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2018-11-19gnu: r-sjstats: Update to 0.17.2.Roel Janssen
* gnu/packages/cran.scm (r-sjstats): Update to 0.17.2.
2018-11-19gnu: r-ggpubr: Update to 0.2.Roel Janssen
* gnu/packages/cran.scm (r-ggpubr): Update to 0.2.
2018-11-19gnu: r-recipes: Update to 0.1.4.Roel Janssen
* gnu/packages/cran.scm (r-recipes): Update to 0.1.4.
2018-11-19gnu: r-dimred: Update to 0.2.2.Roel Janssen
* gnu/packages/cran.scm (r-dimred): Update to 0.2.2.
2018-11-19gnu: r-ensembldb: Update to 2.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
2018-11-19gnu: r-msnbase: Update to 2.8.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
2018-11-19gnu: r-genomeinfodb: Update to 1.18.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
2018-11-19gnu: Add clojure-algo-monads.Alex Vong
* gnu/packages/lisp.scm (clojure-algo-monads): New public variable.
2018-11-19gnu: Add clojure-tools-macro.Alex Vong
* gnu/packages/lisp.scm (clojure-tools-macro): New public variable.
2018-11-19gnu: Add clojure-algo-generic.Alex Vong
* gnu/packages/lisp.scm (clojure-algo-generic): New public variable.
2018-11-19gnu: Add clojure-core-match.Alex Vong
* gnu/packages/lisp.scm (clojure-core-match): New public variable.
2018-11-19gnu: Add clojure-instaparse.Alex Vong
* gnu/packages/lisp.scm (clojure-instaparse): New public variable.
2018-11-19guix: Add clojure-utils.Alex Vong
* guix/build/clojure-utils.scm: New file. * gnu/packages/lisp.scm (clojure)[arguments]: Use it. * Makefile.am (MODULES): Add it.
2018-11-19gnu: clojure: Use (guix build java-utils) to simplify build phases.Alex Vong
* gnu/packages/lisp.scm (clojure)[arguments]: Use 'ant-build-javadoc', 'install-jars' and 'install-javadoc' in build phases.
2018-11-19gnu: clojure: Refactor to ensure there's a single list of libraries.Alex Vong
This avoids having to update multiple lists. * gnu/packages/lisp.scm (clojure)[native-inputs]: Use new local variable. [arguments]: Adjust build phases accordingly.
2018-11-19gnu: clojure: Remove 'remove-archives' snippet.Alex Vong
This is no longer needed since clojure now makes official source releases in github. * gnu/packages/lisp.scm (clojure)[source]: Remove it. [native-inputs]: Remove it in 'submodule'. [arguments]: Adjust 'unpack-submodule-sources' phase accordingly.
2018-11-19gnu: clojure: Move from java to lisp.Alex Vong
* gnu/packages/java.scm (clojure): Move from here... * gnu/packages/lisp.scm (clojure): ...to here.
2018-11-19gnu: python-kivy: Update to 1.10.1Jovany Leandro G.C
* gnu/packages/python.scm (python-kivy): Update to 1.10.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-19gnu: help2man: Add 1.47.8.Ludovic Courtès
* gnu/packages/man.scm (help2man/latest): New variable.
2018-11-19gnu: fuse-exfat: Update to 1.3.0.Ludovic Courtès
* gnu/packages/linux.scm (fuse-exfat): Update to 1.3.0.
2018-11-19gnu: diffoscope: Update to 105.Ludovic Courtès
* gnu/packages/package-management.scm (diffoscope): Update to 105.
2018-11-18gnu: Add libfdk 'FDK AAC' library.Leo Famulari
* gnu/packages/audio.scm (libfdk): New variable.
2018-11-18vm: Remove explicit calls to 'operating-system-derivation'.Ludovic Courtès
* gnu/system/vm.scm (iso9660-image): Change 'os-drv' to 'os' and remove call to 'operating-system-derivation'. (system-qemu-image): Likewise. (system-qemu-image/shared-store): Likewise.
2018-11-18system: De-monadify 'operating-system-bootcfg'.Ludovic Courtès
* gnu/system.scm (operating-system-bootcfg): Remove 'mlet*' and 'lower-object' call. * gnu/system/vm.scm (system-disk-image) (system-qemu-image/shared-store): Adjust accordingly. * guix/scripts/system.scm (perform-action): Add 'lower-object' call for BOOTCFG.
2018-11-18system: Please Emacs.Ludovic Courtès
* gnu/system.scm (operating-system-bootcfg): Remove opening parenthesis at the beginning of the line in the docstring to placate Emacs.
2018-11-18system: De-monadify 'operating-system-boot-parameters'.Ludovic Courtès
* gnu/system.scm (operating-system-boot-parameters): Turn to direct style instead of monadic. (operating-system-bootcfg): Adjust accordingly. (operating-system-boot-parameters-file): Likewise.
2018-11-18linux-initrd: Return file-like objects instead of monadic values.Ludovic Courtès
This is an incompatible change visible to users via the 'initrd' field of 'operating-system'. However, assuming the user's 'initrd' value tail-calls to 'raw-initrd' or 'base-initrd', the switch to non-monadic style is invisible. * gnu/system/linux-initrd.scm (expression->initrd): Use 'computed-file' instead of 'gexp->derivation'. (raw-initrd, base-initrd): Adjust docstring to mention non-monadic return. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Adjust accordingly. * gnu/system.scm (operating-system-directory-base-entries) (operating-system-initrd-file) (operating-system-boot-parameters): Adjust accordingly. * doc/guix.texi (operating-system Reference) (Initial RAM Disk): Update.
2018-11-18system: Simplify kernel argument handling.Ludovic Courtès
* gnu/system.scm (bootable-kernel-arguments): Remove 'kernel-arguments' parameter and return only the base list of kernel arguments. Rename 'system.drv' to 'system'. (operating-system-kernel-arguments): Adjust accordingly and remove 'system.drv' parameter. (read-boot-parameters-file): Adjust accordingly. Remove 'if params' since dominating code assumed PARAMS is always true. (operating-system-boot-parameters): Remove 'system.drv' parameter; add #:system-kernel-arguments? instead and honor it. (operating-system-bootcfg): Adjust accordingly. (operating-system-boot-parameters-file): Likewise. * gnu/system/vm.scm (system-qemu-image/shared-store-script): Remove 'os-drv' variable. Adjust call to 'operating-system-kernel-arguments'.
2018-11-18bootloader: De-monadify configuration file generators.Ludovic Courtès
* gnu/bootloader/extlinux.scm: Remove unneeded imports. (extlinux-configuration-file): Use 'computed-file' instead of 'gexp->derivation'. * gnu/bootloader/grub.scm (svg->png): Likewise. (grub-background-image, eye-candy): Adjust accordingly, return non-monadically. (grub-configuration-file): Likewise, and use 'computed-file' instead of 'gexp->derivation'. * gnu/bootloader/u-boot.scm: Remove unneeded imports. * gnu/system.scm: Add 'lower-object' call.
2018-11-18activation: Aways pass '-d HOME' to 'useradd'.Ludovic Courtès
Fixes <https://bugs.gnu.org/33422>. Reported by fps. * gnu/build/activation.scm (add-user): Always pass "-d HOME" when HOME is true. Pass "--create-home" only when HOME, CREATE-HOME?, and SYSTEM? are true. (activate-users+groups): Pass #:create-home? create-home? to 'ensure-user'. * gnu/tests/base.scm (run-basic-test)["accounts"]: Test 'passwd:dir' as well.
2018-11-18gnu: ocaml: Update to 4.7.0.Julien Lepiller
Update ocaml to the latest version and fixes dependent packages by updating them or by adding new inputs, such as ocaml-num and ocamlbuild, that were removed from the core ocaml package. Rename packages that cannot be built with the new compiler with an ocaml4.02 prefix. Add ocaml4.02 dependencies. * gnu/packages/ocaml.scm (ocaml): Update to 4.7.0. (ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir) (ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip) (ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest) (ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree) (ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned) (ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult) (ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner) (ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools) (ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log) (ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos) (ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf) (ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake) (ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis) (ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq) (ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format) (ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi) (ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages. (opam): Update to 2.0.0. (camlp4): Update to 4.07+1. (camlp5): Update to 7.06. (hevea): Update to 2.32. (coq)[inputs]: Add ocaml-num. (emacs-tuareg): Update to 2.2.0. (ocaml-menhir)[native-inputs]: Add ocamlbuild. (ocaml-lablgtk): Update to 2.18.6. (unison)[inputs]: Use ocaml-4.02. (ocaml-findlib): Update to 1.8.0. (ocaml-ounit)[native-inputs]: Add ocamlbuild. (ocamlmod): Update to 0.0.9. (ocaml-frontc)[arguments]: Use ocaml-4.02. (ocaml-qcheck)[native-inputs]: Add ocamlbuild. (ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild. (ocaml-stringext)[native-inputs]: Add ocamlbuild. (ocaml-bisect): Update to 1.3.1. (ocaml4.01-bisect): Downgrade to 1.3. (ocaml-bitstring): Update to 3.1.0. (ocaml-topkg)[native-inputs]: Add ocamlbuild. (ocaml-rresult)[native-inputs]: Add ocamlbuild. (ocaml-sqlite3)[native-inputs]: Add ocamlbuild. (ocaml-csv)[native-inputs]: Add ocamlbuild. (ocaml-mtime)[native-inputs]: Add ocamlbuild. (ocaml-cmdliner)[native-inputs]: Add ocamlbuild. (ocaml-fmt)[native-inputs]: Add ocamlbuild. (ocaml-astring)[native-inputs]: Add ocamlbuild. (ocaml-alcotest)[native-inputs]: Add ocamlbuild. (ocaml-ppx-tools)[native-inputs]: Add ocamlbuild. (ocaml-react)[native-inputs]: Add ocamlbuild. (ocaml-ssl)[arguments]: Return #t in phases. (ocaml-lwt): Update to 4.1.0. (ocaml-logs)[native-inputs]: Add ocamlbuild. (ocaml-fpath)[native-inputs]: Add ocamlbuild. (ocaml-bos)[native-inputs]: Add ocamlbuild. (ocaml-xmlm): Update to 1.3.0. (ocaml-ulex): Update to 1.2.0. (ocaml-uchar)[native-inputs]: Add ocamlbuild. (ocaml-uutf): Update to 1.0.1. (ocaml-jsonm): Update to 1.0.1. (ocaml-ocurl): Update to 0.8.2. (ocaml-base64)[native-inputs]: Add ocamlbuild. (ocamlify)[native-inputs]: Use ocaml-4.02. (omake): Update to 0.10.3. (ocaml-batteries): Update to 2.9.0. (ocaml-pcre)[native-inputs]: Add ocamlbuild. (ocaml-expect): Update 0.0.6. (ocaml4.02-fileutils): Update to 0.5.3. (ocaml-oasis): Update 0.4.11. (ocaml-js-build-tools)[native-inputs]: Add ocamlbuild. (ocaml-bin-prot): Rename to ocaml4.02-bin-prot. (ocaml-fieldslib): Rename to ocaml4.02-fieldslib. (ocaml-ppx-core): Rename to ocaml4.02-ppx-core. (ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp. (ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver. (ocaml-cppo): Update to 1.6.5. (ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving. (ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv. (ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test. (ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench. (ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare. (ocaml-sexplib): Rename to ocaml4.02-sexplib. (ocaml-typerep): Rename to ocaml4.02-typerep. (ocaml-variantslib): Rename to ocaml4.02-variantslib. (ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv. (ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv. (ocaml-ppx-here): Rename to ocaml4.02-ppx-here. (ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert. (ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate. (ocaml-ppx-let): Rename to ocaml4.02-ppx-let. (ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv. (ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value. (ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang. (ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot. (ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail. (ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf. (ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message. (ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv. (ocaml-re): Update to 1.8.0. (ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect. (ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane. (ocaml-core-kernel): Rename to ocaml4.02-core-kernel. (ocaml-async-kernel): Rename to ocaml4.02-async-kernel. (ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel. (ocaml-core): Rename to ocaml4.02-core. (ocaml-async-unix): Rename to ocaml4.02-async-unix. (ocaml-async-extra): Rename to ocaml4.02-async-extra. (ocaml-async): Rename to ocaml4.02-async. (ocaml-ocplib-endian)[native-inputs]: Update to 1.0. (ocaml-cstruct): Rename to ocaml4.02-cstruct. (ocaml-hex): Rename to ocaml4.02-hex. (ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm. (ocaml-uri): Rename to ocaml4.02-uri. (optcomp): Use ocaml-4.02. (ocaml-piqilib): Update to 0.6.14. (ocaml-uuidm)[native-inputs]: Add ocamlbuild. (ocaml-graph): Update to 1.8.8. (ocaml-piqi): Update to 0.7.6. (bap): Update to 1.3.0. (ocaml-camomile): Update to 1.0.1. (ocaml-jbuilder): Use ocaml-4.02. (ocaml-lambda-term): Update to 1.13. (ocaml-utop): Update to 2.2.0. (ocaml-integers)[native-inputs]: Add ocamlbuild. (ocaml-ctypes): Update to 0.14.0. (ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild. (ocaml-tsdl)[native-inputs]: Add ocamlbuild. * gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02. * gnu/packages/maths.scm (cubicle): Update to 1.1.2. * gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch: Update patch. * guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib) (package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.
2018-11-18gnu: maxima: Fix tests on i686 and x86_64.Kei Kebreau
* gnu/packages/maths.scm (maxima)[arguments]: Replace check phase.
2018-11-18gnu: ccl: Include x86-headers and remove missing "contrib" folder.Pierre Neidhardt
* gnu/packages/lisp.scm (ccl): Include x86-headers and remove missing "contrib" folder.
2018-11-17gnu: mesa: Stay on RTTI-less LLVM.Marius Bakke
* gnu/packages/llvm.scm (llvm-without-rtti): New public variable. * gnu/packages/gl.scm (mesa)[inputs]: Use that instead of LLVM.
2018-11-17gnu: Add ClamAV.Eric Bavier
* gnu/packages/antivirus.scm: New file. * gnu/packages/patches/clamav-system-tomsfastmath.patch, gnu/packages/patches/clamav-config-llvm-libs.patch: New files. * gnu/local.mk (GNU_SYSTEM_MODULES): Add new module. (dist_patch_DATA): Add patches. Co-authored-by: Christopher Baines <mail@cbaines.net>
2018-11-17gnu: Add TomsFastMath.Eric Bavier
* gnu/packages/multiprecision.scm (tomsfastmath): New variable. * gnu/packages/patches/tomsfastmath-constness.patch: New patch. * gnu/local.mk (dist_patch_DATA): Add it.
2018-11-17llvm: Build with RTTI by default.Eric Bavier
Increases size of llvm@6 by 2.5MiB (2.5%), but saves building specialized llvm's with rtti enabled for packages that require RTTI when linking with the llvm libraries. * gnu/packages/llvm.scm (llvm-3.8-with-rtti): Remove variable. (llvm)[arguments]: Add '-DLLVM_REQUIRES_RTTI=1' to #:configure-flags. * gnu/packages/audio.scm (faust-2)[native-inputs]: 'llvm-3.8-with-rtti' -> 'llvm-3.8'.
2018-11-17gnu: u-boot: Update to 2018.11.Vagrant Cascadian
* gnu/packages/bootloaders.scm (u-boot): Update to 2018.11. (u-boot)[native-inputs]: Add lz4.
2018-11-16gnu: Add git-when-merged.Kyle Meyer
* gnu/packages/version-control.scm (git-when-merged): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-16gnu: Add caps-plugins-lv2.Thorsten Wilms
* gnu/packages/audio.scm (caps-plugins-lv2): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-16gnu: tiled: Update to 1.2.1.David Thompson
* gnu/packages/game-development.scm (tiled): Update to 1.2.1.
2018-11-16guile: newt: Update revision to 2.Mathieu Othacehe
* gnu/packages/guile.scm (guile-newt): Update revision to 2.
2018-11-16gnu: Add cmh.Andreas Enge
* gnu/packages/algebra.scm (cmh): New variable.
2018-11-16gnu: gp2c: Update to 0.0.11pl1.Andreas Enge
* gnu/packages/algebra.scm (gp2c): Update to 0.0.11pl1.
2018-11-15gnu: emacs-realgud: Patch configure.ac to repair the build.Maxim Cournoyer
This fixes https://bugs.gnu.org/33196, a build problem caused by a defective Elisp snippet in a check in configure.ac. * gnu/packages/patches/emacs-realgud-fix-configure-ac.patch: Add patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/emacs.scm (emacs-realgud)[source]: Use it.
2018-11-15gnu: Add nanopolish.pimi
* gnu/packages/bioinformatics.scm (nanopolish): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15gnu: sambamba: Update to 0.6.8.Roel Janssen
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-14gnu: linux-libre: Update to 4.19.2.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.2. (%linux-libre-hash): Update hash.
2018-11-14gnu: linux-libre@4.14: Update to 4.14.81.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.81. (%linux-libre-4.14-hash): Update hash.
2018-11-14gnu: linux-libre@4.9: Update to 4.9.137.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.137.
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