gentoo resync : 04.07.2020

18 files changed, 11 insertions, 235 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index d9ab1fab5e1e..a7c8917767f8 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest
index d1449e8aff1c..fe6af898c915 100644
--- a/sci-libs/avogadrolibs/Manifest
+++ b/sci-libs/avogadrolibs/Manifest
@@ -7,6 +7,7 @@ AUX avogadrolibs-1.93.0-fix_AvogadroLibsConfig.patch 695 BLAKE2B 40feb1bfe132fe5
 DIST avogadrolibs-1.91.0_pre20180415.tar.gz 2541101 BLAKE2B 526d2135af123d31220c8dd87351a35464e3dfd6b8d411d6dc9a6b3e74693090adfa3b61198a6a296eac99e6bbd67623f7aeda6a1752a09e3e3bcaa3df4d5008 SHA512 1cc646368f70523fcf20c6cf598025234162e0c81da64a3b5375c1691a6743f2aceb1f13230937bf9da045e725a23c1c89c8121e07b31ef9e2c7987b1feafccc
 DIST avogadrolibs-1.93.0.tar.gz 2735862 BLAKE2B b5d696f23aeeab27358ee390a30b2cf146e7119185a0d2e8d71b34d2744e534cd8b50b36d12928b5aa723118db470272b6428514593d64770d172c4bde730cf6 SHA512 1af220e5614cbd96656679c2879cb7f7c46acd135b4e6f2e5f8d0ba98601ce004e78f019a0a71c643f005451309bd194eb73eb9f66707685e5855b47e95f7eae
 DIST linux64-genXrdPattern 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
+DIST linux64-genXrdPattern-avogadrolibs-1.93.0 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
 EBUILD avogadrolibs-1.91.0_pre20180415.ebuild 2223 BLAKE2B 6a9201d8b944a49fca4a0ef06f227e3d941539666d14a60a12cd72531ff46b1a5845a1543c44a8117b843174a2dacb4b3605e7a5afd4fc893b404bcb9b72304e SHA512 cad3ea94243eccc4f734368a5a8ebdfef1ec7ece172ab6b97e2470b3bc4b5e05c7da2b5ca8c898d4f05ebf5a8531aca6dfbcceea39987dbe5754617bbbe0293e
-EBUILD avogadrolibs-1.93.0.ebuild 2319 BLAKE2B 949191323ba13df889944a1908bbf23417e8770139d8fb060395bc809ce0e0de1bf1ac3927c88a6449979801ba3ca92107d6a15e409a2a703efbe9b59262e19b SHA512 be5e96632b2a43aeb2b33e45ba2048cf982bfb9b2759a9e0d3c755108d05afc53f2f3073e21fdc5f1960f6ac8ee67c70c0154f1a068f6f0c7fd0c4fad03f9289
+EBUILD avogadrolibs-1.93.0.ebuild 2422 BLAKE2B 911019bbe695b030064bd0c23159402d22ddfae058f3a7bcbc87427b76616b125ae283ab0ed35afe16d915957f7468974afc74b8dfb8c4ff3bbb976987ea918e SHA512 a360095e50bee771e34c4be736a1afd5ccf6ad4687a8f0294093a18a095cf2bea6ec4443b79bae2e75ae3edcbeb77439af54d3d0d1a32930554727b7d62acdfc
 MISC metadata.xml 670 BLAKE2B 39737e6ffacaf9284506e41dfa1154f233a6bf37dd514c0eafe6bdf7bd7129a43d81cf4c3e510759b7888277bb403ad933e21abf0ba4dbedd43fda2aa2b55edd SHA512 781b3e67a291253d83d6c2e11124b07dbae652267de2702a1a2b10680f7db19cf35bda8964b320658d849091bd9ead07eeb5fc682a8817101dd1e7a1e9e20757
diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.93.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.93.0.ebuild
index a1cbede0ed28..a2872894639d 100644
--- a/sci-libs/avogadrolibs/avogadrolibs-1.93.0.ebuild
+++ b/sci-libs/avogadrolibs/avogadrolibs-1.93.0.ebuild
@@ -8,7 +8,7 @@ DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries"
 HOMEPAGE="https://www.openchemistry.org/ https://github.com/OpenChemistry/avogadrolibs"
 SRC_URI="
 	https://github.com/OpenChemistry/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
-	vtk? ( https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern )
+	vtk? ( https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern -> linux64-genXrdPattern-${P} )
 "
 
 SLOT="0"
@@ -51,12 +51,13 @@ DEPEND="${RDEPEND}
 PATCHES=(
 	# https://github.com/OpenChemistry/avogadrolibs/issues/449
 	"${FILESDIR}"/${PN}-1.93.0-fix_AvogadroLibsConfig.patch
+	"${FILESDIR}/"${PN}-1.91.0_pre20180406-bundled-genxrdpattern.patch
 )
 
 src_unpack() {
 	default
 	if use vtk; then
-		cp "${DISTDIR}"/linux64-genXrdPattern "${WORKDIR}/genXrdPattern" || die
+		cp "${DISTDIR}"/linux64-genXrdPattern-${P} "${WORKDIR}/genXrdPattern" || die
 	fi
 }
 
diff --git a/sci-libs/deap/Manifest b/sci-libs/deap/Manifest
deleted file mode 100644
index 0581d4b96f03..000000000000
--- a/sci-libs/deap/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-DIST deap-0.9.1.tar.gz 968521 BLAKE2B 2846e98b88164c09133317f7eaca09e096f64b6dec4b824b79b688d5418dc3eb1f3eaeadeab3d582cbbbadbde37c353d451b93861c6415258fa286a659762ff6 SHA512 70786b444a05e4db9c95f132af4308acb058e507a537946979a735025f2ed5bbafe13c3c876d3c73cef6dc034c8e28f4a982afbc4416a4905be5d3b905831107
-DIST deap-1.0.0.tar.gz 847713 BLAKE2B bcf9f862f8d1ae37723f026a3bb06c2e168a2b8d868c99041176747ae02ca2e78d382b241a1ff2707ee352706ec0de5cee90c00432905479de10886fac7fcd12 SHA512 4d7bb72586c3c8bf1b7e353721cf86be6b6a845965a69f03c60fbfcc5995e88d99b094aa6a82cdf8c4cfc4aae7401c1c30348f54702e7d5d91e3f0aeaae4af49
-DIST deap-1.0.1.tar.gz 861409 BLAKE2B f0b37e4fc054b86a4bf08bd010d02281317bacdaf6b3c80fce99a0227907dd0c4c3004692d90471b1dc53b2d30d3bc6fb035f1ccd4886bf7adda33845c5e5c9b SHA512 82e7e60f669d242aba1786d5a9c1f01dd581ff7e77b4e5c2ec173d06c4ea2edc33ebae2390f103b635d8568b2664ca5ad7f9ba81ebd26472251a1c0d04b3e073
-EBUILD deap-0.9.1.ebuild 423 BLAKE2B 7c716bc401d0aa7c78a2c830962f009270506862d6bdf7a961b9a73b346c675956d581eee12c26d0d577ff2286639a8d9edf74cb29a0ca11cd302e977731cb74 SHA512 b0134b6c4a1a8aeae92598860b95be4b232c75b5617b2081f54780c14e28734e628586e79d5b6c01ea3bec6bf60a8c0d0e02f3c3e3e0185b6fc67f8c669569f3
-EBUILD deap-1.0.0.ebuild 452 BLAKE2B 373cfe053f95d3528b254a756082df6a3b6ba8fa98ec67ed767f7c12cd91604ef63bf501cf946a97e63890565ae2d27f2c1262f45be8646b9643fe948b925edd SHA512 3f86601c83201641f102338eae2cb6e07937f8df604fff0c516965a419cb1214cdfe04eb84d9e66c1fbd7a01a8c9269924faae6814008e9189e83c31b662b6db
-EBUILD deap-1.0.1.ebuild 437 BLAKE2B 8bcbe6f25ea826bdae8716f742e4a1d170641e1a2d500ceb061c2bca29453a12718e1ceb0426cd85f7afbba56e5003ad5ecfcf9f32db6040a4dd298f1d400415 SHA512 c3f4b72fd66c84a5a3e81609dd2141c7194bf187ad51d661d6ee7fe98a10a441e4d15e2a3c5c175aec9300739485b9fd893c4b378cd140ed7d324e9899c8a165
-MISC metadata.xml 633 BLAKE2B 59d9b2e51488273f55ab6662aa5d86833aa1419bd5e678dbf92271ad3d193ee15b974d1bb27f9f9f4eb44bed515aabefed84fc763af8076fcd0c363172b13cdd SHA512 7d1fe41bdf5c095cb8e2e330238c1bdb1ea3c1e48198d9c93786659fb9535df84db8af151aa850d2934b18bdee20354126bca28fa047e0c383d984851d43fd63
diff --git a/sci-libs/deap/deap-0.9.1.ebuild b/sci-libs/deap/deap-0.9.1.ebuild
deleted file mode 100644
index ccb293d84705..000000000000
--- a/sci-libs/deap/deap-0.9.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Novel evolutionary computation framework"
-HOMEPAGE="https://code.google.com/p/deap/"
-SRC_URI="https://deap.googlecode.com/files/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="dev-python/setuptools"
diff --git a/sci-libs/deap/deap-1.0.0.ebuild b/sci-libs/deap/deap-1.0.0.ebuild
deleted file mode 100644
index 923a82748ad6..000000000000
--- a/sci-libs/deap/deap-1.0.0.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-inherit distutils-r1
-
-DESCRIPTION="Distributed Evolutionary Algorithms in Python"
-HOMEPAGE="https://code.google.com/p/deap/ https://pypi.org/project/deap/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="dev-python/setuptools"
diff --git a/sci-libs/deap/deap-1.0.1.ebuild b/sci-libs/deap/deap-1.0.1.ebuild
deleted file mode 100644
index b33af7bbecab..000000000000
--- a/sci-libs/deap/deap-1.0.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Novel evolutionary computation framework"
-HOMEPAGE="https://github.com/deap/deap"
-SRC_URI="https://github.com/DEAP/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="dev-python/setuptools"
diff --git a/sci-libs/deap/metadata.xml b/sci-libs/deap/metadata.xml
deleted file mode 100644
index 62d9ca88584a..000000000000
--- a/sci-libs/deap/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<!-- maintainer-needed -->
-	<longdescription>
-		DEAP stands for Distributed Evolutionary Algorithm in Python, it is dedicated to people who
-		wish to learn how to use evolutionary algorithms and to those who wish to
-		rediscover evolutionary algorithms. DEAP is the proof that evolutionary
-		algorithms do **not** need to be neither complex or complicated.
-	</longdescription>
-	<upstream>
-		<remote-id type="pypi">deap</remote-id>
-		<remote-id type="github">DEAP/deap</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/kim-api/Manifest b/sci-libs/kim-api/Manifest
index 31e460f8f35e..98b3ffead8a1 100644
--- a/sci-libs/kim-api/Manifest
+++ b/sci-libs/kim-api/Manifest
@@ -1,5 +1,5 @@
 DIST kim-api-2.1.3.txz 296492 BLAKE2B 707ae2eaeaa737865d9b4f48a7f1ed53fb6453fc3680dee3b5b41f315b60710dfa9546105bc871cf1a4667644434e4a8eab0c95976feef3bed73ff8401613ac3 SHA512 efbc0214234b43a65ed40d23d8faa5264ac1dbd056e9e340548ea7ee5dc530f9cfb2d85a1d9d47fba9dfc7aa660a8ec20374daf4aa8ee605e7c097ae2a12512d
 DIST kim-api-v1.8.2.tgz 1634997 BLAKE2B ab2db24b9bb619aac3fdad6868d36d9615f0b08a8325613cd311d32dadab2f23105fe92b73e32c442d0f64364fde32d1293cc063637ff49eb49760a46bcb4f4b SHA512 fed930d147bfbb7936548eb129fcc403df90d1a8010f0fd5b85eaa35c1529d76c9c7c10b098b8eb74d9878e6d3ba0fad3c10d2a3e5bc9b673841a2abc290bac3
 EBUILD kim-api-1.8.2.ebuild 642 BLAKE2B 8aee22e3c2032ca6df812a1c548420e84296d5a4ed78a499b61f5703ef0d40427b64fdedd705834df508251091ca5ba0f7ef74ed7d4cf59558fd88c1bdd45cee SHA512 3a6a1f11f40af004330ebb4a55edcd12a93249e8c816f695e5a42044096e864c23154dbdb4d0f024d8882e538ef29269fb0c3ab56f4b516ce79b7f5408530405
-EBUILD kim-api-2.1.3.ebuild 384 BLAKE2B cb8fefd8a9141e7921422ec879388a2e604f40e1073d8ece7e7f48aec15454238152e10a8327bce6b887e619ffab3b911cad053fbcbec44f75c171e652accfda SHA512 dd4233a98b5ac9513e48f8761162e89e009c9dd3afbfeb974341df5a7fd2a95d8c290d3a5bdfd79727033ad2f109d80db6ec9795ee028ee1e8d5849112af73f1
+EBUILD kim-api-2.1.3.ebuild 404 BLAKE2B 6473d91267bf97d51779a6f2f63a413f5c7f21a4e72e2e6c1f6e0ca3fa79235124d020fc3f708d43bfbe45141151fc2888fed459a1349ad06720adbd7f8dcc5c SHA512 1da030e9a8f23fc06146dbefe08ecc9775ef00872e987137b8e977e1bb820e235f635a4436deb02569d3a7db01465db9122a19cec2cf75c2479e18d14ba95fe5
 MISC metadata.xml 367 BLAKE2B cc3fc8e9dbc98eef49a88d43c68b358b5d2f658316247637a9a3925de3784eb2e82de849e0a49217d5b49be74c280b81a66abbfdd9310fd18b77d67451a480c2 SHA512 455c79e8837ba1ed980967e3236d4a0ac0edbd1b88b056a06d715894e03e7fc802079440752e60a06c9ce4acb62fd68d4020a7847a154a14065afd995257f685
diff --git a/sci-libs/kim-api/kim-api-2.1.3.ebuild b/sci-libs/kim-api/kim-api-2.1.3.ebuild
index 60c0e882f990..b97d6cf0670f 100644
--- a/sci-libs/kim-api/kim-api-2.1.3.ebuild
+++ b/sci-libs/kim-api/kim-api-2.1.3.ebuild
@@ -14,5 +14,5 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
+DEPEND="app-editors/vim-core"
 RDEPEND="${DEPEND}"
diff --git a/sci-libs/pcl/Manifest b/sci-libs/pcl/Manifest
index 5c0604fc2fcf..457203a6cbbc 100644
--- a/sci-libs/pcl/Manifest
+++ b/sci-libs/pcl/Manifest
@@ -1,6 +1,4 @@
 DIST pcl-1.11.0.tar.gz 67091890 BLAKE2B 77dcaf99e19cd3042a01176e57441a38e7f5095d7bd9b08c9ad4464384eb6c603eab9734a6bcbb52eff9da55c3aaa69b3744a10137b8264e5729c2432a678f71 SHA512 1cde48349b2630d1bb89fa50b2844054802fe02d22c810516bc41a712823a26cd5fa1b14297718f517b88c371a637567b31fb8c4c9b4908e94fb3a7208095127
-DIST pcl-1.9.1.tar.gz 67158067 BLAKE2B 472422930e08feba11f42a2df49d68e0c55484744e0649164b113dc3b654188e598b1c0a55f1b75680150090749b00378ae0f70b35b1695a7914a16be7415bf7 SHA512 ca95028c23861ac2df0fa7e18fdd0202255cb2e49ab714325eb36c35289442c6eedbf489e6f9f232b30fa2a93eff4c9619f8a14d3fdfe58f353a4a6e26206bdf
-EBUILD pcl-1.11.0.ebuild 2173 BLAKE2B 5bf60542a71815e62d08dd31bc79146bee3a3bc9a3db90fa0f334ab6bf7d9430fb9441fe9dbba301567ff3d10185794449292c35c4cc54ce75f69179c072d78c SHA512 9635a58f08d3a1ec9c6053ec3ac24e913811ae02ca2b58bd91315680031b7122394718cdfe62be4619dfc49ef35531283d435fdc51b925b03d59545832eb5d2a
-EBUILD pcl-1.9.1.ebuild 2252 BLAKE2B 3a488488afb1d0d18da684f9fa35c490a8f70ebd3f08d0668cdd265f17384adfa89228ee7034573040e90a9b78301693256fefa6361ff8754fff84517007714c SHA512 b0d94f742f20576b2adc6277c05b53dd78463432b3892f2ebaf58332cb2726cf6d436903f85a8e69c5ac9c350a839d27dc1c521a13ecab05d1e6f6e176225232
-EBUILD pcl-9999.ebuild 2173 BLAKE2B 5bf60542a71815e62d08dd31bc79146bee3a3bc9a3db90fa0f334ab6bf7d9430fb9441fe9dbba301567ff3d10185794449292c35c4cc54ce75f69179c072d78c SHA512 9635a58f08d3a1ec9c6053ec3ac24e913811ae02ca2b58bd91315680031b7122394718cdfe62be4619dfc49ef35531283d435fdc51b925b03d59545832eb5d2a
+EBUILD pcl-1.11.0.ebuild 2174 BLAKE2B 0e8893788a3c82015da257ee9a06bd89cf065ca5eaaeefb4a7988f98fc289d8dfd44c74c1eddfe23e062c434fb6a425d0b1572232eea0a1d6f362b06a4e142c0 SHA512 86b6eeeaa5c3b2da5f0458cd53bd3b370554fe2ce4583c3b2618b8f1d4362c648d05ea7328bc6504bd1d7aec169add0c414dac1162743acb361e3bf7601a22f9
+EBUILD pcl-9999.ebuild 2174 BLAKE2B 0e8893788a3c82015da257ee9a06bd89cf065ca5eaaeefb4a7988f98fc289d8dfd44c74c1eddfe23e062c434fb6a425d0b1572232eea0a1d6f362b06a4e142c0 SHA512 86b6eeeaa5c3b2da5f0458cd53bd3b370554fe2ce4583c3b2618b8f1d4362c648d05ea7328bc6504bd1d7aec169add0c414dac1162743acb361e3bf7601a22f9
 MISC metadata.xml 1125 BLAKE2B 27e8b272d41bf690e99b28e7b9af140412e3d5641f56131c1c8ece113262f3222444a487a3e6a050fcf7fb8c8c404f284bc731780fa557d56241e0e0ad18613f SHA512 d5676bf63401993065215538dd0725f13a99251117e7e61cf9614ea765eb0b9388a8866aa74fb6840dba4ead49f763070076cd328c60ab0830ff11bee827e7cf
diff --git a/sci-libs/pcl/pcl-1.11.0.ebuild b/sci-libs/pcl/pcl-1.11.0.ebuild
index 340870c8b8e2..04c17c371e91 100644
--- a/sci-libs/pcl/pcl-1.11.0.ebuild
+++ b/sci-libs/pcl/pcl-1.11.0.ebuild
@@ -20,7 +20,7 @@ else
 	S="${WORKDIR}/${PN}-${P}"
 fi
 
-HOMEPAGE="http://pointclouds.org/"
+HOMEPAGE="https://pointclouds.org/"
 DESCRIPTION="2D/3D image and point cloud processing"
 LICENSE="BSD"
 SLOT="0/1.11"
diff --git a/sci-libs/pcl/pcl-1.9.1.ebuild b/sci-libs/pcl/pcl-1.9.1.ebuild
deleted file mode 100644
index 19c912a12d8c..000000000000
--- a/sci-libs/pcl/pcl-1.9.1.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-SCM=""
-if [ "${PV#9999}" != "${PV}" ] ; then
-	SCM="git-r3"
-	EGIT_REPO_URI="https://github.com/PointCloudLibrary/pcl"
-fi
-
-inherit ${SCM} cmake-utils multilib
-
-if [ "${PV#9999}" != "${PV}" ] ; then
-	KEYWORDS=""
-	SRC_URI=""
-else
-	KEYWORDS="~amd64 ~arm"
-	SRC_URI="https://github.com/PointCloudLibrary/pcl/archive/${P}.tar.gz"
-	S="${WORKDIR}/${PN}-${P}"
-fi
-
-HOMEPAGE="http://pointclouds.org/"
-DESCRIPTION="2D/3D image and point cloud processing"
-LICENSE="BSD"
-SLOT="0/1.9"
-IUSE="cuda doc opengl openni openni2 pcap png +qhull qt5 usb vtk cpu_flags_x86_sse test tutorials"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	>=sci-libs/flann-1.7.1
-	dev-libs/boost:=[threads]
-	dev-cpp/eigen:3
-	opengl? ( virtual/opengl media-libs/freeglut )
-	openni? ( dev-libs/OpenNI )
-	openni2? ( dev-libs/OpenNI2 )
-	pcap? ( net-libs/libpcap )
-	png? ( media-libs/libpng:0= )
-	qhull? ( media-libs/qhull )
-	qt5? (
-		dev-qt/qtgui:5
-		dev-qt/qtcore:5
-		dev-qt/qtconcurrent:5
-		dev-qt/qtopengl:5
-	)
-	usb? ( virtual/libusb:1 )
-	vtk? ( >=sci-libs/vtk-5.6:=[imaging,rendering] )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4 )
-"
-DEPEND="${RDEPEND}
-	!!dev-cpp/metslib
-	doc? ( app-doc/doxygen )
-	tutorials? ( dev-python/sphinx dev-python/sphinxcontrib-doxylink )
-	test? ( >=dev-cpp/gtest-1.6.0 )
-	virtual/pkgconfig"
-
-REQUIRED_USE="
-	openni? ( usb )
-	openni2? ( usb )
-	tutorials? ( doc )
-"
-
-src_configure() {
-	local mycmakeargs=(
-		"-DLIB_INSTALL_DIR=$(get_libdir)"
-		"-DWITH_CUDA=$(usex cuda TRUE FALSE)"
-		"-DWITH_LIBUSB=$(usex usb TRUE FALSE)"
-		"-DWITH_OPENGL=$(usex opengl TRUE FALSE)"
-		"-DWITH_PNG=$(usex png TRUE FALSE)"
-		"-DWITH_QHULL=$(usex qhull TRUE FALSE)"
-		"-DWITH_QT=$(usex qt5 TRUE FALSE)"
-		"-DWITH_VTK=$(usex vtk TRUE FALSE)"
-		"-DWITH_PCAP=$(usex pcap TRUE FALSE)"
-		"-DWITH_OPENNI=$(usex openni TRUE FALSE)"
-		"-DBUILD_OPENNI=$(usex openni TRUE FALSE)"
-		"-DWITH_OPENNI2=$(usex openni2 TRUE FALSE)"
-		"-DBUILD_OPENNI2=$(usex openni2 TRUE FALSE)"
-		"-DPCL_ENABLE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)"
-		"-DWITH_DOCS=$(usex doc TRUE FALSE)"
-		"-DWITH_TUTORIALS=$(usex tutorials TRUE FALSE)"
-		"-DBUILD_TESTS=$(usex test TRUE FALSE)"
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/pcl/pcl-9999.ebuild b/sci-libs/pcl/pcl-9999.ebuild
index 340870c8b8e2..04c17c371e91 100644
--- a/sci-libs/pcl/pcl-9999.ebuild
+++ b/sci-libs/pcl/pcl-9999.ebuild
@@ -20,7 +20,7 @@ else
 	S="${WORKDIR}/${PN}-${P}"
 fi
 
-HOMEPAGE="http://pointclouds.org/"
+HOMEPAGE="https://pointclouds.org/"
 DESCRIPTION="2D/3D image and point cloud processing"
 LICENSE="BSD"
 SLOT="0/1.11"
diff --git a/sci-libs/pycifrw/Manifest b/sci-libs/pycifrw/Manifest
deleted file mode 100644
index ee8f9d61201d..000000000000
--- a/sci-libs/pycifrw/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST PyCifRW-3.6.2.tar.gz 356813 BLAKE2B d1b774a3603dd2b69004f7209e05a539f8be1dd5a2313c13c273a35d0190ef9888d5c926a254d2920d105f90b0ab9aea9b6894e9ea4e1ed8193718da06af0df8 SHA512 21b5738deb54a7293faef2d0cb578047be15feb1e2a0f4e6566777977ec8955c4281e6eddc920c08705f553acec4a574b52ca60b37b8bc0269d6b2cdaec7bf71
-DIST PyCifRW-4.1.1.tar.gz 446258 BLAKE2B 61df861f64b67c6d064a6af588d8f94416fc855f3b0b9284d98348636b7fe9b972dfbfcac3a3e32b15846338df835ac07c4f89317f8dad2b166615e38466e856 SHA512 5358080528851b1341c5294ade0741450963bea26b731ec1cb820e012d921dd329137413b3ca1ffb7d7915a4796415f8b3f9654711052ac744d8db7d6104e18d
-EBUILD pycifrw-3.6.2.ebuild 520 BLAKE2B ae21c61d9e4854144d92c0083cc6a494220b752fb8322003d84c2e50c120821c48e8adad73ea1d44976f46b7dd89e6a1cd236e43dbdbcbb7a00cc1cc29c6caa9 SHA512 b8d323d0c76fd1a2872507933f3f1a4f4950ea7ac560dd98880f6061de1666f9b83ff5592d9fe7d72c38d207e0b3257b3e667a4961f00d4e81dfbace5a0d2c05
-EBUILD pycifrw-4.1.1.ebuild 527 BLAKE2B 51bbf749f9146636b964680a08963349075e387562084d7daaca1e05242f640c18d221baa072b21926db9d2a1df2eb9c0447610b52a885aca72afce9131e852a SHA512 3ba36d4cc7853def7c3142ea5c0035ed3e583573e286c383ba45c1178b0b51a0aae33f68337bb5413711de82f70f214317d6fd3b88b31d03d1ede979d615b082
-MISC metadata.xml 410 BLAKE2B 1d6c55fdb666301a5a49eae059702b2e54949fe2f67467c1e87d0cc676e286311bbdd2ac705c400f62b9c3d21b5cdc3b2a0eed6685a086f22732dcc22f2eb2d1 SHA512 9eeb0a15f8e2066fa9d10aad5042985bd97d0b0e81e7a2842c859f35064b1a9d1b685a25cf38aac854d027c091859c7f0e5a40c3f95570c15929ea7c9edabc8e
diff --git a/sci-libs/pycifrw/metadata.xml b/sci-libs/pycifrw/metadata.xml
deleted file mode 100644
index b763b4f1a8ae..000000000000
--- a/sci-libs/pycifrw/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="pypi">PyCifRW</remote-id>
-    <remote-id type="bitbucket">jamesrhester/pycifrw</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-libs/pycifrw/pycifrw-3.6.2.ebuild b/sci-libs/pycifrw/pycifrw-3.6.2.ebuild
deleted file mode 100644
index 19fd43d8f8a5..000000000000
--- a/sci-libs/pycifrw/pycifrw-3.6.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="PyCifRW"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Provides support for reading and writing of CIF using python"
-HOMEPAGE="https://pypi.org/project/PyCifRW/ https://bitbucket.org/jamesrhester/pycifrw/wiki/Home"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="ASRP"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
diff --git a/sci-libs/pycifrw/pycifrw-4.1.1.ebuild b/sci-libs/pycifrw/pycifrw-4.1.1.ebuild
deleted file mode 100644
index 17841ce359a7..000000000000
--- a/sci-libs/pycifrw/pycifrw-4.1.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="PyCifRW"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Reading and writing CIF (Crystallographic Information Format) files"
-HOMEPAGE="https://pypi.org/project/PyCifRW/ https://bitbucket.org/jamesrhester/pycifrw/wiki/Home"
-SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-LICENSE="ASRP"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"