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branch core-updates updated (b03f270 -> 0171019)
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From: |
Marius Bakke |
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Subject: |
branch core-updates updated (b03f270 -> 0171019) |
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Date: |
Sun, 9 Sep 2018 12:15:14 -0400 (EDT) |
mbakke pushed a change to branch core-updates
in repository guix.
from b03f270 gnu: guile: Remove "share/guile/site" from
GUILE_LOAD_COMPILED_PATH.
adds 38fe644 gnu: Add transset-df.
adds 5108c18 gnu: perl: Add support for cross-compilation
adds fd95f37 Revert "gnu: perl: Add support for cross-compilation"
adds 9c4b522 gnu: Add ghc-wcwidth.
adds 3ad6b89 gnu: ghc-tasty: Update to 1.1.0.3.
adds 8374cc4 gnu: ghc-tasty-ant-xml: Update to 1.1.4.
adds 6300ba5 gnu: ghc-integer-logarithms: Allow building with newer
tasty.
adds 906a396 gnu: ghc-zlib: Enable tests.
adds b50658f gnu: kicad: Update to 5.0.0.
adds 71ca16b gnu: petsc-openmpi: Configure with support for hdf5 data
format.
adds 1bf7587 gnu: Add emacs-picpocket.
adds 7e1d229 inferior: Add home-page and location package accessors.
adds ca71942 Switch to Guile-Gcrypt.
adds 95681e5 gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}].
adds fcf4841 gnu: Zsh: Patch some tests that began failing in 5.6.
adds fefe17b gnu: dolphin-emu: Update to commit 5f0d825.
adds ca1dc4c gnu: nss-pam-ldapd: Update to 0.9.10.
adds 0d7974c gnu: libbigwig: Update to 0.4.2.
adds 8afdeb8 gnu: python-pybigwig: Update to 0.3.12.
adds 4fd2622 gnu: python-tables: Update to 3.4.4.
adds 030f136 channels: Add 'latest-channel-derivation' convenience
procedure.
adds 185948b gnu: xorg: Fix typo.
adds 3d43017 tests: Adjust 'add-file-tree-to-store' test for lack of
/bin/sh.
adds 53166ae gnu: guix: Update to 3d43017.
adds 998100e gnu: eyed3: Update home page.
adds 296f091 gnu: packages: mp3: Use HTTPS where possible.
adds b26e4f2 gnu: Add SUNDIALS.
adds a3a99e2 petsc: Move example code to "examples" output.
adds c15be12 petsc: Upgrade to 3.9.3.
adds 3f5e6cc slepc: Upgrade to 3.9.2.
adds 5e3082d gnu: guile-fibers: Install .go files to "…/site-ccache".
adds 7903f00 gnu: cuirass: Add dependency on Guile-Gcrypt.
adds 3b0153b gnu: guix-daemon: Add dependency on Guile-Gcrypt.
adds 356230d gnu: Add r-fansi.
adds 5371865 gnu: Add r-polynom.
adds dd954dd gnu: Add r-gbrd.
adds 6a84697 gnu: Add r-rdpack.
adds 88e4ed5 gnu: Add r-clipr.
adds 6505016 gnu: r-chippeakanno: Update to 3.14.1.
adds ce0e762 gnu: r-annotationforge: Update to 1.22.2.
adds 3c04375 gnu: r-biocviews: Update to 1.48.3.
adds 5728d9c gnu: r-iranges: Update to 2.14.11.
adds 1adf459 gnu: r-edger: Update to 3.22.3.
adds 33a103a gnu: r-variantannotation: Update to 1.26.1.
adds 688cb08 gnu: r-limma: Update to 3.36.3.
adds 1d56c79 gnu: r-genomicranges: Update to 1.32.6.
adds a023400 gnu: r-biocparallel: Update to 1.14.2.
adds 3e61c2a gnu: r-rsamtools: Update to 1.32.3.
adds aea1b6f gnu: r-delayedarray: Update to 0.6.5.
adds f2e7982 gnu: r-rtracklayer: Update to 1.40.6.
adds ad2ed8d gnu: r-genomicfeatures: Update to 1.32.2.
adds 48b21f8 gnu: r-seqminer: Update to 6.1.
adds 4ee8c37 gnu: r-maldiquant: Update to 1.18.
adds 07bd90c gnu: r-msnbase: Update to 2.6.3.
adds 6f6aef8 gnu: r-seurat: Update to 2.3.4.
adds c273bcd gnu: r-diffusionmap: Update to 1.1-0.1.
adds eb251fe gnu: r-igraph: Update to 1.2.2.
adds 3c55304 gnu: r-edaseq: Update to 2.14.1.
adds ff7c7d6 gnu: r-keggrest: Update to 1.20.1.
adds 70daf93 gnu: r-biovizbase: Update to 1.28.2.
adds 16527f1 gnu: r-ggbio: Update to 1.28.5.
adds e69c07e gnu: r-hdf5array: Update to 1.8.1.
adds 8e44ff0 gnu: r-scater: Update to 1.8.4.
adds f077174 gnu: r-scran: Update to 1.8.4.
adds 1ec1989 gnu: r-httpuv: Update to 1.4.5.
adds 4f8247b gnu: Add r-pkgbuild.
adds e362be8 gnu: Add r-pkgload.
adds 97c81cc gnu: r-stringi: Update to 1.2.4.
adds 3bf3902 gnu: r-scales: Update to 1.0.0.
adds 2a96a09 gnu: r-evaluate: Update to 0.11.
adds 3299bc1 gnu: r-yaml: Update to 2.2.0.
adds 6b02569 gnu: r-dbplyr: Update to 1.2.2.
adds 7f38b31 gnu: r-xtable: Update to 1.8-3.
adds 9b7e8df gnu: r-ade4: Update to 1.7-13.
adds 2848c52 gnu: r-roxygen2: Update to 6.1.0.
adds 19cb93b gnu: r-git2r: Update to 0.23.0.
adds 41f6685 gnu: r-rcpparmadillo: Update to 0.9.100.5.0.
adds 2aafa73 gnu: r-xml: Update to 3.98-1.16.
adds e926159 gnu: r-e1071: Update to 1.7-0.
adds eefa7c7 gnu: r-r-utils: Update to 2.7.0.
adds e2a2c33 gnu: r-r-rsp: Update to 0.43.0.
adds 195eec7 gnu: r-matrixstats: Update to 0.54.0.
adds 88cb7aa gnu: r-plotly: Update to 4.8.0.
adds 5dbe7aa gnu: r-googlesheets: Update to 0.3.0.
adds c183fa2 gnu: Add r-officer.
adds bfee9ce gnu: Add r-snakecase.
adds de059e4 gnu: Add r-prediction.
adds cfc0631 gnu: Add r-sjlabelled.
adds 1f560b9 gnu: Add r-sjmisc.
adds aaed237 gnu: Add r-nortest.
adds 0fd7d59 gnu: Add r-moonbook.
adds 9070832 Revert "gnu: ghc-base-compat: Update to 0.10.4."
adds f9f4578 Revert "gnu: ghc-tasty: Update to 1.1.0.3."
adds 78f2c08 gnu: r-rmarkdown: Use latest version of Pandoc.
adds 589bd1c gnu: Add r-flextable.
adds cb96d81 gnu: r-doby: Update to 4.6-2.
adds 2cdd9d4 gnu: r-reticulate: Update to 1.10.
adds e3c1e93 gnu: r-reprex: Update to 0.2.0.
adds b72de5b gnu: r-callr: Update to 3.0.0.
adds b00e8ae gnu: r-glue: Update to 1.3.0.
adds c73752c gnu: r-pls: Update to 2.7-0.
adds 2d2b95d gnu: r-ipred: Update to 0.9-7.
adds 45c156b gnu: r-broom: Update to 0.5.0.
adds dc66835 gnu: Add r-ucminf.
adds b8f6e2f gnu: Add r-ordinal.
adds e7630cc gnu: r-jomo: Update to 2.6-4.
adds a726559 gnu: r-pan: Update to 1.6.
adds 1b3b2a7 gnu: r-mice: Update to 3.3.0.
adds 69bf449 gnu: r-xts: Update to 0.11-0.
adds 6f5b157 gnu: r-pillar: Update to 1.3.0.
adds d97d98e gnu: r-tinytex: Update to 0.8.
adds e32368c gnu: r-metap: Update to 1.0.
adds be5642e gnu: r-statnet-common: Update to 4.1.4.
adds 1fe9919 gnu: r-tsa: Update to 1.2.
adds 1995082 gnu: r-heatmaply: Update to 0.15.2.
adds 7a96c4e gnu: r-fnn: Update to 1.1.2.1.
adds 1213222 gnu: r-maptools: Update to 0.9-3.
adds 2e6909b gnu: r-later: Update to 0.7.4.
adds a9b02dd gnu: r-codedepends: Update to 0.6.5.
adds caaec88 gnu: r-ggpubr: Update to 0.1.8.
adds 5dfe491 gnu: r-graph: Move from bioinformatics to bioconductor.
adds a207bca gnu: r-codedepends: Move from cran to bioconductor.
adds c0608f8 gnu: r-adaptivesparsity: Update to 1.6.
adds c28d8d8 gnu: r-kernlab: Update to 0.9-27.
adds 8da236a gnu: r-gtools: Update to 3.8.1.
adds f0519c8 gnu: r-zoo: Update to 1.8-3.
adds e5db689 gnu: r-ztable: Update to 0.2.0.
adds 314e8e7 gnu: r-ggthemes: Update to 4.0.1.
adds 8e499d7 gnu: r-rann: Update to 2.6.
adds 0d279d6 gnu: r-robustbase: Update to 0.93-2.
adds f33a474 gnu: r-modelmetrics: Update to 1.2.0.
adds dff5640 gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.
adds ca248f1 gnu: pigx-rnaseq: Use latest version of Pandoc.
adds 7cd40c8 gnu: pigx-chipseq: Use latest version of Pandoc.
adds c2b4f81 gnu: pigx-bsseq: Use latest version of Pandoc.
adds 00a43cb gnu: pigx-scrnaseq: Use latest version of Pandoc.
adds cb341c1 channels: Fix external channel builds.
adds 37a6cdb git: Don't require users to specifiy "origin/" for
branches.
adds a5c70c2 gnu: libmpdclient: Update to 2.15.
adds d83477a gnu: font-fira-code: Update to 1.205.
adds 79b283e gnu: ccache: Update to 3.4.3.
adds d53aeea Add missing use-modules clause.
adds 96d6c41 gnu: guile-commonmark: Install .go files to libdir.
adds b3ca2d8 gnu: hpcguix-web: Update to 9ff40fc.
adds 89874fd gnu: guile-charting: Install .go files to libdir.
adds b290a63 gnu: guile-present: Install .go files to libdir.
adds 888b640 build: Remove -L flag when $LIBGCRYPT_LIBDIR is empty.
adds f66be84 gnu: gfortran, gcc-objc, gcc-objc++: Add version 8.
adds 3ffcad7 build-self: Accomodate upgrades from May 2016 and earlier.
adds 7df9456 services: hpcguix-web: Set SSL_CERT_DIR.
adds fd3a643 doc: Update hpcguix-web configuration documentation.
adds 21f5f35 gnu: libgme: Update to 0.6.2.
adds 1e066f0 gnu: curl: Update replacement to 7.61.1 [fixes
CVE-2018-14618].
adds 91cc2a3 gnu: Wireshark: Update to 2.6.3 [fixes
CVE-2018-{14994,16056,16057,16058}].
adds 0012e0d gnu: knot: Update to 2.7.2.
adds 1540075 vm: Make UUID computation really deterministic.
adds 12498b5 gnu: emacs-ess: Update to 17.11.
adds 40c1091 gnu: Add r-abcp2.
adds cadc10a gnu: Add r-abcrf.
adds 12da2a5 gnu: Add r-abctools.
adds 77b33e0 gnu: Add r-ggstance.
adds c61f7bc gnu: Add r-mosaiccore.
adds 214452f gnu: Add r-ggformula.
adds ee94cfe pull: Add '--profile'.
adds bd74701 Add 'guix describe'.
adds 2b73d82 guix package: Record package provenance in manifest
entries.
adds da34a19 guix describe: Display information about the current
generation.
adds 1521482 gnu: guile-json: Update to 1.2.0.
adds 6b4f991 gnu: gdb: Update to 8.2.
adds afdd155 gnu: indent: Add version 2.2.12.
adds 9f1f200 gnu: diffoscope: Update to 100.
adds 9b6c435 services: 'instantiate-missing-services' reaches fixed
point.
adds 48d17ba gnu: address@hidden: Update to 4.4.154.
adds ddb419c gnu: address@hidden: Update to 4.9.125.
adds 4be8fdd gnu: address@hidden: Update to 4.14.68.
adds 090e376 gnu: linux-libre: Update to 4.18.6.
adds 39b5d8f gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl.
adds 445ecce gnu: nyacc: Update to 0.86.0.
adds c665774 gnu: mes: Update to 0.17.1.
adds 985975a services: nginx: Don't read PID file when passed a custom
config file.
adds e80c725 services: nginx: 'stop' returns #f.
adds 5dec93b gexp: 'file-union' accepts directory names.
adds 4ab6a2f tests: base: Add Guile-Gcrypt & co. to the search path.
adds d7f99b3 gnu: perl: Improve description.
adds 6930ea3 gnu: aircrack-ng: Use HTTPS.
adds b9114cc gnu: aircrack-ng: Update to 1.3.
adds a0fad03 gnu: links: Update to 2.17.
adds 2d32a65 gnu: perl-params-validate: Update to 1.29.
adds 49e63e3 gnu: perl-datetime: Update to 1.50.
adds 04fc0b9 gnu: perl-namespace-clean: Update to 0.27.
adds 748e6e1 gnu: perl-getopt-long-descriptive: Update to 0.103.
adds 4e77b75 gnu: perl-extutils-helpers: Update to 0.026.
adds 15dbc91 gnu: perl-extutils-installpaths: Update to 0.012.
adds 9ad8099 gnu: perl-config-autoconf: Update to 0.317.
adds bb5e06a gnu: perl-pegex: Update to 0.67.
adds bb10567 gnu: musl: Update to 1.1.20.
adds c231164 gnu: signify: Update to 24.
adds b64e67a gnu: cloc: Update to 1.78.
adds 81bf0fd gnu: julia: Update objconv input.
adds 617cf5d gnu: mpfr: Update home page.
adds 249846b gnu: libsoup: Update to 2.64.0.
adds 37f9cfa gnu: msmtp: Update to 1.8.0.
adds 91b3a6d gnu: msmtp: Remove unneeded input.
adds e9c1492 gnu: glm: Update to 0.9.9.1.
adds 1448fa2 gnu: openal: Update to 1.19.0.
adds a617fd5 gnu: OpenBLAS: Update source URI.
adds 910a20e gnu: jbig2dec: Replace with 0.15 [security fixes].
adds 0084744 gnu: ghostscript: Update replacement to 9.24 [security
fixes].
new 0aeb134 Merge branch 'master' into core-updates
new 842c44c gnu: ghostscript: Remove graft for 9.24.
new 16676fc gnu: curl: Remove graft for 7.61.1.
new 0171019 gnu: openssl: Update to 1.0.2p.
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Makefile.am | 7 +-
README | 3 +-
build-aux/build-self.scm | 93 ++-
config-daemon.ac | 2 +-
configure.ac | 13 +-
doc/guix.texi | 120 +++-
gnu/local.mk | 8 +-
gnu/packages/audio.scm | 4 +-
gnu/packages/bash.scm | 2 +-
gnu/packages/bioconductor.scm | 51 +-
gnu/packages/bioinformatics.scm | 206 +++---
gnu/packages/ccache.scm | 11 +-
gnu/packages/ci.scm | 30 +-
gnu/packages/code.scm | 19 +-
gnu/packages/cran.scm | 736 ++++++++++++++++++---
gnu/packages/crypto.scm | 4 +-
gnu/packages/curl.scm | 4 +-
gnu/packages/dns.scm | 4 +-
gnu/packages/emacs.scm | 78 ++-
gnu/packages/emulators.scm | 6 +-
gnu/packages/engineering.scm | 25 +-
gnu/packages/fonts.scm | 4 +-
gnu/packages/games.scm | 157 +++++
gnu/packages/gcc.scm | 22 +
gnu/packages/gdb.scm | 4 +-
gnu/packages/ghostscript.scm | 23 +-
gnu/packages/gnome.scm | 5 +-
gnu/packages/graph.scm | 9 +-
gnu/packages/gtk.scm | 9 +-
gnu/packages/guile.scm | 28 +-
gnu/packages/haskell-check.scm | 4 +-
gnu/packages/haskell.scm | 39 +-
gnu/packages/image.scm | 17 +
gnu/packages/julia.scm | 6 +-
gnu/packages/linux.scm | 16 +-
gnu/packages/machine-learning.scm | 12 +-
gnu/packages/mail.scm | 7 +-
gnu/packages/maths.scm | 129 +++-
gnu/packages/mes.scm | 26 +-
gnu/packages/mp3.scm | 16 +-
gnu/packages/mpd.scm | 4 +-
gnu/packages/multiprecision.scm | 2 +-
gnu/packages/music.scm | 11 +-
gnu/packages/musl.scm | 6 +-
gnu/packages/networking.scm | 56 +-
gnu/packages/openldap.scm | 4 +-
gnu/packages/package-management.scm | 16 +-
.../patches/ghostscript-CVE-2018-10194.patch | 52 --
.../patches/ghostscript-CVE-2018-16509.patch | 193 ++++++
gnu/packages/patches/ghostscript-bug-699708.patch | 160 +++++
gnu/packages/patches/ghostscript-runpath.patch | 18 -
gnu/packages/patches/mes-nyacc-0.86.0.patch | 197 ++++++
gnu/packages/patches/nyacc-binary-literals.patch | 29 +
.../patches/openssl-1.0.2-CVE-2018-0495.patch | 215 ------
.../patches/openssl-1.0.2-CVE-2018-0732.patch | 50 --
gnu/packages/perl.scm | 38 +-
gnu/packages/plotutils.scm | 12 +-
gnu/packages/python.scm | 4 +-
gnu/packages/shells.scm | 17 +-
gnu/packages/statistics.scm | 137 ++--
gnu/packages/tls.scm | 6 +-
gnu/packages/web-browsers.scm | 4 +-
gnu/packages/web.scm | 20 +-
gnu/packages/xorg.scm | 42 ++
gnu/services.scm | 24 +-
gnu/services/web.scm | 19 +-
gnu/system/vm.scm | 81 ++-
gnu/tests/base.scm | 16 +-
guix/channels.scm | 30 +-
guix/derivations.scm | 2 +-
guix/describe.scm | 4 +-
guix/docker.scm | 2 +-
guix/gcrypt.scm | 49 --
guix/gexp.scm | 39 +-
guix/git.scm | 19 +-
guix/hash.scm | 184 ------
guix/http-client.scm | 2 +-
guix/import/cpan.scm | 2 +-
guix/import/cran.scm | 2 +-
guix/import/crate.scm | 2 +-
guix/import/elpa.scm | 2 +-
guix/import/gnu.scm | 2 +-
guix/import/hackage.scm | 2 +-
guix/import/texlive.scm | 2 +-
guix/import/utils.scm | 2 +-
guix/inferior.scm | 20 +-
guix/nar.scm | 4 +-
guix/pk-crypto.scm | 407 ------------
guix/pki.scm | 2 +-
guix/profiles.scm | 6 +-
guix/scripts/archive.scm | 2 +-
guix/scripts/authenticate.scm | 2 +-
guix/scripts/describe.scm | 159 +++++
guix/scripts/download.scm | 2 +-
guix/scripts/hash.scm | 6 +-
guix/scripts/pack.scm | 60 +-
guix/scripts/package.scm | 57 +-
guix/scripts/publish.scm | 4 +-
guix/scripts/pull.scm | 22 +-
guix/scripts/refresh.scm | 2 +-
guix/scripts/substitute.scm | 4 +-
guix/self.scm | 26 +-
guix/store.scm | 2 +-
guix/store/deduplication.scm | 2 +-
guix/tests.scm | 2 +-
m4/guix.m4 | 18 -
po/guix/POTFILES.in | 1 +
tests/base32.scm | 2 +-
tests/builders.scm | 2 +-
tests/challenge.scm | 2 +-
tests/cpan.scm | 2 +-
tests/crate.scm | 2 +-
tests/derivations.scm | 2 +-
tests/gem.scm | 2 +-
tests/gexp.scm | 18 +
.../bash/guix-daemon => tests/guix-describe.sh | 39 +-
tests/guix-system.sh | 8 +
tests/hash.scm | 128 ----
tests/inferior.scm | 26 +-
tests/nar.scm | 2 +-
tests/opam.scm | 2 +-
tests/packages.scm | 2 +-
tests/pk-crypto.scm | 290 --------
tests/pki.scm | 4 +-
tests/publish.scm | 4 +-
tests/pypi.scm | 2 +-
tests/services.scm | 25 +
tests/store-deduplication.scm | 2 +-
tests/store.scm | 10 +-
tests/substitute.scm | 4 +-
130 files changed, 2929 insertions(+), 2200 deletions(-)
delete mode 100644 gnu/packages/patches/ghostscript-CVE-2018-10194.patch
create mode 100644 gnu/packages/patches/ghostscript-CVE-2018-16509.patch
create mode 100644 gnu/packages/patches/ghostscript-bug-699708.patch
delete mode 100644 gnu/packages/patches/ghostscript-runpath.patch
create mode 100644 gnu/packages/patches/mes-nyacc-0.86.0.patch
create mode 100644 gnu/packages/patches/nyacc-binary-literals.patch
delete mode 100644 gnu/packages/patches/openssl-1.0.2-CVE-2018-0495.patch
delete mode 100644 gnu/packages/patches/openssl-1.0.2-CVE-2018-0732.patch
delete mode 100644 guix/gcrypt.scm
delete mode 100644 guix/hash.scm
delete mode 100644 guix/pk-crypto.scm
create mode 100644 guix/scripts/describe.scm
copy etc/completion/bash/guix-daemon => tests/guix-describe.sh (50%)
delete mode 100644 tests/hash.scm
delete mode 100644 tests/pk-crypto.scm
- branch core-updates updated (b03f270 -> 0171019),
Marius Bakke <=