2022-08-23 12:17:00 UTC

10 files changed, 23 insertions, 40 deletions

diff --git a/metadata/md5-cache/sci-biology/biosql-1.0.1-r2 b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2
index 54c0036aa974..2db325d864b6 100644
--- a/metadata/md5-cache/sci-biology/biosql-1.0.1-r2
+++ b/metadata/md5-cache/sci-biology/biosql-1.0.1-r2
@@ -2,11 +2,11 @@ DEFINED_PHASES=install postinst
 DEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg )
 DESCRIPTION=A generic bioinformatics relational database model
 EAPI=8
-HOMEPAGE=http://www.biosql.org/
+HOMEPAGE=https://biosql.org/
 IUSE=mysql postgres
 KEYWORDS=amd64 x86
 LICENSE=LGPL-3
 RDEPEND=mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) dev-lang/perl
 SLOT=0
-SRC_URI=http://biosql.org/DIST/biosql-1.0.1.tar.bz2
-_md5_=6438fefd6b37886a8a237f7e9b0c1258
+SRC_URI=https://biosql.org/DIST/biosql-1.0.1.tar.bz2
+_md5_=17f139bd8463877fe11118d9b9cc16e2
diff --git a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3 b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3
index 99e6baa842cf..38d1cf5ce831 100644
--- a/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3
+++ b/metadata/md5-cache/sci-biology/exonerate-2.2.0-r3
@@ -12,6 +12,6 @@ RDEPEND=dev-libs/glib:2
 REQUIRED_USE=test? ( utils )
 RESTRICT=!test? ( test )
 SLOT=0
-SRC_URI=http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz
+SRC_URI=https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz
 _eclasses_=gnuconfig	b6b3e92f8b8c996400074b5f61a59256	toolchain-funcs	1542e649be915f43f6908a9e93909961	multilib	5ca4e49abed8e3a2f7b56920eadee157	libtool	241a8f577b9781a42a7421e53448a44e	autotools	9e6965bfaa00f52cc61e0d4bc44c87b3
-_md5_=1e7139985e79a73dd3eda616d23bafc0
+_md5_=4bd132dac9c502e76b3000e9c6d1e897
diff --git a/metadata/md5-cache/sci-biology/iedera-1.05-r2 b/metadata/md5-cache/sci-biology/iedera-1.05-r2
index 7f838d5765dd..68c8c694ea07 100644
--- a/metadata/md5-cache/sci-biology/iedera-1.05-r2
+++ b/metadata/md5-cache/sci-biology/iedera-1.05-r2
@@ -1,12 +1,12 @@
 BDEPEND=sys-devel/gnuconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.5:1.16 ) >=sys-devel/autoconf-2.71 >=sys-devel/libtool-2.4
 DEFINED_PHASES=prepare
-DESCRIPTION=A subset seed design tool for DNA sequence alignment
+DESCRIPTION=Subset seed design tool for DNA sequence alignment
 EAPI=8
-HOMEPAGE=http://bioinfo.lifl.fr/yass/iedera.php
+HOMEPAGE=https://bioinfo.lifl.fr/yass/iedera.php
 INHERIT=autotools
 KEYWORDS=~amd64 ~x86
 LICENSE=GPL-2
 SLOT=0
-SRC_URI=http://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz
+SRC_URI=https://bioinfo.lifl.fr/yass/files/iedera-1.05.tar.gz
 _eclasses_=gnuconfig	b6b3e92f8b8c996400074b5f61a59256	toolchain-funcs	1542e649be915f43f6908a9e93909961	multilib	5ca4e49abed8e3a2f7b56920eadee157	libtool	241a8f577b9781a42a7421e53448a44e	autotools	9e6965bfaa00f52cc61e0d4bc44c87b3
-_md5_=a94a95bf7657c616d7b48d8bc45068c7
+_md5_=c1df71458cdeda01ad17b744ef31dc36
diff --git a/metadata/md5-cache/sci-biology/muscle-3.8.31 b/metadata/md5-cache/sci-biology/muscle-3.8.31
index eea33522ee27..9719a5db923f 100644
--- a/metadata/md5-cache/sci-biology/muscle-3.8.31
+++ b/metadata/md5-cache/sci-biology/muscle-3.8.31
@@ -1,12 +1,12 @@
 DEFINED_PHASES=configure install
 DESCRIPTION=Multiple sequence comparison by log-expectation
 EAPI=7
-HOMEPAGE=http://www.drive5.com/muscle/
+HOMEPAGE=https://www.drive5.com/muscle/
 INHERIT=toolchain-funcs
 KEYWORDS=amd64 ~ppc x86
 LICENSE=public-domain
 RDEPEND=!sci-libs/libmuscle
 SLOT=0
-SRC_URI=http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
+SRC_URI=https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
 _eclasses_=toolchain-funcs	1542e649be915f43f6908a9e93909961	multilib	5ca4e49abed8e3a2f7b56920eadee157
-_md5_=70730a85bf27816f07c7b7498e5adc91
+_md5_=373aea64d7c96030dbc1a9c4404f3985
diff --git a/metadata/md5-cache/sci-biology/pals-1.0-r2 b/metadata/md5-cache/sci-biology/pals-1.0-r2
index d65994a35198..79ce26cc1a2f 100644
--- a/metadata/md5-cache/sci-biology/pals-1.0-r2
+++ b/metadata/md5-cache/sci-biology/pals-1.0-r2
@@ -1,11 +1,11 @@
 DEFINED_PHASES=configure install
 DESCRIPTION=Pairwise Aligner for Long Sequences
 EAPI=8
-HOMEPAGE=http://www.drive5.com/pals/
+HOMEPAGE=https://www.drive5.com/pals/
 INHERIT=toolchain-funcs
 KEYWORDS=amd64 x86
 LICENSE=public-domain
 SLOT=0
-SRC_URI=http://www.drive5.com/pals/pals_source.tar.gz -> pals-1.0.tar.gz
+SRC_URI=https://www.drive5.com/pals/pals_source.tar.gz -> pals-1.0.tar.gz
 _eclasses_=toolchain-funcs	1542e649be915f43f6908a9e93909961	multilib	5ca4e49abed8e3a2f7b56920eadee157
-_md5_=0374a4cc1893f560fdb963ab9e27c56b
+_md5_=03270366228400ac56642b59fb067532
diff --git a/metadata/md5-cache/sci-biology/trf-4.04-r2 b/metadata/md5-cache/sci-biology/trf-4.04-r2
index 30e1962524fe..46eab303fe68 100644
--- a/metadata/md5-cache/sci-biology/trf-4.04-r2
+++ b/metadata/md5-cache/sci-biology/trf-4.04-r2
@@ -1,10 +1,10 @@
 DEFINED_PHASES=install unpack
 DESCRIPTION=Tandem Repeats Finder
 EAPI=8
-HOMEPAGE=http://tandem.bu.edu/trf/trf.html
+HOMEPAGE=https://tandem.bu.edu/trf/trf.html
 KEYWORDS=amd64 x86
 LICENSE=trf
 RESTRICT=mirror bindist
 SLOT=0
-SRC_URI=http://tandem.bu.edu/trf/downloads/trf404.linux
-_md5_=7a6d356b931b70a39c33d922bd23adb1
+SRC_URI=https://tandem.bu.edu/trf/downloads/trf404.linux
+_md5_=44fad2daec87377702c578544bf008e5
diff --git a/metadata/md5-cache/sci-libs/med-4.1.1 b/metadata/md5-cache/sci-libs/med-4.1.1
index 6d84789a6929..5c24a6e7ab18 100644
--- a/metadata/md5-cache/sci-libs/med-4.1.1
+++ b/metadata/md5-cache/sci-libs/med-4.1.1
@@ -4,7 +4,7 @@ DEPEND=!sci-libs/libmed dev-lang/tk:0= >=sci-libs/hdf5-1.10.2:=[fortran?,mpi(+)?
 DESCRIPTION=A library to store and exchange meshed data or computation results
 EAPI=8
 HOMEPAGE=https://www.salome-platform.org/user-section/about/med
-INHERIT=cmake fortran-2 python-single-r1
+INHERIT=cmake flag-o-matic fortran-2 python-single-r1
 IUSE=doc fortran mpi python test python_single_target_python3_8 python_single_target_python3_9 python_single_target_python3_10 python_single_target_python3_11
 KEYWORDS=~amd64 ~x86
 LICENSE=LGPL-3
@@ -14,4 +14,4 @@ RESTRICT=!test? ( test ) python? ( test )
 SLOT=0
 SRC_URI=https://files.salome-platform.org/Salome/other/med-4.1.1.tar.gz
 _eclasses_=toolchain-funcs	1542e649be915f43f6908a9e93909961	multilib	5ca4e49abed8e3a2f7b56920eadee157	flag-o-matic	38d6ec96711cea42a5cb1cc723a6e906	multiprocessing	b4e253ab22cef7b1085e9b67c7a3b730	ninja-utils	58ec4e54962bf45d065fb95030701514	xdg-utils	fffb53a53cf17c9c0c998a3c0a590c7e	cmake	44afbf15c35884f7c840470f1cf05d0d	fortran-2	72d28c6872beb1e7cb99684b0ae4715d	python-utils-r1	dd5e1098e305ad508d21f496e9e37046	python-single-r1	a5747fe6dc0651d95cb78eddd5e160a8
-_md5_=97b96af2c1d97842f7eefce3b017bb17
+_md5_=0fad2338bf66b487f50ae9e9a876355c
diff --git a/metadata/md5-cache/sci-libs/vtk-9.0.3-r4 b/metadata/md5-cache/sci-libs/vtk-9.0.3-r4
deleted file mode 100644
index 6ba7d6dac164..000000000000
--- a/metadata/md5-cache/sci-libs/vtk-9.0.3-r4
+++ /dev/null
@@ -1,17 +0,0 @@
-BDEPEND=mpi? ( app-admin/chrpath ) openmp? ( || ( sys-devel/gcc[openmp(+)] sys-devel/clang-runtime[openmp(+)] ) ) >=dev-util/ninja-1.8.2 >=dev-util/cmake-3.20.5 test? ( x11-base/xorg-server[xvfb] x11-apps/xhost )
-DEFINED_PHASES=compile configure install postinst preinst prepare prerm pretend setup test
-DEPEND=app-arch/lz4 app-arch/xz-utils dev-db/sqlite dev-cpp/eigen[cuda?,openmp?] dev-libs/double-conversion:= dev-libs/expat dev-libs/icu:= dev-libs/libxml2:2 dev-libs/pugixml media-libs/freetype media-libs/libogg media-libs/libpng media-libs/libtheora media-libs/tiff <sci-libs/hdf5-1.12:=[mpi=] sci-libs/kissfft[openmp?] sci-libs/netcdf:=[mpi=] sys-libs/zlib virtual/jpeg all-modules? ( sci-geosciences/liblas[gdal] ) boost? ( dev-libs/boost:=[mpi?] ) cuda? ( dev-util/nvidia-cuda-toolkit:= ) ffmpeg? ( media-video/ffmpeg:= ) gdal? ( sci-libs/gdal:= ) java? ( >=virtual/jdk-1.8:* ) json? ( dev-libs/jsoncpp:= ) mpi? ( sci-libs/h5part sys-cluster/openmpi[cxx,romio] ) mysql? ( dev-db/mariadb-connector-c ) odbc? ( dev-db/unixODBC ) offscreen? ( media-libs/mesa[osmesa] ) postgres? ( dev-db/postgresql:= ) python? ( python_single_target_python3_8? ( >=dev-lang/python-3.8.13:3.8 ) python_single_target_python3_9? ( >=dev-lang/python-3.9.12:3.9 ) python_single_target_python3_10? ( >=dev-lang/python-3.10.4:3.10 ) ) qt5? ( dev-qt/qtcore:5 dev-qt/qtsql:5 dev-qt/qtwidgets:5 ) rendering? ( media-libs/freeglut media-libs/glew:= <sci-libs/proj-8:= virtual/opengl x11-libs/gl2ps ) tbb? ( <dev-cpp/tbb-2021:= ) tk? ( dev-lang/tk:= ) video_cards_nvidia? ( x11-drivers/nvidia-drivers[tools,static-libs] ) views? ( x11-libs/libICE x11-libs/libXext ) web? ( app-admin/webapp-config ) python_single_target_python3_8? ( python? ( boost? ( dev-libs/boost:=[mpi?,python?,python_targets_python3_8(-)] ) gdal? ( sci-libs/gdal:=[python?,python_targets_python3_8(-)] ) mpi? ( dev-python/mpi4py[python_targets_python3_8(-)] ) ) ) python_single_target_python3_9? ( python? ( boost? ( dev-libs/boost:=[mpi?,python?,python_targets_python3_9(-)] ) gdal? ( sci-libs/gdal:=[python?,python_targets_python3_9(-)] ) mpi? ( dev-python/mpi4py[python_targets_python3_9(-)] ) ) ) python_single_target_python3_10? ( python? ( boost? ( dev-libs/boost:=[mpi?,python?,python_targets_python3_10(-)] ) gdal? ( sci-libs/gdal:=[python?,python_targets_python3_10(-)] ) mpi? ( dev-python/mpi4py[python_targets_python3_10(-)] ) ) ) dev-libs/jsoncpp dev-libs/utfcpp pegtl? ( <dev-libs/pegtl-3 ) java? ( >=dev-java/java-config-2.2.0-r3 )
-DESCRIPTION=The Visualization Toolkit
-EAPI=7
-HOMEPAGE=https://www.vtk.org/
-INHERIT=check-reqs cmake cuda flag-o-matic java-pkg-opt-2 python-single-r1 toolchain-funcs virtualx webapp
-IUSE=+X all-modules boost cuda doc examples ffmpeg gdal imaging java +json kits mpi mysql odbc offscreen openmp pegtl postgres python qt5 +rendering tbb theora tk video_cards_nvidia views web java python_single_target_python3_8 python_single_target_python3_9 python_single_target_python3_10 test
-KEYWORDS=amd64 ~arm ~arm64 ~x86 ~amd64-linux ~x86-linux
-LICENSE=BSD LGPL-2
-RDEPEND=app-arch/lz4 app-arch/xz-utils dev-db/sqlite dev-cpp/eigen[cuda?,openmp?] dev-libs/double-conversion:= dev-libs/expat dev-libs/icu:= dev-libs/libxml2:2 dev-libs/pugixml media-libs/freetype media-libs/libogg media-libs/libpng media-libs/libtheora media-libs/tiff <sci-libs/hdf5-1.12:=[mpi=] sci-libs/kissfft[openmp?] sci-libs/netcdf:=[mpi=] sys-libs/zlib virtual/jpeg all-modules? ( sci-geosciences/liblas[gdal] ) boost? ( dev-libs/boost:=[mpi?] ) cuda? ( dev-util/nvidia-cuda-toolkit:= ) ffmpeg? ( media-video/ffmpeg:= ) gdal? ( sci-libs/gdal:= ) java? ( >=virtual/jdk-1.8:* ) json? ( dev-libs/jsoncpp:= ) mpi? ( sci-libs/h5part sys-cluster/openmpi[cxx,romio] ) mysql? ( dev-db/mariadb-connector-c ) odbc? ( dev-db/unixODBC ) offscreen? ( media-libs/mesa[osmesa] ) postgres? ( dev-db/postgresql:= ) python? ( python_single_target_python3_8? ( >=dev-lang/python-3.8.13:3.8 ) python_single_target_python3_9? ( >=dev-lang/python-3.9.12:3.9 ) python_single_target_python3_10? ( >=dev-lang/python-3.10.4:3.10 ) ) qt5? ( dev-qt/qtcore:5 dev-qt/qtsql:5 dev-qt/qtwidgets:5 ) rendering? ( media-libs/freeglut media-libs/glew:= <sci-libs/proj-8:= virtual/opengl x11-libs/gl2ps ) tbb? ( <dev-cpp/tbb-2021:= ) tk? ( dev-lang/tk:= ) video_cards_nvidia? ( x11-drivers/nvidia-drivers[tools,static-libs] ) views? ( x11-libs/libICE x11-libs/libXext ) web? ( app-admin/webapp-config ) python_single_target_python3_8? ( python? ( boost? ( dev-libs/boost:=[mpi?,python?,python_targets_python3_8(-)] ) gdal? ( sci-libs/gdal:=[python?,python_targets_python3_8(-)] ) mpi? ( dev-python/mpi4py[python_targets_python3_8(-)] ) ) ) python_single_target_python3_9? ( python? ( boost? ( dev-libs/boost:=[mpi?,python?,python_targets_python3_9(-)] ) gdal? ( sci-libs/gdal:=[python?,python_targets_python3_9(-)] ) mpi? ( dev-python/mpi4py[python_targets_python3_9(-)] ) ) ) python_single_target_python3_10? ( python? ( boost? ( dev-libs/boost:=[mpi?,python?,python_targets_python3_10(-)] ) gdal? ( sci-libs/gdal:=[python?,python_targets_python3_10(-)] ) mpi? ( dev-python/mpi4py[python_targets_python3_10(-)] ) ) ) java? ( >=dev-java/java-config-2.2.0-r3 )
-REQUIRED_USE=all-modules? ( boost ffmpeg gdal imaging mysql odbc postgres qt5 rendering theora views ) cuda? ( X video_cards_nvidia ) java? ( rendering ) python? ( ^^ ( python_single_target_python3_8 python_single_target_python3_9 python_single_target_python3_10 ) ) qt5? ( X rendering ) tk? ( X rendering python ) web? ( python ) ^^ ( X offscreen )
-RESTRICT=!test? ( test )
-SLOT=0/9.0
-SRC_URI=https://www.vtk.org/files/release/9.0/VTK-9.0.3.tar.gz https://www.vtk.org/files/release/9.0/VTKData-9.0.3.tar.gz doc? ( https://www.vtk.org/files/release/9.0/vtkDocHtml-9.0.3.tar.gz ) examples? ( https://www.vtk.org/files/release/9.0/VTKLargeData-9.0.3.tar.gz ) test? ( https://www.vtk.org/files/release/9.0/VTKLargeData-9.0.3.tar.gz )
-_eclasses_=check-reqs	5e6dfbd7a8d3238a79f009fae7ac469c	toolchain-funcs	1542e649be915f43f6908a9e93909961	multilib	5ca4e49abed8e3a2f7b56920eadee157	edos2unix	33e347e171066657f91f8b0c72ec8773	strip-linguas	ac3ee41ee2d31d8c41a77c0838320cc7	wrapper	4a1902f969e5718126434fc35f3a0d9c	eutils	8f942ebdcf04334697649d4a0bf65a32	flag-o-matic	38d6ec96711cea42a5cb1cc723a6e906	multiprocessing	b4e253ab22cef7b1085e9b67c7a3b730	ninja-utils	58ec4e54962bf45d065fb95030701514	xdg-utils	fffb53a53cf17c9c0c998a3c0a590c7e	cmake	44afbf15c35884f7c840470f1cf05d0d	cuda	15edbf8fd9df209322f42c06ecf59a96	java-utils-2	c79d65661a9f4f72b60376c9e4b3dfa1	java-pkg-opt-2	a71433e535af8faae0c0f6c861a32054	eapi8-dosym	cd7d420bb5be5ee079f27239ce76b8f5	python-utils-r1	dd5e1098e305ad508d21f496e9e37046	python-single-r1	a5747fe6dc0651d95cb78eddd5e160a8	virtualx	644887c82aefdf12001489391fca4f02	webapp	d872f28d7595b70dd46545199ef35fb0
-_md5_=b81b4b929c9525c0a188646e8daf8d57
diff --git a/metadata/pkg_desc_index b/metadata/pkg_desc_index
index 748bdb2ee97c..f8f4a28e37c3 100644
--- a/metadata/pkg_desc_index
+++ b/metadata/pkg_desc_index
@@ -16264,7 +16264,7 @@ sci-biology/glimmer 3.02b: An HMM-based microbial gene finding system from TIGR
 sci-biology/glimmerhmm 3.0.1-r1: A eukaryotic gene finding system from TIGR
 sci-biology/gmap 2020.10.27: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
 sci-biology/hmmer 2.3.2-r5 3.1_beta2-r1: Sequence analysis using profile hidden Markov models
-sci-biology/iedera 1.05-r2: A subset seed design tool for DNA sequence alignment
+sci-biology/iedera 1.05-r2: Subset seed design tool for DNA sequence alignment
 sci-biology/infernal 1.0.2-r1: Inference of RNA alignments
 sci-biology/iqpnni 3.3.2-r2: Important Quartet Puzzling and NNI Operation
 sci-biology/kalign 2.03-r3: Global and progressive multiple sequence alignment
@@ -16783,7 +16783,7 @@ sci-libs/umfpack 5.7.9: Unsymmetric multifrontal sparse LU factorization library
 sci-libs/volk 2.4.1 2.5.0: vector optimized library of kernels
 sci-libs/voro++ 0.4.6-r1: 3D Voronoi cell software library
 sci-libs/votca-tools 1.6.4 2021.2: Votca tools library
-sci-libs/vtk 9.0.3-r4 9.0.3-r5 9.1.0-r2: The Visualization Toolkit
+sci-libs/vtk 9.0.3-r5 9.1.0-r2: The Visualization Toolkit
 sci-libs/xdmf2 1.0_p141226-r4: eXtensible Data Model and Format
 sci-libs/xdrfile 1.1.4: Library to read gromacs trajectory and topology files
 sci-libs/xgks-pmel 2.5.5: PMEL fork of XGKS, an X11-based version of the ANSI Graphical Kernel System
diff --git a/metadata/timestamp.chk b/metadata/timestamp.chk
index 388f96cc5081..38abb5065ae7 100644
--- a/metadata/timestamp.chk
+++ b/metadata/timestamp.chk
@@ -1 +1 @@
-Tue, 23 Aug 2022 12:02:03 +0000
+Tue, 23 Aug 2022 12:17:00 +0000