[gentoo-commits] proj/sci:master commit in: sci-biology/conrad/, sci-biology/InterMine/, sci-biology/tigr-foundation-libs/, ...

[Aisha Tammy]

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"