[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
branch core-updates updated (a56bf10 -> f167595)
|
From: |
Mark H. Weaver |
|
Subject: |
branch core-updates updated (a56bf10 -> f167595) |
|
Date: |
Sun, 6 Aug 2017 00:26:21 -0400 (EDT) |
mhw pushed a change to branch core-updates
in repository guix.
from a56bf10 gnu: perl: Work around more "dotless @INC" build issues.
new e3df693 gnu: libtasn1: Add replacement to fix CVE-2017-10790.
adds 7441f1d build: Make Guile-Git a hard requirement.
adds 59a1627 pull: Fetch source code from Git.
adds 3085b50 pull: Use the commit ID as the version string.
adds c53fc48 pull: Honor '--no-grafts'.
adds aa18480 gnu: Add r-pkgconfig.
adds 796237a gnu: Add r-blob.
adds 8060a61 gnu: r-rsqlite: Update to 2.0.
adds bfa0d1e gnu: r-sva: Update to 3.24.4.
adds 9eb2714 gnu: r-copywriter: Update to 2.8.1.
adds 8cfaa9a gnu: r-genomicfeatures: Update to 1.28.4.
adds 15afa9b gnu: r-rtracklayer: Update to 1.36.4.
adds 26760c8 gnu: r-genomicalignments: Update to 1.12.1.
adds f41150f gnu: r-summarizedexperiment: Update to 1.6.3.
adds adf5d0a gnu: r-delayedarray: Update to 0.2.7.
adds 5077bc3 gnu: r-biostrings: Update to 2.44.2.
adds 1ff74d0 gnu: r-biocparallel: Update to 1.10.1.
adds 0c6494a gnu: r-biomart: Update to 2.32.1.
adds 62eb93a gnu: r-annotationdbi: Update to 1.38.2.
adds 1898a78 gnu: r-biobase: Update to 2.36.2.
adds 1b4738e gnu: r-limma: Update to 3.32.5.
adds 48f5d28 gnu: r-variantannotation: Update to 1.22.3.
adds 6252dd0 gnu: r-genomeinfodb: Update to 1.12.2.
adds 3ec25eb gnu: r-iranges: Update to 2.10.2.
adds 9c4348d gnu: r-dnacopy: Update to 1.50.1.
adds 0ff4783 gnu: r-biocstyle: Update to 2.4.1.
adds bd4a0ba gnu: r-category: Update to 2.42.1.
adds fd215c2 gnu: r-annotationforge: Update to 1.18.1.
adds f1915a5 gnu: r-deseq2: Update to 1.16.1.
adds 2f06dc0 gnu: Add r-rlang.
adds 2e508b6 gnu: libvirt: Use HTTPS.
adds ced2d2b gnu: libvirt: Update to 3.6.0.
adds 0abf526 gnu: hdf4: Update to 4.12.13.
adds a70b03d gnu: Add python-grako
adds 33485fa gnu: eyed3: Update to 0.8, build with python3.
adds e0958c2 gnu: libpng-apng: Update to 1.6.28.
adds 696f1d0 gnu: libpng-apng: Be sure to apply the APNG patch.
adds 721d7a6 gnu: address@hidden: Don't built on aarch64.
adds 9ef5940 gnu: calibre: Add python2-msgpack as an input.
adds 2c5cf84 gnu: python2-conda: Fix build by building with enum34.
adds 575e5e4 gnu: address@hidden: Fix CVE-2015-5180.
adds a0ae64a gnu: address@hidden: Fix CVE-2015-5180,
CVE-2016-{3075,3706,4429}.
adds edd08fb gnu: address@hidden: Fix security issues.
adds ec5495b doc: 'patches' field of <origin> can list file-like
objects.
adds 49962b1 activation: Make sure /etc exists.
adds 6862c72 gnu: tor: Update to 0.3.0.10.
adds 5d8312f gnu: youtube-dl: Update to 2017.07.30.1.
adds 68a29ab gnu: Add LeoCAD.
adds 5638d71 gnu: openscenegraph: Add 'Release' configure flag.
adds a8ead6f gnu: vc: Limit to x86_64 and i686.
adds 92971d6 gnu: htseq: Update to 0.9.1.
adds 75e6639 gnu: htseq: Use PyPI URI.
adds dd4b747 gnu: Add grub-hybrid.
adds 5bee6bf gnu: Add r-glue.
adds 847b457 gnu: r-plogr: Move to (gnu packages cran).
adds 736332c gnu: r-rcpp: Update to 0.12.12.
adds a8cba9d gnu: r-rcpp: Move to (gnu packages cran).
adds eed58a0 gnu: Add r-bindr.
adds 4bb0b4c gnu: Add r-bindrcpp.
adds a40b2c2 gnu: r-dplyr: Update to 0.7.2.
adds aad948a gnu: r-tibble: Update to 1.3.3.
adds 5fc74f2 gnu: r-devtools: Update to 1.13.3.
adds 7b36881 gnu: r-purrr: Update to 0.2.2.2.
adds d590508 gnu: r-igraph: Update to 1.1.2.
adds f9b3760 gnu: r-plotly: Update to 4.7.1.
adds cc9a778 gnu: r-hmisc: Update to 4.0-3.
adds c628b84 gnu: r-ranger: Update to 0.8.0.
adds 64c6712 gnu: r-knitrbootstrap: Update to 1.0.1.
adds 0f2eee0 gnu: r-pracma: Update to 2.0.7.
adds 2d81bc1 gnu: r-httpuv: Update to 1.3.5.
adds 9fe794f gnu: r-jsonlite: Update to 1.5.
adds a1e54db gnu: r-servr: Update to 0.6.
adds 8501510 gnu: r-htmltools: Update to 0.3.6.
adds 53deffe gnu: r-htmlwidgets: Update to 0.9.
adds e584b9f gnu: r-curl: Update to 2.8.1.
adds af1eeab gnu: r-boot: Update to 1.3-20.
adds 74b037d gnu: r-foreign: Update to 0.8-69.
adds dbeda1b gnu: r-matrix: Update to 1.2-10.
adds 6fb21ed gnu: r-mgcv: Update to 1.8-18.
adds 831858a gnu: r-bit64: Update to 0.9-7.
adds d5ce380 gnu: r-dbi: Update to 0.7.
adds 12cd797 gnu: r-evaluate: Update to 0.10.1.
adds 6dc86e8 gnu: r-formatr: Update to 1.5.
adds b07c8c0 gnu: r-knitr: Update to 1.16.
adds f05c627 gnu: r-r6: Update to 2.2.2.
adds c832d32 gnu: r-formula: Update to 1.2-2.
adds 63f934e gnu: r-backports: Update to 1.1.0.
adds 58e1ce8 gnu: r-checkmate: Update to 1.8.3.
adds f212bf8 gnu: r-git2r: Update to 0.19.0.
adds d8048a1 gnu: r-withr: Update to 2.0.0.
adds 76040b8 gnu: r-readr: Update to 1.1.1.
adds 1c41d51 gnu: r-plotrix: Update to 3.6-5.
adds 7c172ea gnu: r-rcpparmadillo: Update to 0.7.900.2.0.
adds cc8ba9b gnu: r-rmarkdown: Update to 1.6.
adds fe99172 gnu: r-xml: Update to 3.98-1.9.
adds 127b926 gnu: r-segmented: Update to 0.5-2.1.
adds 81c057c gnu: r-sparsem: Update to 1.77.
adds 1c576cb gnu: r-irlba: Update to 2.2.1.
adds e1cd25b gnu: r-glmnet: Update to 2.0-10.
adds 9b9fef0 gnu: r-tidyr: Update to 0.6.3.
adds 1d25643 gnu: r-googlesheets: Update to 0.2.2.
adds 2c75199 gnu: r-sfsmisc: Update to 1.1-1.
adds 80d1185 gnu: r-gdata: Update to 2.18.0.
adds a8c2706 gnu: r-statmod: Update to 1.4.30.
adds d58faa7 gnu: r-rann: Update to 2.5.1.
adds df03b6f gnu: r-cowplot: Update to 0.8.0.
adds 62d3afc gnu: r-fastica: Update to 1.2-1.
adds 60869fb gnu: r-flexmix: Update to 2.3-14.
adds 41692b2 gnu: r-mclust: Update to 5.3.
adds 4431dd3 gnu: r-vgam: Update to 1.0-4.
adds 12c3bbb gnu: r-pbapply: Update to 1.3-3.
adds 0f008ab gnu: r-rcppeigen: Update to 0.3.3.3.0.
adds 6bb4bfa gnu: r-car: Update to 2.1-5.
adds 85cd755 gnu: r-tclust: Update to 1.2-7.
adds 3f6ec08 gnu: r-bookdown: Update to 0.4.
adds 7150f1c gnu: r-optparse: Update to 1.4.4.
adds 023aa8f gnu: r-seqinr: Update to 3.4-5.
adds c8a9b2b gnu: r-qtl: Update to 1.41-6.
adds 4e0c847 gnu: r-wgcna: Update to 1.60.
adds 5e0de29 gnu: r-seqminer: Update to 6.0.
adds ceb802a gnu: r-desc: Update to 1.1.1.
adds 2267e4d gnu: r-purrr: Update to 0.2.3.
adds cf18970 vm: Use grub-hybrid's grub-mkrescue.
adds 7cb6155 gnu: bioinformatics.scm: Use (gnu packages cran) module.
adds 9e37e53 gnu: Add missing references to (gnu packages cran).
adds 81ca29a gnu: address@hidden: Update to 1.4.22 [fixes
CVE-2017-7526].
adds c9f4f56 gnu: git: Enable tests.
adds c890914 gnu: freerdp: Update to 2.0.0-rc0 [security fixes].
adds 20f8d1d gnu: sshfs-fuse: Update to 2.10.
adds 0f08917 gnu: zerofree: Use ‘modify-phases’ syntax.
adds 7a06845 gnu: zerofree: Use ‘install-file’.
adds 4de4a1c gnu: zerofree: Expand description.
adds 30ac4cc gnu: zerofree: Update to 1.1.0.
adds 0a3ecfd gnu: thefuck: Update to 3.19.
adds b55d15e gnu: cmark: Update to 0.28.0.
adds 9a7fd37 gnu: xonsh: Update to 0.5.12.
adds 19dd509 gnu: certbot, python-acme: Update to 0.17.0.
adds f58be41 gnu: fabric: Update to 1.13.2.
adds 3b4018d gnu: sshoot: Update to 1.2.6.
adds 54360c9 gnu: diffoscope: Use HTTPS.
adds e9f6a93 gnu: python-lz4: Update to 0.10.1.
adds b316caa gnu: python-lz4: Fix typo in synopsis.
adds 88c8f24 build: Add minify build system.
adds ed69963 gnu: Add js-html5shiv.
adds 68ffb6c gnu: Add js-json2.
adds 3f48403 gnu: Add js-strftime.
adds a6bbb2a gnu: Add js-highlight.
adds c4abc94 gnu: Add js-datatables.
adds 4f65067 gnu: Add js-selectize.
adds 0b0aa76 gnu: Add js-es5-shim.
adds a3cd23b gnu: Add r-shiny.
adds 8d6c845 gnu: Add r-crosstalk.
adds 1cec346 gnu: php: Update to 7.1.8.
adds 7656739 Revert "daemon: Ensure proper alignment on the stack."
adds 3d5d87a gnu: Add cubicle.
adds eedcfa7 gnu: lftp: Update to 4.7.8.
adds 7f171fd gnu: git: Update to 2.14.0.
adds e78e38a gnu: emacs-exwm: Update to 0.15.
adds 91d94e2 gnu: emacs-exwm-x: Do not set DISPLAY.
adds 9833bcf build: Allow mounting of entire disks.
adds 31ed845 daemon: On aarch64, use increments of 16 on the stack.
adds 6a43643 doc: Suggest running guix-daemon with 'sudo -E'.
adds 01a61d7 gnu: libtasn1: Fix CVE-2017-10790.
new f167595 Merge branch 'master' into core-updates
The 2 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 | 10 +-
build-aux/build-self.scm | 17 +
configure.ac | 10 +-
doc/contributing.texi | 7 +-
doc/guix.texi | 47 +-
gnu/bootloader/grub.scm | 6 +
gnu/build/activation.scm | 1 +
gnu/build/file-systems.scm | 17 +-
gnu/local.mk | 10 +-
gnu/packages/admin.scm | 22 +-
gnu/packages/base.scm | 10 +
gnu/packages/bioinformatics.scm | 135 ++---
gnu/packages/bootloaders.scm | 33 ++
gnu/packages/compression.scm | 9 +-
gnu/packages/cran.scm | 106 ++++
gnu/packages/ebook.scm | 3 +
gnu/packages/emacs.scm | 10 +-
gnu/packages/ftp.scm | 4 +-
gnu/packages/gcc.scm | 7 +-
gnu/packages/gnupg.scm | 4 +-
gnu/packages/graphics.scm | 6 +-
gnu/packages/image.scm | 44 +-
gnu/packages/javascript.scm | 191 ++++++-
gnu/packages/lego.scm | 61 ++-
gnu/packages/linux.scm | 42 +-
gnu/packages/machine-learning.scm | 1 +
gnu/packages/markup.scm | 4 +-
gnu/packages/maths.scm | 54 +-
gnu/packages/mp3.scm | 13 +-
gnu/packages/package-management.scm | 9 +-
gnu/packages/patches/fabric-tests.patch | 15 -
gnu/packages/patches/gd-CVE-2017-7890.patch | 30 ++
gnu/packages/patches/glibc-CVE-2015-5180.patch | 311 +++++++++++
gnu/packages/patches/glibc-CVE-2015-7547.patch | 590 +++++++++++++++++++++
gnu/packages/patches/glibc-CVE-2016-3075.patch | 43 ++
gnu/packages/patches/glibc-CVE-2016-3706.patch | 188 +++++++
gnu/packages/patches/glibc-CVE-2016-4429.patch | 58 ++
gnu/packages/patches/libtasn1-CVE-2017-10790.patch | 63 +++
gnu/packages/php.scm | 17 +-
gnu/packages/python.scm | 28 +
gnu/packages/rdesktop.scm | 22 +-
gnu/packages/shells.scm | 4 +-
gnu/packages/statistics.scm | 333 ++++++------
gnu/packages/tls.scm | 16 +-
gnu/packages/tor.scm | 4 +-
gnu/packages/version-control.scm | 39 +-
gnu/packages/video.scm | 4 +-
gnu/packages/virtualization.scm | 10 +-
gnu/packages/vpn.scm | 6 +-
gnu/packages/web.scm | 156 +++++-
gnu/system/vm.scm | 7 +
guix/build-system/minify.scm | 127 +++++
guix/build/minify-build-system.scm | 73 +++
guix/scripts/pull.scm | 250 +++++----
nix/libstore/build.cc | 11 +-
55 files changed, 2766 insertions(+), 532 deletions(-)
delete mode 100644 gnu/packages/patches/fabric-tests.patch
create mode 100644 gnu/packages/patches/gd-CVE-2017-7890.patch
create mode 100644 gnu/packages/patches/glibc-CVE-2015-5180.patch
create mode 100644 gnu/packages/patches/glibc-CVE-2015-7547.patch
create mode 100644 gnu/packages/patches/glibc-CVE-2016-3075.patch
create mode 100644 gnu/packages/patches/glibc-CVE-2016-3706.patch
create mode 100644 gnu/packages/patches/glibc-CVE-2016-4429.patch
create mode 100644 gnu/packages/patches/libtasn1-CVE-2017-10790.patch
create mode 100644 guix/build-system/minify.scm
create mode 100644 guix/build/minify-build-system.scm
- branch core-updates updated (a56bf10 -> f167595),
Mark H. Weaver <=