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2018-09-10gnu: Add hstr.Benjamin Slade
* gnu/packages/shellutils.scm (hstr): New variable.
2018-09-10substitute: Ignore exceptions thrown by 'set-thread-name'.Ludovic Courtès
Fixes <https://bugs.gnu.org/32669>. Reported by Ricardo Wurmus <rekado@elephly.net>. * guix/scripts/substitute.scm (guix-substitute): Swallow 'system-error' exceptions around 'set-thread-name' call.
2018-09-10syscalls: Report lack of a libc symbol as ENOSYS.Ludovic Courtès
* guix/build/syscalls.scm (syscall->procedure): Throw to 'system-error with ENOSYS when NAME cannot be found.
2018-09-10gnu: emacs-guix: Update to 0.5.Alex Kost
* gnu/packages/emacs.scm (emacs-guix): Update to 0.5. [propagated-inputs]: Add 'guile-gcrypt'. [arguments]: Adjust #:configure-flags accordingly.
2018-09-10gnu: emacs-build-farm: Update to 0.2.1.Alex Kost
* gnu/packages/emacs.scm (emacs-build-farm): Update to 0.2.1. Change source from gitlab to notabug.
2018-09-10gnu: emacs-bui: Update to 1.2.0.Alex Kost
* gnu/packages/emacs.scm (emacs-bui): Update to 1.2.0. Change source from github to notabug.
2018-09-10gnu: Add python-pygenometracks.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
2018-09-10gnu: Add python-hicexplorer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
2018-09-10gnu: Add python-cooler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
2018-09-10gnu: Add python-pyfaidx.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
2018-09-10gnu: Add python-pypairix.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
2018-09-10gnu: Add python-intervaltree.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
2018-09-10gnu: Add python-dask.Ricardo Wurmus
* gnu/packages/python.scm (python-dask): New variable.
2018-09-10gnu: Add python-partd.Ricardo Wurmus
* gnu/packages/python.scm (python-partd): New variable.
2018-09-10gnu: Add python-blosc.Ricardo Wurmus
* gnu/packages/python.scm (python-blosc): New variable.
2018-09-10gnu: Add python-locket.Ricardo Wurmus
* gnu/packages/python.scm (python-locket): New variable.
2018-09-10gnu: Add python-cloudpickle.Ricardo Wurmus
* gnu/packages/python.scm (python-cloudpickle): New variable.
2018-09-10gnu: Add python-sortedcontainers.Ricardo Wurmus
* gnu/packages/python.scm (python-sortedcontainers): New variable.
2018-09-10gnu: Add python-cytoolz.Ricardo Wurmus
* gnu/packages/python.scm (python-cytoolz): New variable.
2018-09-10gnu: Add python-toolz.Ricardo Wurmus
* gnu/packages/python.scm (python-toolz): New variable.
2018-09-10gnu: Add python-multiprocess.Ricardo Wurmus
* gnu/packages/python.scm (python-multiprocess): New variable.
2018-09-10gnu: Add python-dill.Ricardo Wurmus
* gnu/packages/python.scm (python-dill): New variable.
2018-09-10gnu: python-typing: Update to 3.6.6.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-typing): Update to 3.6.6.
2018-09-10gnu: tinyproxy: Update to 1.10.0.Tobias Geerinckx-Rice
* gnu/packages/web.scm (tinyproxy): Update to 1.10.0. [native-inputs]: Remove asciidoc.
2018-09-10gnu: spectrwm: Update to 3.2.0.Tobias Geerinckx-Rice
* gnu/packages/wm.scm (spectrwm): Update to 3.2.0. [arguments]: Remove 'fix-freetype-include' phase.
2018-09-10gnu: Add yad.Mădălin Ionel Patrașcu
* gnu/packages/gtk.scm (yad): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-09-10gnu: hpcguix-web: Update to 53e09ea.Ludovic Courtès
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
2018-09-10services: hpcguix-web: Produce a log file and rotate it.Ludovic Courtès
* gnu/services/web.scm (%hpcguix-web-log-file) (%hpcguix-web-log-rotations): New variables. (hpcguix-web-shepherd-service): Pass #:log-file. (hpcguix-web-service-type): Extend ROTTLOG-SERVICE-TYPE.
2018-09-10services: tailon: Move to (gnu services web).Ludovic Courtès
This allows (gnu services admin) to remain deeper in the module graph and to be used by (gnu services web). * gnu/services/admin.scm (<tailon-configuration-file>) (tailon-configuration-files-string) (tailon-configuration-file-compiler, <tailon-configuration>) (tailon-shepherd-service, %tailon-accounts) (tailon-service-type): Move to... * gnu/services/web.scm: ... here. * gnu/tests/admin.scm: Remove. Move test to... * gnu/tests/web.scm (%tailon-os) (run-tailon-test, %test-tailon): ... here.
2018-09-10gnu: youtube-dl: Update to 2018.08.04.Alex Vong
* gnu/packages/video.scm (youtube-dl): Update to 2018.08.04.
2018-09-09gnu: Add asignify.Leo Famulari
* gnu/packages/crypto.scm (asignify): New variable.
2018-09-09gnu: certbot: Update to 0.27.1.Leo Famulari
* gnu/packages/tls.scm (python-acme): Update to 0.27.1. [arguments]: Use invoke. (certbot): Update to 0.27.1. [native-inputs]: Use python-sphinx-1.6.
2018-09-09gnu: libgd: Fix CVE-2018-{5711,1000222}.Leo Famulari
* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gd.scm (gd/fixed): New variable. * gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'.
2018-09-09ui: Add soft port for styling and filtering build output.Ricardo Wurmus
* guix/ui.scm (build-output-port): New procedure. * guix/scripts/package.scm (%default-options): Print build trace. (guix-package): Use build-output-port. * guix/scripts/build.scm (guix-build): Use build-output-port. Co-authored-by: Sahithi Yarlagadda <sahi@swecha.net>
2018-09-09ui: Add support for colorization.Sahithi Yarlagadda
* guix/ui.scm (ansi-color-tables): New variable. (color, colorize-string): New procedures. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-09-09gnu: r-chron: Update to 2.3-53.Ricardo Wurmus
* gnu/packages/statistics.scm (r-chron): Update to 2.3-53.
2018-09-09gnu: r-annotationhub: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
2018-09-09gnu: r-chippeakanno: Update to 3.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2.
2018-09-09gnu: Update texmaker to 5.0.2.Roel Janssen
* gnu/packages/tex.scm (texmaker): Update to 5.0.2.
2018-09-09gnu: ghostscript: Update replacement to 9.24 [security fixes].Marius Bakke
The following CVEs are fixed with this release: CVE-2018-15908, CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509, CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539, CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543. * gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file. * gnu/packages/patches/ghostscript-CVE-2018-16509.patch, gnu/packages/patches/ghostscript-bug-699708.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24. [source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and 'ghostscript-runpath.patch'. Add 'ghostscript-CVE-2018-16509.patch' and 'ghostscript-bug-699708.patch'. [arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output directory.
2018-09-09gnu: jbig2dec: Replace with 0.15 [security fixes].Marius Bakke
* gnu/packages/image.scm (jbig2dec-0.15): New public variable. (jbig2dec)[replacement]: New field.
2018-09-09gnu: OpenBLAS: Update source URI.Marius Bakke
* gnu/packages/maths.scm (openblas)[source](uri): Use the more stable SourceForge mirror.
2018-09-09gnu: openal: Update to 1.19.0.Marius Bakke
* gnu/packages/audio.scm (openal): Update to 1.19.0.
2018-09-09gnu: glm: Update to 0.9.9.1.Marius Bakke
* gnu/packages/maths.scm (glm): Update to 0.9.9.1.
2018-09-09gnu: msmtp: Remove unneeded input.Marius Bakke
* gnu/packages/mail.scm (msmtp)[inputs]: Remove LIBIDN, which is only required when using OpenSSL (or GnuTLS sans IDN support).
2018-09-09gnu: msmtp: Update to 1.8.0.Marius Bakke
* gnu/packages/mail.scm (msmtp): Update to 1.8.0.
2018-09-09gnu: libsoup: Update to 2.64.0.Marius Bakke
* gnu/packages/gnome.scm (libsoup): Update to 2.64.0. [inputs]: Add LIBPSL.
2018-09-09gnu: mpfr: Update home page.Marius Bakke
* gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS.
2018-09-09gnu: julia: Update objconv input.Marius Bakke
* gnu/packages/julia.scm (julia)[inputs]: Update the hash of "objconv", which does not have a stable URL. Add a file name and use HTTPS while at it.
2018-09-09gnu: cloc: Update to 1.78.Tobias Geerinckx-Rice
* gnu/packages/code.scm (cloc): Update to 1.78. [source]: Update URI.
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