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-rw-r--r--metadata/md5-cache/dev-lang/gnat-gpl-2017-r12
-rw-r--r--metadata/md5-cache/dev-libs/cyberjack-3.99.5_p1314
-rw-r--r--metadata/md5-cache/sci-biology/infernal-1.0.2-r15
-rw-r--r--metadata/md5-cache/sci-biology/poa-2-r19
-rw-r--r--metadata/md5-cache/sci-biology/vienna-rna-2.1.114
-rw-r--r--metadata/md5-cache/sci-biology/wgs-assembler-7.0-r29
-rw-r--r--metadata/pkg_desc_index4
-rw-r--r--metadata/timestamp.chk2
8 files changed, 15 insertions, 44 deletions
diff --git a/metadata/md5-cache/dev-lang/gnat-gpl-2017-r1 b/metadata/md5-cache/dev-lang/gnat-gpl-2017-r1
index 3ad5bd91d9c4..78cface05905 100644
--- a/metadata/md5-cache/dev-lang/gnat-gpl-2017-r1
+++ b/metadata/md5-cache/dev-lang/gnat-gpl-2017-r1
@@ -12,4 +12,4 @@ RESTRICT=!test? ( test )
SLOT=6.3.0
SRC_URI=http://mirrors.cdn.adacore.com/art/591adbb4c7a4473fcc4532a3 -> gnat-gpl-2017-src.tar.gz http://mirrors.cdn.adacore.com/art/591adb65c7a4473fcbb153ac -> gcc-6-gpl-2017-src.tar.gz http://mirrors.cdn.adacore.com/art/591adbc5c7a4473fcbb153ae -> gcc-interface-6-gpl-2017-src.tar.gz bootstrap? ( amd64? ( http://mirrors.cdn.adacore.com/art/564b3ebec8e196b040fbe66c -> gnat-gpl-2014-x86_64-linux-bin.tar.gz ) x86? ( http://mirrors.cdn.adacore.com/art/564b3e9dc8e196b040fbe248 -> gnat-gpl-2014-x86-linux-bin.tar.gz ) ) mirror://gentoo/gcc-6.3.0-patches-1.0.tar.bz2 https://dev.gentoo.org/~vapier/dist/gcc-6.3.0-patches-1.0.tar.bz2 https://dev.gentoo.org/~rhill/dist/gcc-6.3.0-patches-1.0.tar.bz2 https://dev.gentoo.org/~zorry/patches/gcc/gcc-6.3.0-patches-1.0.tar.bz2 https://dev.gentoo.org/~blueness/dist/gcc-6.3.0-patches-1.0.tar.bz2 https://dev.gentoo.org/~tamiko/distfiles/gcc-6.3.0-patches-1.0.tar.bz2 https://dev.gentoo.org/~slyfox/distfiles/gcc-6.3.0-patches-1.0.tar.bz2 gcj? ( ftp://sourceware.org/pub/java/ecj-4.5.jar )
_eclasses_=desktop 7fd20552ce4cc97e8acb132a499a7dd8 eapi7-ver f9ec87e93172b25ce65a85303dc06964 epatch ed88001f77c6dd0d5f09e45c1a5b480e estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 fixheadtails 662e80584ee2337b981d7188078e7c74 flag-o-matic f1194291b9a1baca337c1c89b5f7f365 gnuconfig b8ec1c34be4ff9dac7ad4034d277936b libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 2477ebe553d3e4d2c606191fe6c33602 pax-utils a41d1fd1c111289ffa04490de6ee79d7 prefix c2993e4c430c1ee24f278983d6189501 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain 3c5c1f58d3da32714ebe931369218569 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=2100f920fa3478c15db3e673bfdd382c
+_md5_=8cf44353748b23db21a47555d5211b1f
diff --git a/metadata/md5-cache/dev-libs/cyberjack-3.99.5_p13 b/metadata/md5-cache/dev-libs/cyberjack-3.99.5_p13
deleted file mode 100644
index 8d493f075291..000000000000
--- a/metadata/md5-cache/dev-libs/cyberjack-3.99.5_p13
+++ /dev/null
@@ -1,14 +0,0 @@
-BDEPEND=virtual/pkgconfig >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 virtual/pkgconfig
-DEFINED_PHASES=compile configure install prepare setup
-DEPEND=sys-apps/pcsc-lite usb? ( virtual/libusb:1 ) udev? ( virtual/udev ) xml? ( dev-libs/libxml2:2= )
-DESCRIPTION=REINER SCT cyberJack USB chipcard reader user space driver
-EAPI=7
-HOMEPAGE=https://www.reiner-sct.de/
-IUSE=static-libs threads tools +udev +usb xml kernel_linux
-KEYWORDS=amd64 x86
-LICENSE=GPL-2+ LGPL-2.1+
-RDEPEND=sys-apps/pcsc-lite usb? ( virtual/libusb:1 ) udev? ( virtual/udev ) xml? ( dev-libs/libxml2:2= )
-SLOT=0
-SRC_URI=https://support.reiner-sct.de/downloads/LINUX/V3.99.5_SP13/pcsc-cyberjack_3.99.5final.SP13.tar.gz
-_eclasses_=autotools 7d999b62b8749fad43fff00620cedf47 eutils fcb2aa98e1948b835b5ae66ca52868c5 flag-o-matic f1194291b9a1baca337c1c89b5f7f365 libtool f143db5a74ccd9ca28c1234deffede96 linux-info 5d5cc2632ef6b3c817019fa4fa3d8508 multilib 2477ebe553d3e4d2c606191fe6c33602 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb udev 452708c3f55cf6e918b045adb949a9e6
-_md5_=1917ff3c708a102f0da86298b10eb7e7
diff --git a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1 b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1
index e3d478338308..b43dc9f10d3a 100644
--- a/metadata/md5-cache/sci-biology/infernal-1.0.2-r1
+++ b/metadata/md5-cache/sci-biology/infernal-1.0.2-r1
@@ -1,7 +1,7 @@
DEFINED_PHASES=configure install
DEPEND=mpi? ( virtual/mpi )
DESCRIPTION=Inference of RNA alignments
-EAPI=6
+EAPI=7
HOMEPAGE=http://infernal.janelia.org/
IUSE=mpi
KEYWORDS=amd64 x86
@@ -9,4 +9,5 @@ LICENSE=GPL-3
RDEPEND=mpi? ( virtual/mpi )
SLOT=0
SRC_URI=ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz
-_md5_=a3cee86cfd4ecbef4e39563bc652a64b
+_eclasses_=multilib 2477ebe553d3e4d2c606191fe6c33602 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb
+_md5_=a3b1f788e8f5b38e41b3a9e38f91fe88
diff --git a/metadata/md5-cache/sci-biology/poa-2-r1 b/metadata/md5-cache/sci-biology/poa-2-r1
index 793985885507..91bb06718743 100644
--- a/metadata/md5-cache/sci-biology/poa-2-r1
+++ b/metadata/md5-cache/sci-biology/poa-2-r1
@@ -1,11 +1,10 @@
-DEFINED_PHASES=compile install postinst prepare
+DEFINED_PHASES=compile configure install postinst
DESCRIPTION=Fast multiple sequence alignments using partial-order graphs
-EAPI=5
+EAPI=7
HOMEPAGE=http://bioinfo.mbi.ucla.edu/poa/
-IUSE=static-libs
KEYWORDS=~amd64 ~x86
LICENSE=GPL-2
SLOT=0
SRC_URI=mirror://sourceforge/poamsa/poaV2.tar.gz
-_eclasses_=desktop 7fd20552ce4cc97e8acb132a499a7dd8 epatch ed88001f77c6dd0d5f09e45c1a5b480e estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 2477ebe553d3e4d2c606191fe6c33602 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=ab2bece5c6a9c68d3f07555c962d382d
+_eclasses_=multilib 2477ebe553d3e4d2c606191fe6c33602 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb
+_md5_=d7bb9c94a05320cd21ff72a8beb56406
diff --git a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1 b/metadata/md5-cache/sci-biology/vienna-rna-2.1.1
deleted file mode 100644
index 7938cb23c810..000000000000
--- a/metadata/md5-cache/sci-biology/vienna-rna-2.1.1
+++ /dev/null
@@ -1,14 +0,0 @@
-DEFINED_PHASES=compile configure install prepare test unpack
-DEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) python? ( dev-lang/swig:0 ) >=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4 dev-lang/perl:=[-build(-)]
-DESCRIPTION=RNA secondary structure prediction and comparison
-EAPI=5
-HOMEPAGE=http://www.tbi.univie.ac.at/~ivo/RNA/
-IUSE=doc openmp python static-libs python_targets_python2_7
-KEYWORDS=amd64 ppc x86
-LICENSE=vienna-rna
-RDEPEND=dev-lang/perl media-libs/gd doc? ( dev-texlive/texlive-latex ) python? ( python_targets_python2_7? ( >=dev-lang/python-2.7.5-r2:2.7 ) >=dev-lang/python-exec-2:=[python_targets_python2_7(-)?,-python_single_target_python2_7(-)] ) dev-lang/perl:=[-build(-)]
-REQUIRED_USE=python? ( || ( python_targets_python2_7 ) )
-SLOT=0
-SRC_URI=http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-2.1.1.tar.gz
-_eclasses_=autotools 7d999b62b8749fad43fff00620cedf47 autotools-utils 95db0904ad0f62535e18e5ccb67cce5e desktop 7fd20552ce4cc97e8acb132a499a7dd8 distutils-r1 44725b3eb803b8abcd6978759c231210 epatch ed88001f77c6dd0d5f09e45c1a5b480e estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 libtool f143db5a74ccd9ca28c1234deffede96 ltprune 2729691420b6deeda2a90b1f1183fb55 multibuild 40fe59465edacd730c644ec2bc197809 multilib 2477ebe553d3e4d2c606191fe6c33602 multiprocessing cac3169468f893670dac3e7cb940e045 perl-functions 6ec4c4d8fc8324200f1c14e8d158c59b perl-module 97206c028d9bdc9f248e022ac5c9fc83 preserve-libs ef207dc62baddfddfd39a164d9797648 python-r1 8386b016a2b3bbefa88443fdaa898057 python-utils-r1 ace0a9a129fcfeaae542c0d15c07f36a toolchain-funcs 605c126bed8d87e4378d5ff1645330cb unpacker b5891c9326ad2e7905c011d44c927c34 vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf xdg-utils ff2ff954e6b17929574eee4efc5152ba
-_md5_=1e58c830b49ced05ae9960fcc2dead13
diff --git a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2 b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2
index 063894d236f3..202f9f785ee1 100644
--- a/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2
+++ b/metadata/md5-cache/sci-biology/wgs-assembler-7.0-r2
@@ -1,13 +1,12 @@
-DEFINED_PHASES=compile configure install prepare
+DEFINED_PHASES=compile configure install
DEPEND=net-libs/libtirpc x11-libs/libXt !x11-terms/terminator
DESCRIPTION=The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG
-EAPI=6
+EAPI=7
HOMEPAGE=https://sourceforge.net/projects/wgs-assembler/
-IUSE=static-libs
KEYWORDS=amd64 x86
LICENSE=GPL-2
RDEPEND=net-libs/libtirpc x11-libs/libXt !x11-terms/terminator app-shells/tcsh dev-perl/Log-Log4perl
SLOT=0
SRC_URI=mirror://sourceforge/wgs-assembler/wgs-7.0.tar.bz2
-_eclasses_=desktop 7fd20552ce4cc97e8acb132a499a7dd8 epatch ed88001f77c6dd0d5f09e45c1a5b480e estack 686eaab303305a908fd57b2fd7617800 eutils fcb2aa98e1948b835b5ae66ca52868c5 ltprune 2729691420b6deeda2a90b1f1183fb55 multilib 2477ebe553d3e4d2c606191fe6c33602 preserve-libs ef207dc62baddfddfd39a164d9797648 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb vcs-clean 2a0f74a496fa2b1552c4f3398258b7bf
-_md5_=cb4182fc2947f2a3efa19db296a6a76f
+_eclasses_=multilib 2477ebe553d3e4d2c606191fe6c33602 toolchain-funcs 605c126bed8d87e4378d5ff1645330cb
+_md5_=8de6fdef210cdf37e56e086c61983865
diff --git a/metadata/pkg_desc_index b/metadata/pkg_desc_index
index a8e18b7476aa..93a38cb62fd7 100644
--- a/metadata/pkg_desc_index
+++ b/metadata/pkg_desc_index
@@ -4888,7 +4888,7 @@ dev-libs/crypto++ 5.6.5-r1 7.0.0-r3 8.2.0 8.2.0-r2: C++ class library of cryptog
dev-libs/cudnn 6.0 7.0.5-r1 7.1.4 7.4.1.5 7.4.2.24 7.5.0.56 7.6.0.64 7.6.1.34 7.6.2.24 7.6.5.32 7.6.5.32-r2: NVIDIA Accelerated Deep Learning on GPU library
dev-libs/cvector 1.0.3.1: An ANSI C implementation of dynamic arrays (approximation of C++ vectors)
dev-libs/cxxtools 2.2.1: Collection of general purpose C++-classes
-dev-libs/cyberjack 3.99.5_p13 3.99.5_p14: REINER SCT cyberJack USB chipcard reader user space driver
+dev-libs/cyberjack 3.99.5_p14: REINER SCT cyberJack USB chipcard reader user space driver
dev-libs/cyrus-sasl 2.1.27-r3 2.1.27-r4: The Cyrus SASL (Simple Authentication and Security Layer)
dev-libs/d0_blind_id 0.5 1.0: Blind-ID library for user identification using RSA blind signatures
dev-libs/darts 0.32 0.32h_pre20181117064816 9999: Darts-clone (Double-ARray Trie System) C++ library
@@ -15610,7 +15610,7 @@ sci-biology/unafold 3.8-r1: Unified Nucleic Acid Folding and hybridization packa
sci-biology/update-blastdb 12.0.0: update_blastdb.pl for local blast db maintainance
sci-biology/vcftools 0.1.14: Tools for working with VCF (Variant Call Format) files
sci-biology/velvet 1.2.10: A sequence assembler for very short reads
-sci-biology/vienna-rna 2.1.1 2.1.8: RNA secondary structure prediction and comparison
+sci-biology/vienna-rna 2.1.8: RNA secondary structure prediction and comparison
sci-biology/wgs-assembler 7.0-r2: The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG
sci-biology/wise 2.4.0_alpha: Intelligent algorithms for DNA searches
sci-biology/yass 1.14-r2: Genomic similarity search with multiple transition constrained spaced seeds
diff --git a/metadata/timestamp.chk b/metadata/timestamp.chk
index c6f1b08c3985..5aaf788ef16f 100644
--- a/metadata/timestamp.chk
+++ b/metadata/timestamp.chk
@@ -1 +1 @@
-Sun, 21 Jun 2020 17:35:17 +0000
+Sun, 21 Jun 2020 18:05:50 +0000