.ebuild | 4 ++-- dev-java/hdf-java/hdf-java-2.9.ebuild | 10 +++++----- dev-java/jogl/jogl-2.1.4.ebuild | 4 ++-- dev-java/jogl/jogl-2.2.4.ebuild | 4 ++-- dev-lang/icc/icc-18.0.2.199-r1.ebuild | 2 +- dev-lang/icc/icc-19.0.4.243.ebuild | 3 +-- dev-lang/icc/icc-19.1.1.217.ebuild | 3 +-- sci-biology/BBmap/BBmap-34.97.ebuild | 6 +++--- sci-biology/BBmap/BBmap-35.92.ebuild | 6 +++--- sci-biology/BBmap/BBmap-36.02.ebuild | 6 +++--- sci-biology/BBmap/BBmap-36.86.ebuild | 6 +++--- sci-biology/BBmap/BBmap-37.67.ebuild | 6 +++--- sci-biology/FLASH/FLASH-1.2.9.ebuild | 6 +++--- sci-biology/IMAGE/IMAGE-2.4.1.ebuild | 4 ++-- sci-biology/InterMine/InterMine-0.98.ebuild | 4 ++-- sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 2 +- .../files/NGSEPcore_fix_compilation.patch | 0 sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild | 8 ++++---- sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild | 8 ++++---- sci-biology/SnpEff/SnpEff-4.3i.ebuild | 8 ++++---- sci-biology/SolexaQA/SolexaQA-2.2.ebuild | 6 +++--- sci-biology/autoeditor/autoeditor-1.20.ebuild | 8 ++++---- sci-biology/bambus/bambus-2.33.ebuild | 11 +++++------ sci-biology/clview/clview-0.1.ebuild | 6 +++--- sci-biology/conrad/conrad-1.ebuild | 7 +++---- sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 8 ++++---- sci-biology/estscan/estscan-3.0.3.ebuild | 22 +++++++++++----------- sci-biology/glean/glean-1.0.1.ebuild | 6 +++--- .../jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild | 8 ++++---- sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild | 8 ++++---- sci-biology/jtreeview/jtreeview-9999.ebuild | 4 ++-- sci-biology/kraken/kraken-1.0.ebuild | 4 ++-- sci-biology/lucy/lucy-1.20.ebuild | 6 +++--- sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 6 +++--- sci-biology/parafly/parafly-20130121.ebuild | 6 +++--- sci-biology/quast/quast-4.4.ebuild | 6 +++--- sci-biology/samstat/samstat-1.5.1.ebuild | 6 +++--- .../scaffold_builder-20131122-r1.ebuild | 12 ++++++------ sci-biology/screed/screed-0.9.ebuild | 4 ++-- sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild | 8 ++++---- sci-biology/smalt/smalt-0.7.6.ebuild | 6 +++--- sci-biology/staden/staden-2.0.0_beta10.ebuild | 6 +++--- sci-biology/staden/staden-2.0.0_beta11.ebuild | 6 +++--- sci-biology/staden/staden-9999.ebuild | 4 ++-- .../staden_doc/staden_doc-2.0.0_beta11.ebuild | 6 +++--- .../staden_doc/staden_doc-2.0.0_beta9.ebuild | 6 +++--- sci-biology/subread/subread-1.4.6.ebuild | 6 +++--- .../tigr-foundation-libs-2.0-r1.ebuild | 4 ++-- sci-biology/trowel/trowel-0.1.4.1.ebuild | 8 ++++---- sci-chemistry/pesto/pesto-9999.ebuild | 4 ++-- sci-libs/fdlibm/fdlibm-5.3.ebuild | 4 ++-- sci-libs/geom/geom-5.1.2.7.ebuild | 4 ++-- sci-libs/libmatheval/libmatheval-1.1.10.ebuild | 4 ++-- sci-libs/modglue/modglue-1.19.ebuild | 4 ++-- sci-libs/pytorch/pytorch-1.4.0_p0-r1.ebuild | 2 +- sci-libs/zarja/zarja-1.1.1.ebuild | 4 ++-- sci-mathematics/cipi/cipi-1.0.ebuild | 4 ++-- sci-mathematics/lie/lie-2.2.2.ebuild | 4 ++-- sci-mathematics/netgen/netgen-4.9.13.ebuild | 4 ++-- sci-mathematics/netgen/netgen-5.0.0.ebuild | 4 ++-- sci-mathematics/netgen/netgen-5.3.1.ebuild | 4 ++-- sci-mathematics/scilab/scilab-5.5.2-r1.ebuild | 6 +++--- sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild | 4 ++-- sci-misc/elmer-meta/elmer-meta-9999.ebuild | 4 ++-- sci-physics/genfit/genfit-02.00.00.ebuild | 4 ++-- sci-physics/genfit/genfit-9999.ebuild | 4 ++-- 66 files changed, 184 insertions(+), 188 deletions(-) diff --git a/app-doc/blacs-docs/blacs-docs-1.1.ebuild b/app-doc/blacs-docs/blacs-docs-1.1.ebuild index 7bb93e833..d1915e0f6 100644 --- a/app-doc/blacs-docs/blacs-docs-1.1.ebuild +++ b/app-doc/blacs-docs/blacs-docs-1.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 DESCRIPTION="Documentation reference for BLACS implementations" -HOMEPAGE="http://www.netlib.org/blacs/"; +HOMEPAGE="https://www.netlib.org/blacs/"; SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"; LICENSE="BSD" diff --git a/dev-java/hdf-java/hdf-java-2.9.ebuild b/dev-java/hdf-java/hdf-java-2.9.ebuild index 248df280d..7a0ba9261 100644 --- a/dev-java/hdf-java/hdf-java-2.9.ebuild +++ b/dev-java/hdf-java/hdf-java-2.9.ebuild @@ -1,14 +1,14 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 JAVA_PKG_IUSE="doc examples" -inherit autotools eutils fdo-mime java-pkg-2 +inherit autotools eutils java-pkg-2 xdg-utils DESCRIPTION="Java interface to the HDF5 library" -HOMEPAGE="http://www.hdfgroup.org/hdf-java-html/index.html"; +HOMEPAGE="https://www.hdfgroup.org/"; SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/${P}/src/${P}-src.tar"; LICENSE="NCSA-HDF" @@ -122,9 +122,9 @@ src_install() { } pkg_postinst() { - use hdfview && fdo-mime_desktop_database_update + use hdfview && xdg_desktop_database_update } pkg_postrm() { - use hdfview && fdo-mime_desktop_database_update + use hdfview && xdg_desktop_database_update } diff --git a/dev-java/jogl/jogl-2.1.4.ebuild b/dev-java/jogl/jogl-2.1.4.ebuild index fbf84aba8..8811c0a32 100644 --- a/dev-java/jogl/jogl-2.1.4.ebuild +++ b/dev-java/jogl/jogl-2.1.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -21,7 +21,7 @@ KEYWORDS="~amd64 ~x86" IUSE="cg" CDEPEND=" - =dev-java/gluegen-${PV}:${SLOT} + ~dev-java/gluegen-${PV}:${SLOT} dev-java/antlr:0 dev-java/ant-core:0 x11-libs/libX11 diff --git a/dev-java/jogl/jogl-2.2.4.ebuild b/dev-java/jogl/jogl-2.2.4.ebuild index edccee222..3af40058d 100644 --- a/dev-java/jogl/jogl-2.2.4.ebuild +++ b/dev-java/jogl/jogl-2.2.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -18,7 +18,7 @@ KEYWORDS="~amd64 ~x86" IUSE="cg" CDEPEND=" - =dev-java/gluegen-${PV}:${SLOT} + ~dev-java/gluegen-${PV}:${SLOT} dev-java/antlr:0 dev-java/ant-core:0 x11-libs/libX11 diff --git a/dev-lang/icc/icc-18.0.2.199-r1.ebuild b/dev-lang/icc/icc-18.0.2.199-r1.ebuild index 7f2c36e82..84641de62 100644 --- a/dev-lang/icc/icc-18.0.2.199-r1.ebuild +++ b/dev-lang/icc/icc-18.0.2.199-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 diff --git a/dev-lang/icc/icc-19.0.4.243.ebuild b/dev-lang/icc/icc-19.0.4.243.ebuild index c388143bd..9a166f221 100644 --- a/dev-lang/icc/icc-19.0.4.243.ebuild +++ b/dev-lang/icc/icc-19.0.4.243.ebuild @@ -1,4 +1,4 @@ -# Copyright 2439-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -38,4 +38,3 @@ pkg_setup() { "icc-doc-ps-19.0-19.0.4-243.noarch.rpm") fi } - diff --git a/dev-lang/icc/icc-19.1.1.217.ebuild b/dev-lang/icc/icc-19.1.1.217.ebuild index 7d7379690..226b9c784 100644 --- a/dev-lang/icc/icc-19.1.1.217.ebuild +++ b/dev-lang/icc/icc-19.1.1.217.ebuild @@ -1,4 +1,4 @@ -# Copyright 2439-2020 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -39,4 +39,3 @@ pkg_setup() { INTEL_DIST_DAT_RPMS+=( "icc-doc-19.1-${MY_PV}.noarch.rpm" ) fi } - diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild index cf80ed6c8..25627cf02 100644 --- a/sci-biology/BBmap/BBmap-34.97.ebuild +++ b/sci-biology/BBmap/BBmap-34.97.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit java-pkg-2 java-ant-2 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" -HOMEPAGE="http://sourceforge.net/projects/bbmap/"; -SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/bbmap/"; +SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; LICENSE="BSD" SLOT="0" diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-35.92.ebuild index d8d2042ce..3bc328b4c 100644 --- a/sci-biology/BBmap/BBmap-35.92.ebuild +++ b/sci-biology/BBmap/BBmap-35.92.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit java-pkg-2 java-ant-2 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" -HOMEPAGE="http://sourceforge.net/projects/bbmap/"; -SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/bbmap/"; +SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; LICENSE="BSD" SLOT="0" diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild index d8d2042ce..3bc328b4c 100644 --- a/sci-biology/BBmap/BBmap-36.02.ebuild +++ b/sci-biology/BBmap/BBmap-36.02.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit java-pkg-2 java-ant-2 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" -HOMEPAGE="http://sourceforge.net/projects/bbmap/"; -SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/bbmap/"; +SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; LICENSE="BSD" SLOT="0" diff --git a/sci-biology/BBmap/BBmap-36.86.ebuild b/sci-biology/BBmap/BBmap-36.86.ebuild index d8d2042ce..3bc328b4c 100644 --- a/sci-biology/BBmap/BBmap-36.86.ebuild +++ b/sci-biology/BBmap/BBmap-36.86.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit java-pkg-2 java-ant-2 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" -HOMEPAGE="http://sourceforge.net/projects/bbmap/"; -SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/bbmap/"; +SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; LICENSE="BSD" SLOT="0" diff --git a/sci-biology/BBmap/BBmap-37.67.ebuild b/sci-biology/BBmap/BBmap-37.67.ebuild index d8d2042ce..3bc328b4c 100644 --- a/sci-biology/BBmap/BBmap-37.67.ebuild +++ b/sci-biology/BBmap/BBmap-37.67.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit java-pkg-2 java-ant-2 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" -HOMEPAGE="http://sourceforge.net/projects/bbmap/"; -SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/bbmap/"; +SRC_URI="https://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; LICENSE="BSD" SLOT="0" diff --git a/sci-biology/FLASH/FLASH-1.2.9.ebuild b/sci-biology/FLASH/FLASH-1.2.9.ebuild index 823f2eba7..c2c05eb4a 100644 --- a/sci-biology/FLASH/FLASH-1.2.9.ebuild +++ b/sci-biology/FLASH/FLASH-1.2.9.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 DESCRIPTION="Paired-end mates merge from fragments" -HOMEPAGE="http://sourceforge.net/projects/flashpage"; -SRC_URI="http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.9.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/flashpage"; +SRC_URI="https://downloads.sourceforge.net/project/flashpage/${P}.tar.gz"; LICENSE="GPL-3" SLOT="0" diff --git a/sci-biology/IMAGE/IMAGE-2.4.1.ebuild b/sci-biology/IMAGE/IMAGE-2.4.1.ebuild index 82447fb2b..d0969c344 100644 --- a/sci-biology/IMAGE/IMAGE-2.4.1.ebuild +++ b/sci-biology/IMAGE/IMAGE-2.4.1.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="Iterative Mapping and Assembly for Gap Elimination using paired-end Illumina" HOMEPAGE="https://sourceforge.net/apps/mediawiki/image2"; -SRC_URI="http://sourceforge.net/projects/image2/files/IMAGE_version2.4.1_64bit.zip"; +SRC_URI="https://sourceforge.net/projects/image2/files/IMAGE_version${PV}_64bit.zip"; #http://genomebiology.com/2010/11/4/R41 LICENSE="CC-BY-2.0" diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild b/sci-biology/InterMine/InterMine-0.98.ebuild index 2159f4dba..1d06d2c15 100644 --- a/sci-biology/InterMine/InterMine-0.98.ebuild +++ b/sci-biology/InterMine/InterMine-0.98.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 [ "$PV" == "9999" ] && inherit git-r3 DESCRIPTION="Biological data warehouse integrating complex data" -HOMEPAGE="http://github.com/intermine/intermine"; +HOMEPAGE="https://github.com/intermine/intermine"; if [ "$PV" == "9999" ]; then EGIT_REPO_URI="https://github.com/intermine/intermine"; KEYWORDS="" diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild index 24445eb0d..0addb08b8 100644 --- a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild +++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild @@ -25,7 +25,7 @@ RDEPEND="${DEPEND}" S="${WORKDIR}/${PN}_${PV}" -PATCHES=( "${FILESDIR}"/NGSEPcore_drop_utf8_chars.patch "${FILESDIR}"/NGSEPcore_fix_compilation.patch ) +PATCHES=( "${FILESDIR}"/NGSEPcore_drop_utf8_chars.patch ) src_prepare(){ rm lib/htsjdk-1.129.jar || die diff --git a/sci-biology/NGSEPcore/files/NGSEPcore_fix_compilation.patch b/sci-biology/NGSEPcore/files/NGSEPcore_fix_compilation.patch deleted file mode 100644 index e69de29bb..000000000 diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild index 4b948623a..1724e13c3 100644 --- a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild +++ b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,10 +8,10 @@ inherit eutils toolchain-funcs versionator java-pkg-2 MY_PV=$(replace_all_version_separators '-') DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" -HOMEPAGE="http://www.oboedit.org/"; +HOMEPAGE="http://www.oboedit.org/"; # no https, invalid certificate SRC_URI=" - http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/${MY_PV}_unix_install4j.sh/download -> OBO-Edit_unix_install4j-${PV}.sh - http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/ReleaseNotes-${PV}.txt"; + https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/${MY_PV}_unix_install4j.sh/download -> OBO-Edit_unix_install4j-${PV}.sh + https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/ReleaseNotes-${PV}.txt"; LICENSE="OBO-Edit" # Artistic-like SLOT="0" diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild index 6163c6728..e4d3b9304 100644 --- a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild +++ b/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -11,10 +11,10 @@ MY_VER="2.1.1-b6" MY_PV=$(replace_all_version_separators '-') DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" -HOMEPAGE="http://www.oboedit.org/"; +HOMEPAGE="http://www.oboedit.org/"; # no https, invalid certificate SRC_URI=" - http://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_VER}/${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh - http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_PV}/ReleaseNotes-${MY_VER}.txt -> ${PN}_ReleaseNotes-${PV}.txt" + https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_VER}/${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh + https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_PV}/ReleaseNotes-${MY_VER}.txt -> ${PN}_ReleaseNotes-${PV}.txt" LICENSE="OBO-Edit" # Artistic-like SLOT="0" diff --git a/sci-biology/SnpEff/SnpEff-4.3i.ebuild b/sci-biology/SnpEff/SnpEff-4.3i.ebuild index 9921b3394..2bd2bfb1d 100644 --- a/sci-biology/SnpEff/SnpEff-4.3i.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3i.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -8,10 +8,10 @@ inherit java-pkg-2 java-ant-2 MY_PV=${PV/./_} DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF" -HOMEPAGE="http://snpeff.sourceforge.net"; +HOMEPAGE="https://pcingola.github.io/SnpEff/"; SRC_URI=" - http://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip - http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html" + https://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip + https://pcingola.github.io/SnpEff/index.html -> ${P}.html" LICENSE="LGPL-3" SLOT="0" diff --git a/sci-biology/SolexaQA/SolexaQA-2.2.ebuild b/sci-biology/SolexaQA/SolexaQA-2.2.ebuild index 62fc3dc8b..3ef15d780 100644 --- a/sci-biology/SolexaQA/SolexaQA-2.2.ebuild +++ b/sci-biology/SolexaQA/SolexaQA-2.2.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="Analyze and trim single-end and paired-end reads, show quality statistics" -HOMEPAGE="http://sourceforge.net/projects/clview"; -SRC_URI="http://sourceforge.net/projects/solexaqa/files/src/SolexaQA_v.2.2.zip"; +HOMEPAGE="https://sourceforge.net/projects/clview"; +SRC_URI="https://sourceforge.net/projects/solexaqa/files/src/SolexaQA_v.${PV}.zip"; LICENSE="GPL-3" SLOT="0" diff --git a/sci-biology/autoeditor/autoeditor-1.20.ebuild b/sci-biology/autoeditor/autoeditor-1.20.ebuild index 5e4c631b7..776133aa2 100644 --- a/sci-biology/autoeditor/autoeditor-1.20.ebuild +++ b/sci-biology/autoeditor/autoeditor-1.20.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,10 +6,10 @@ EAPI=5 inherit eutils DESCRIPTION="Automatic correct of discrepancies in multiple sequence alignments" -HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor"; +HOMEPAGE="https://sourceforge.net/projects/amos/"; SRC_URI=" - ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz - test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20-sample.tar.gz )" + ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-${PV}.tar.gz + test? ( ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-${PV}-sample.tar.gz )" LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild index 71cc10aa5..4391801b0 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,12 +8,11 @@ inherit perl-module eutils toolchain-funcs DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle" HOMEPAGE=" - http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS - http://sourceforge.net/projects/amos/files/bambus - http://www.tigr.org/software/bambus"; + https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS + https://sourceforge.net/projects/amos/files/bambus"; SRC_URI=" - http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz - http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"; + https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz + http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"; # no https LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild index 8b5d9b34d..7b2387dc6 100644 --- a/sci-biology/clview/clview-0.1.ebuild +++ b/sci-biology/clview/clview-0.1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools" -HOMEPAGE="http://sourceforge.net/projects/clview"; +HOMEPAGE="https://sourceforge.net/projects/clview"; SRC_URI=" - http://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz + https://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz"; diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild index 6de809361..66acb381f 100644 --- a/sci-biology/conrad/conrad-1.ebuild +++ b/sci-biology/conrad/conrad-1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,9 +6,8 @@ EAPI=5 inherit java-pkg-2 java-ant-2 DESCRIPTION="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor" -HOMEPAGE="http://www.broadinstitute.org/annotation/conrad - http://sourceforge.net/projects/conradcrf"; -SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"; +HOMEPAGE="https://sourceforge.net/projects/conradcrf"; +SRC_URI="https://downloads.sourceforge.net/project/conradcrf/conradcrf/Version%201/conradSrc.zip -> ${P}.zip" LICENSE="LGPL-2.1" SLOT="0" diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild index b700de820..13151d643 100644 --- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild +++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -6,9 +6,9 @@ EAPI=6 inherit perl-functions DESCRIPTION="Genotype variant discovery without reference sequence" -HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"; +HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"; # no https SRC_URI=" - http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz + https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"; LICENSE="GPL-3" @@ -25,7 +25,7 @@ DEPEND=" dev-lang/perl" RDEPEND="${DEPEND}" -S="${WORKDIR}"/CORTEX_release_v1.0.5.21 +S="${WORKDIR}/CORTEX_release_v${PV}" src_prepare(){ default diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild index e933c59b8..3d2581553 100644 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ b/sci-biology/estscan/estscan-3.0.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,17 +6,17 @@ EAPI=5 inherit eutils fortran-2 perl-module toolchain-funcs DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" -HOMEPAGE="http://sourceforge.net/projects/${PN}/"; +HOMEPAGE="https://sourceforge.net/projects/${PN}/"; SRC_URI=" - http://downloads.sourceforge.net/${PN}/${P}.tar.gz - http://downloads.sourceforge.net/${PN}/At.smat.gz - http://downloads.sourceforge.net/${PN}/Dm.smat.gz - http://downloads.sourceforge.net/${PN}/Dr.smat.gz - http://downloads.sourceforge.net/${PN}/Hs.smat.gz - http://downloads.sourceforge.net/${PN}/Mm.smat.gz - http://downloads.sourceforge.net/${PN}/Rn.smat.gz - http://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf - http://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"; + https://downloads.sourceforge.net/${PN}/${P}.tar.gz + https://downloads.sourceforge.net/${PN}/At.smat.gz + https://downloads.sourceforge.net/${PN}/Dm.smat.gz + https://downloads.sourceforge.net/${PN}/Dr.smat.gz + https://downloads.sourceforge.net/${PN}/Hs.smat.gz + https://downloads.sourceforge.net/${PN}/Mm.smat.gz + https://downloads.sourceforge.net/${PN}/Rn.smat.gz + https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf + https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"; SLOT="0" LICENSE="estscan" diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild index 48b4238f4..8fdfcd3cf 100644 --- a/sci-biology/glean/glean-1.0.1.ebuild +++ b/sci-biology/glean/glean-1.0.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -7,8 +7,8 @@ PERL_EXPORT_PHASE_FUNCTIONS=no inherit perl-module eutils toolchain-funcs DESCRIPTION="Merge various gene prediction into one (unsupervised learning system)" -HOMEPAGE="http://sourceforge.net/projects/glean-gene"; -SRC_URI="http://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-1-0-1/glean-1-0-1.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/glean-gene"; +SRC_URI="https://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-1-0-1/glean-1-0-1.tar.gz"; LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild index 365c534bf..6b84fd7db 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild +++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -9,10 +9,10 @@ inherit java-pkg-2 java-ant-2 eutils perl-module S="${WORKDIR}"/TreeView-1.1.6r4-bin DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats" -HOMEPAGE="http://jtreeview.sourceforge.net/"; +HOMEPAGE="http://jtreeview.sourceforge.net/"; # no https SRC_URI=" - http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz - http://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"; + https://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz + https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"; LICENSE="GPL-2" SLOT="0" diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild index f1e58af01..e89e14cf0 100644 --- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild +++ b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -9,10 +9,10 @@ inherit java-pkg-2 java-ant-2 eutils perl-module S="${WORKDIR}"/TreeView-1.1.6r4-src DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats" -HOMEPAGE="http://jtreeview.sourceforge.net/"; +HOMEPAGE="http://jtreeview.sourceforge.net/"; # no https SRC_URI=" - http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz - http://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"; + https://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz + https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"; #http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz LICENSE="GPL-2" diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild index 0d7a1be51..159448ab7 100644 --- a/sci-biology/jtreeview/jtreeview-9999.ebuild +++ b/sci-biology/jtreeview/jtreeview-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -7,7 +7,7 @@ inherit java-pkg-2 git-r3 DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats" HOMEPAGE="http://jtreeview.sourceforge.net - https://bitbucket.org/TreeView3Dev/treeview3"; + https://bitbucket.org/TreeView3Dev/treeview3"; # no https EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"; LICENSE="MIT" diff --git a/sci-biology/kraken/kraken-1.0.ebuild b/sci-biology/kraken/kraken-1.0.ebuild index efad890ce..2a021a329 100644 --- a/sci-biology/kraken/kraken-1.0.ebuild +++ b/sci-biology/kraken/kraken-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,7 +8,7 @@ inherit perl-module DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" HOMEPAGE="http://ccb.jhu.edu/software/kraken - http://genomebiology.com/2014/15/3/R46"; + https://genomebiology.com/2014/15/3/R46"; SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz -> ${P}.tar.gz http://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html" diff --git a/sci-biology/lucy/lucy-1.20.ebuild b/sci-biology/lucy/lucy-1.20.ebuild index 8f4ed8edd..27c425e9a 100644 --- a/sci-biology/lucy/lucy-1.20.ebuild +++ b/sci-biology/lucy/lucy-1.20.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="DNA sequence quality and vector trimming tool" -HOMEPAGE="http://lucy.sourceforge.net/"; -SRC_URI="http://sourceforge.net/projects/lucy/files/lucy/lucy%201.20/lucy1.20.tar.gz"; +HOMEPAGE="http://lucy.sourceforge.net/"; # no https +SRC_URI="https://sourceforge.net/projects/lucy/files/lucy/lucy%201.20/lucy${PV}.tar.gz"; LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild index 774224625..65dda0367 100644 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild +++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema" -HOMEPAGE="http://manatee.sourceforge.net/igs"; +HOMEPAGE="http://manatee.sourceforge.net/igs"; # no https SRC_URI=" - http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz + https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz http://manatee.sourceforge.net/igs/docs/README_Linux.txt"; LICENSE="Artistic-Manatee" diff --git a/sci-biology/parafly/parafly-20130121.ebuild b/sci-biology/parafly/parafly-20130121.ebuild index 4df553a85..fe3e26c6c 100644 --- a/sci-biology/parafly/parafly-20130121.ebuild +++ b/sci-biology/parafly/parafly-20130121.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="Some dependency for transdecoder" -HOMEPAGE="http://sourceforge.net/projects/transdecoder/"; -SRC_URI="http://sourceforge.net/projects/transdecoder/files/OLDER/TransDecoder_r20140704.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/transdecoder/"; +SRC_URI="https://sourceforge.net/projects/transdecoder/files/OLDER/TransDecoder_r20140704.tar.gz"; # are current sources available only from here? # https://github.com/trinityrnaseq/trinityrnaseq/tree/f81f0497a211c84ba4299063086604760933e6e3/trinity-plugins/parafly-code diff --git a/sci-biology/quast/quast-4.4.ebuild b/sci-biology/quast/quast-4.4.ebuild index 8a566b7e0..7ac6905c3 100644 --- a/sci-biology/quast/quast-4.4.ebuild +++ b/sci-biology/quast/quast-4.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,8 +8,8 @@ PYTHON_COMPAT=( python2_7 ) inherit python-r1 DESCRIPTION="Compare quality of multiple genome assemblies to each other" -HOMEPAGE="http://bioinf.spbau.ru/QUAST"; -SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz"; +HOMEPAGE="http://bioinf.spbau.ru/QUAST"; # no https +SRC_URI="https://sourceforge.net/projects/quast/files/${P}.tar.gz"; LICENSE="GPL-2" # and some other for the bundled copies, see http://quast.bioinf.spbau.ru/LICENSE SLOT="0" diff --git a/sci-biology/samstat/samstat-1.5.1.ebuild b/sci-biology/samstat/samstat-1.5.1.ebuild index af0f76cb2..cf409eeb0 100644 --- a/sci-biology/samstat/samstat-1.5.1.ebuild +++ b/sci-biology/samstat/samstat-1.5.1.ebuild @@ -6,13 +6,13 @@ EAPI=6 inherit eutils DESCRIPTION="Statistics of BAM/SAM files" -HOMEPAGE="http://samstat.sourceforge.net"; -SRC_URI="http://sourceforge.net/projects/samstat/files/${P}.tar.gz"; +HOMEPAGE="http://samstat.sourceforge.net"; # no https +SRC_URI="https://sourceforge.net/projects/samstat/files/${P}.tar.gz"; LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" IUSE="" -DEPEND="sci-biology/samtools" +DEPEND="sci-biology/samtools:=" RDEPEND="${DEPEND}" diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild index ab9a50360..46a0f5792 100644 --- a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild +++ b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -9,12 +9,12 @@ inherit python-r1 DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds" HOMEPAGE=" - http://sourceforge.net/projects/scaffold-b - http://edwards.sdsu.edu/scaffold_builder"; + https://sourceforge.net/projects/scaffold-b + https://edwards.sdsu.edu/scaffold_builder"; SRC_URI=" - http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip - http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc - http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"; + https://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip + https://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc + https://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf"; #http://www.scfbm.org/content/8/1/23 LICENSE="GPL-3" diff --git a/sci-biology/screed/screed-0.9.ebuild b/sci-biology/screed/screed-0.9.ebuild index 017ff4376..fe8f49405 100644 --- a/sci-biology/screed/screed-0.9.ebuild +++ b/sci-biology/screed/screed-0.9.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 python3_3 python3_4 python3_5 ) inherit distutils-r1 DESCRIPTION="Short read sequence utilities" -HOMEPAGE="https://pypi.python.org/pypi/screed http://github.com/ged-lab/screed/"; +HOMEPAGE="https://pypi.python.org/pypi/screed https://github.com/ged-lab/screed/"; SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" SLOT="0" diff --git a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild index 3de2417b9..b7a9af9bb 100644 --- a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild +++ b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="Adaptor and MID removal / trimming tool" -HOMEPAGE="http://sourceforge.net/projects/skewer"; +HOMEPAGE="https://sourceforge.net/projects/skewer"; SRC_URI=" - http://sourceforge.net/projects/skewer/files/Binaries/skewer-0.1.104-linux-x86_64 - http://sourceforge.net/projects/skewer/files/Scripts/srna-scripts-0.1.2.tar.gz"; + https://sourceforge.net/projects/skewer/files/Binaries/skewer-${PV}-linux-x86_64 + https://sourceforge.net/projects/skewer/files/Scripts/srna-scripts-0.1.2.tar.gz"; LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild b/sci-biology/smalt/smalt-0.7.6.ebuild index 141269ae4..b385c32ef 100644 --- a/sci-biology/smalt/smalt-0.7.6.ebuild +++ b/sci-biology/smalt/smalt-0.7.6.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -7,8 +7,8 @@ MY_PN="${PN%-bin}" MY_P="${MY_PN}-${PV}" DESCRIPTION="DNA read mapper using k=20 (successor of ssaha2)" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"; -SRC_URI="http://sourceforge.net/projects/${PN}/files/${P}.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/smalt/"; +SRC_URI="https://sourceforge.net/projects/${PN}/files/${P}.tar.gz"; LICENSE="GPL-3" SLOT="0" diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild index e2fb8bf37..53c4d2212 100644 --- a/sci-biology/staden/staden-2.0.0_beta10.ebuild +++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,8 +8,8 @@ AUTOTOOLS_AUTORECONF=yes inherit autotools-utils eutils flag-o-matic fortran-2 multilib DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="http://sourceforge.net/projects/staden"; -SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/staden"; +SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"; LICENSE="staden" SLOT="0" diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild index a84e6c178..b8e5425c7 100644 --- a/sci-biology/staden/staden-2.0.0_beta11.ebuild +++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,8 +8,8 @@ AUTOTOOLS_AUTORECONF=yes inherit autotools-utils eutils flag-o-matic fortran-2 multilib DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="http://sourceforge.net/projects/staden"; -SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz" +HOMEPAGE="https://sourceforge.net/projects/staden"; +SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz" LICENSE="staden" SLOT="0" diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild index 4be43217f..961155bf6 100644 --- a/sci-biology/staden/staden-9999.ebuild +++ b/sci-biology/staden/staden-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,7 +8,7 @@ AUTOTOOLS_AUTORECONF=yes inherit autotools-utils flag-o-matic fortran-2 multilib subversion DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="http://sourceforge.net/projects/staden/"; +HOMEPAGE="https://sourceforge.net/projects/staden/"; ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk"; LICENSE="staden" diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild index cc58b4334..8d9011858 100644 --- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild +++ b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit eutils DESCRIPTION="Documentation files for the staden package" -HOMEPAGE="http://sourceforge.net/projects/staden"; -SRC_URI="http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/staden"; +SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"; # https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/doc/ LICENSE="staden" diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild index cc58b4334..8d9011858 100644 --- a/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild +++ b/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,8 +6,8 @@ EAPI=5 inherit eutils DESCRIPTION="Documentation files for the staden package" -HOMEPAGE="http://sourceforge.net/projects/staden"; -SRC_URI="http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/staden"; +SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"; # https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/doc/ LICENSE="staden" diff --git a/sci-biology/subread/subread-1.4.6.ebuild b/sci-biology/subread/subread-1.4.6.ebuild index 7b6cff913..aa8290e1a 100644 --- a/sci-biology/subread/subread-1.4.6.ebuild +++ b/sci-biology/subread/subread-1.4.6.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,12 +6,12 @@ EAPI=5 [ "$PV" == "9999" ] && inherit subversion DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts" -HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/"; +HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/"; # no https if [ "$PV" == "9999" ]; then ESVN_REPO_URI="https://subread.svn.sourceforge.net/svnroot/subread/trunk"; #KEYWORDS="~amd64 ~x86" else - SRC_URI="http://sourceforge.net/projects/subread/files/"${P}"/"${P}"-source.tar.gz"; + SRC_URI="https://sourceforge.net/projects/subread/files/"${P}"/"${P}"-source.tar.gz"; KEYWORDS="~amd64 ~x86" fi diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild index 330e67f3d..8c2b46567 100644 --- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild +++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -6,7 +6,7 @@ EAPI=6 inherit eutils DESCRIPTION="TIGR Foundation for C++" -HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor"; +HOMEPAGE="https://sourceforge.net/projects/amos/"; SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/autoEditor/autoEditor-1.20.tar.gz"; # the one bundled in autoEditor-1.20/TigrFoundation-2.0/ is same with the one in bambus diff --git a/sci-biology/trowel/trowel-0.1.4.1.ebuild b/sci-biology/trowel/trowel-0.1.4.1.ebuild index 4f4e5283e..931ca5371 100644 --- a/sci-biology/trowel/trowel-0.1.4.1.ebuild +++ b/sci-biology/trowel/trowel-0.1.4.1.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="Error corrector for genomic Illumina FASTQ reads" -HOMEPAGE="http://sourceforge.net/projects/trowel-ec"; -SRC_URI="http://downloads.sourceforge.net/project/trowel-ec/src/trowel.0.1.4.1.src.tar.gz"; +HOMEPAGE="https://sourceforge.net/projects/trowel-ec"; +SRC_URI="https://downloads.sourceforge.net/project/trowel-ec/src/trowel.${PV}.src.tar.gz"; LICENSE="GPL-3" SLOT="0" @@ -16,4 +16,4 @@ DEPEND=">=dev-libs/boost-1.53.0 >=dev-cpp/sparsehash-2.0.2" RDEPEND="${DEPEND}" -S="${WORKDIR}"/trowel.0.1.4.1.src +S="${WORKDIR}/trowel.${PV}.src" diff --git a/sci-chemistry/pesto/pesto-9999.ebuild b/sci-chemistry/pesto/pesto-9999.ebuild index b9bfb2c0b..302608937 100644 --- a/sci-chemistry/pesto/pesto-9999.ebuild +++ b/sci-chemistry/pesto/pesto-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -12,7 +12,7 @@ SRC_URI="" EHG_REPO_URI="http://hg.code.sf.net/p/pesto/code-1"; DESCRIPTION="Potential Energy Surface Tools" -HOMEPAGE="http://sourceforge.net/projects/pesto/"; +HOMEPAGE="https://sourceforge.net/projects/pesto/"; LICENSE="BSD" SLOT="0" diff --git a/sci-libs/fdlibm/fdlibm-5.3.ebuild b/sci-libs/fdlibm/fdlibm-5.3.ebuild index 4876249fc..d8324a0bc 100644 --- a/sci-libs/fdlibm/fdlibm-5.3.ebuild +++ b/sci-libs/fdlibm/fdlibm-5.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 inherit toolchain-funcs flag-o-matic versionator multilib DESCRIPTION="C math library supporting IEEE 754 floating-point arithmetic" -HOMEPAGE="http://www.netlib.org/fdlibm"; +HOMEPAGE="https://www.netlib.org/fdlibm"; SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"; LICENSE="freedist" diff --git a/sci-libs/geom/geom-5.1.2.7.ebuild b/sci-libs/geom/geom-5.1.2.7.ebuild index a739b1e34..6e47ca14b 100644 --- a/sci-libs/geom/geom-5.1.2.7.ebuild +++ b/sci-libs/geom/geom-5.1.2.7.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 inherit autotools eutils DESCRIPTION="A complete OpenCascade - OCAF based CAD framework" -HOMEPAGE="http://sourceforge.net/projects/salomegeometry/"; +HOMEPAGE="https://sourceforge.net/projects/salomegeometry/"; SRC_URI="mirror://sourceforge/salomegeometry/${P}.tar.gz" LICENSE="LGPL-2" diff --git a/sci-libs/libmatheval/libmatheval-1.1.10.ebuild b/sci-libs/libmatheval/libmatheval-1.1.10.ebuild index 9b0144249..0509b166b 100644 --- a/sci-libs/libmatheval/libmatheval-1.1.10.ebuild +++ b/sci-libs/libmatheval/libmatheval-1.1.10.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -7,7 +7,7 @@ inherit autotools-utils DESCRIPTION="library to parse and evaluate symbolic expressions" -HOMEPAGE="http://www.gnu.org/software/libmatheval/"; +HOMEPAGE="https://www.gnu.org/software/libmatheval/"; SRC_URI="mirror://gnu/${PN}/${PF}.tar.gz" LICENSE="GPL-2" diff --git a/sci-libs/modglue/modglue-1.19.ebuild b/sci-libs/modglue/modglue-1.19.ebuild index 9005c3f2b..f2dd8d4cb 100644 --- a/sci-libs/modglue/modglue-1.19.ebuild +++ b/sci-libs/modglue/modglue-1.19.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 inherit autotools-utils eutils DESCRIPTION="C++ library for handling of multiple co-processes" -HOMEPAGE="http://cadabra.phi-sci.com"; +HOMEPAGE="https://cadabra.science"; SRC_URI="http://cadabra.phi-sci.com/${P}.tar.gz"; RESTRICT="mirror" diff --git a/sci-libs/pytorch/pytorch-1.4.0_p0-r1.ebuild b/sci-libs/pytorch/pytorch-1.4.0_p0-r1.ebuild index ca6a3c251..8c84e7a09 100644 --- a/sci-libs/pytorch/pytorch-1.4.0_p0-r1.ebuild +++ b/sci-libs/pytorch/pytorch-1.4.0_p0-r1.ebuild @@ -195,7 +195,7 @@ src_configure() { fi # do not rerun cmake and the build process in src_install - sed '/RERUN/,+1d' -i ${BUILD_DIR}/build.ninja || die + sed '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die } src_compile() { diff --git a/sci-libs/zarja/zarja-1.1.1.ebuild b/sci-libs/zarja/zarja-1.1.1.ebuild index d5ce3856c..d4a82cb00 100644 --- a/sci-libs/zarja/zarja-1.1.1.ebuild +++ b/sci-libs/zarja/zarja-1.1.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 DESCRIPTION="Scientific multi-agent simulation library" -HOMEPAGE="http://sourceforge.net/projects/zarja/"; +HOMEPAGE="https://sourceforge.net/projects/zarja/"; SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" LICENSE="GPL-2" diff --git a/sci-mathematics/cipi/cipi-1.0.ebuild b/sci-mathematics/cipi/cipi-1.0.ebuild index 03c1afef3..2665a6837 100644 --- a/sci-mathematics/cipi/cipi-1.0.ebuild +++ b/sci-mathematics/cipi/cipi-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 inherit cmake-utils DESCRIPTION="Computing information projections iteratively" -HOMEPAGE="http://github.com/tom111/cipi"; +HOMEPAGE="https://github.com/tom111/cipi"; SRC_URI="https://github.com/tom111/cipi/archive/1.0.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" diff --git a/sci-mathematics/lie/lie-2.2.2.ebuild b/sci-mathematics/lie/lie-2.2.2.ebuild index 1e386d356..96ffc3d5b 100644 --- a/sci-mathematics/lie/lie-2.2.2.ebuild +++ b/sci-mathematics/lie/lie-2.2.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 inherit eutils toolchain-funcs DESCRIPTION="A Computer algebra package for Lie group computations" -HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/"; +HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/"; # no https, invalid certificate SRC_URI="http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/conLiE.tar.gz -> ${P}.tar.gz" #### Remove the following line when moving this ebuild to the main tree! RESTRICT="mirror" diff --git a/sci-mathematics/netgen/netgen-4.9.13.ebuild b/sci-mathematics/netgen/netgen-4.9.13.ebuild index ef4f19b3e..22f900973 100644 --- a/sci-mathematics/netgen/netgen-4.9.13.ebuild +++ b/sci-mathematics/netgen/netgen-4.9.13.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -6,7 +6,7 @@ EAPI=5 inherit eutils flag-o-matic multilib versionator DESCRIPTION="Automatic 3d tetrahedral mesh generator" -HOMEPAGE="http://www.hpfem.jku.at/netgen/"; +HOMEPAGE="https://sourceforge.net/projects/netgen/"; SRC_URI="mirror://sourceforge/netgen-mesher/${P}.tar.gz" SLOT="0" diff --git a/sci-mathematics/netgen/netgen-5.0.0.ebuild b/sci-mathematics/netgen/netgen-5.0.0.ebuild index 2e5d37fde..7c245c883 100644 --- a/sci-mathematics/netgen/netgen-5.0.0.ebuild +++ b/sci-mathematics/netgen/netgen-5.0.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -8,7 +8,7 @@ inherit autotools eutils flag-o-matic multilib versionator MY_PN=${PN}-mesher MY_PV=$(get_version_component_range 1-2) DESCRIPTION="NETGEN is an automatic 3d tetrahedral mesh generator" -HOMEPAGE="http://www.hpfem.jku.at/netgen/"; +HOMEPAGE="https://sourceforge.net/projects/netgen/"; SRC_URI="mirror://sourceforge/project/${MY_PN}/${MY_PN}/${MY_PV}/${P}.tar.gz" SLOT="0" diff --git a/sci-mathematics/netgen/netgen-5.3.1.ebuild b/sci-mathematics/netgen/netgen-5.3.1.ebuild index 4dd089d1a..5ccbcea2f 100644 --- a/sci-mathematics/netgen/netgen-5.3.1.ebuild +++ b/sci-mathematics/netgen/netgen-5.3.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -8,7 +8,7 @@ inherit autotools eutils flag-o-matic multilib versionator MY_PN=${PN}-mesher MY_PV=$(get_version_component_range 1-2) DESCRIPTION="Automatic 3d tetrahedral mesh generator" -HOMEPAGE="http://www.hpfem.jku.at/netgen/"; +HOMEPAGE="https://sourceforge.net/projects/netgen/"; SRC_URI="mirror://sourceforge/project/${MY_PN}/${MY_PN}/${MY_PV}/${P}.tar.gz" SLOT="0" diff --git a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild index c655c1324..4bbbde779 100644 --- a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild +++ b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -68,13 +68,13 @@ CDEPEND=" dev-java/commons-logging:0 >=dev-java/flexdock-1.2.4:0 >=dev-java/fop-2.0:0 - =dev-java/gluegen-2.2.4:2.2 + ~dev-java/gluegen-2.2.4:2.2 dev-java/javahelp:0 dev-java/jeuclid-core:0 dev-java/jgoodies-looks:2.6 >=dev-java/jlatexmath-1.0.3:1 >=dev-java/jlatexmath-fop-1.0.3:1 - =dev-java/jogl-2.2.4:2.2 + ~dev-java/jogl-2.2.4:2.2 >=dev-java/jrosetta-1.0.4:0 dev-java/skinlf:0 dev-java/xmlgraphics-commons:2 diff --git a/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild b/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild index c4c866374..74e8cd7bb 100644 --- a/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild +++ b/sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 DESCRIPTION="Collection of finite element programs, libraries, and visualization tools" -HOMEPAGE="http://www.csc.fi/english/pages/elmer"; +HOMEPAGE="https://www.csc.fi/web/elmer"; LICENSE="GPL-2" SLOT="0" diff --git a/sci-misc/elmer-meta/elmer-meta-9999.ebuild b/sci-misc/elmer-meta/elmer-meta-9999.ebuild index 9bd892a40..d57349411 100644 --- a/sci-misc/elmer-meta/elmer-meta-9999.ebuild +++ b/sci-misc/elmer-meta/elmer-meta-9999.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 DESCRIPTION="Collection of finite element programs, libraries, and visualization tools" -HOMEPAGE="http://www.csc.fi/english/pages/elmer"; +HOMEPAGE="https://www.csc.fi/web/elmer"; LICENSE="GPL-2" SLOT="0" diff --git a/sci-physics/genfit/genfit-02.00.00.ebuild b/sci-physics/genfit/genfit-02.00.00.ebuild index 40a4cce10..2230d6415 100644 --- a/sci-physics/genfit/genfit-02.00.00.ebuild +++ b/sci-physics/genfit/genfit-02.00.00.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -21,7 +21,7 @@ else fi DESCRIPTION="Generic toolkit for track reconstruction in physics experiments" -HOMEPAGE="http://genfit.sourceforge.net/Main.html"; +HOMEPAGE="http://genfit.sourceforge.net/Main.html"; # no https LICENSE="LGPL-3" SLOT="0" diff --git a/sci-physics/genfit/genfit-9999.ebuild b/sci-physics/genfit/genfit-9999.ebuild index d4960e9fd..2061c4dc1 100644 --- a/sci-physics/genfit/genfit-9999.ebuild +++ b/sci-physics/genfit/genfit-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -20,7 +20,7 @@ else fi DESCRIPTION="Generic toolkit for track reconstruction in physics experiments" -HOMEPAGE="http://genfit.sourceforge.net/Main.html"; +HOMEPAGE="http://genfit.sourceforge.net/Main.html"; # no https LICENSE="LGPL-3" SLOT="0"
