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2018-11-19gnu: r-mclust: Update to 5.4.2.Roel Janssen
* gnu/packages/statistics.scm (r-mclust): Update to 5.4.2.
2018-11-19gnu: r-openssl: Update to 1.1.Roel Janssen
* gnu/packages/statistics.scm (r-openssl): Update to 1.1.
2018-11-19gnu: r-biocmanager: Update to 1.30.4.Roel Janssen
* gnu/packages/cran.scm (r-biocmanager): Update to 1.30.4.
2018-11-19gnu: r-ggeffects: Update to 0.7.0.Roel Janssen
* gnu/packages/cran.scm (r-ggeffects): Update to 0.7.0.
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.
2018-11-19build-system: Add 'clojure-build-system'.Alex Vong
* guix/build-system/clojure.scm, guix/build/clojure-build-system.scm: New files. * guix/build/clojure-utils.scm (@*, @@*): New macros. (%source-dirs, %test-dirs, %compile-dir, %main-class, %omit-source?, %aot-include, %aot-exclude, %tests?, %test-include, %test-exclude, %clojure-regex): New variables. (package-name->jar-names, canonicalize-relative-path, find-files*, file-sans-extension, relative-path->clojure-lib-string, find-clojure-libs, compiled-from?, include-list\exclude-list, eval-with-clojure, create-jar): New procedures. * Makefile.am (MODULES): Add them. * doc/guix.texi (Build Systems): Document 'clojure-build-system'.
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.
2018-11-19guix system: Fix 'init'.Ludovic Courtès
Fixes a regression introduced in 52ee4479ef26826a53b9929cd00ca7738be687b1, whereby 'install' would now be passed a <computed-file> object instead of a derivation. * guix/scripts/system.scm (install): Call 'lower-object' on BOOTCFG.
2018-11-18gnu: Add libfdk 'FDK AAC' library.Leo Famulari
* gnu/packages/audio.scm (libfdk): New variable.
2018-11-18guix system: Clarify 'perform-action'.Ludovic Courtès
* guix/scripts/system.scm (perform-action): Move non-monadic local variables outside the 'mlet' form.
2018-11-18guix system: De-monadify bootloader installation script.Ludovic Courtès
* guix/scripts/system.scm (bootloader-installer-derivation): Rename to... (bootloader-installer-script): ... this. Use 'scheme-file' instead of 'gexp->file'. (perform-action): Adjust accordingly. Move 'lower-object' call to the point where DRVS is computed.
2018-11-18guix system: Simplify bootloader package handling.Ludovic Courtès
* guix/scripts/system.scm (perform-action): Remove 'bootloader-package' variable. Pass (bootloader-package bootloader) as the 2nd argument to 'bootloader-installer-derivation'. Remove BOOTLOADER-PACKAGE from DRVS since it's redundant.
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: hurd: Build against glibc 2.28.Ludovic Courtès
Version 2.28 of glibc is the first in a long time that fully supports GNU/Hurd. This change updates the Hurd and Mach to provide the features glibc 2.28 expects and adjusts the cross-compilation tool chain for "i586-pc-gnu". * gnu/packages/base.scm (glibc/linux): Rename to... (glibc): ... this. [propagated-inputs]: Add 'hurd-target?' case. [arguments]: Use '--disable-werror' when 'hurd-target?'. Add 'augment-libc.so' phase when 'hurd-target?'. [native-inputs]: Add MIG and PERL when 'hurd-target?'. (glibc/hurd, glibc-for-target): Remove (glibc/hurd-headers): Inherit from GLIBC, not GLIBC/HURD. [arguments]: Remove "--enable-obsolete-rpc" configure flag and 'patch-configure-script' phase. * gnu/packages/cross-base.scm (cross-kernel-headers)[xglibc/hurd-headers]: Move 'set-cross-headers-path' after 'unpack'. * gnu/packages/cross-base.scm (cross-libc)[cross-libc-for-target]: Remove. Pass "--disable-werror" when TARGET matches 'hurd-triplet?'. * gnu/packages/hurd.scm (hurd-target?, patch-url): New procedures. (gnumach-headers)[source](patches, modules, snippet): New fields. (hurd-headers): Use Git commit 98b3390. [native-inputs]: Add AUTOCONF and AUTOMAKE. [arguments]: Add "ac_cv_func_*" configure flags. (hurd-minimal)[native-inputs]: Remove. [arguments]: In 'build' phase, build "include/assert-backtrace.h" first.
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.
2018-11-18build-system/ocaml: Use invoke and return #t.Julien Lepiller
* guix/build/ocaml-build-system.scm (configure, build, check, install) (prepare-install): Use invoke and return #t.
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: spice: Run tests sequentially.Ludovic Courtès
* gnu/packages/spice.scm (spice)[arguments]: Add #:parallel-tests?.
2018-11-18gnu: qt@5: Fix build failure on glibc 2.28.Ludovic Courtès
* gnu/packages/patches/qt-5-renameat2.patch: New file. * gnu/packages/qt.scm (qt)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
2018-11-18gnu: linkchecker: Use 'git-file-name' for the source.Efraim Flashner
* gnu/packages/web.scm (linkchecker)[source]: Add missing 'file-name' field.
2018-11-18gnu: python-pytest-localserver: Update to 0.5.0.Efraim Flashner
* gnu/packages/check.scm (python-pytest-localserver): Update to 0.5.0.
2018-11-18gnu: python-pytest-localserver: Fix test suite.Efraim Flashner
* gnu/packages/check.scm (python-pytest-localserver): Replace custom '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.
2018-11-18gnu: libgtextutils: Re-instate custom bootstrap phase.Efraim Flashner
The source lacks a standard bootstrap script so the bootstrap phase is skipped otherwise. * gnu/packages/textutils.smc (libgtextutils)[arguments]: Replace 'bootstrap phase with upstream's bootstrap phase.
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