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authorRicardo Wurmus <rekado@elephly.net>2023-04-28 17:59:55 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-04-29 20:27:56 +0200
commitb962e908a0a3a88d01ea5d30d26641139d64a1f1 (patch)
tree240d418460d1138fa5356f151fca58ad380a3aac /gnu
parent2c32ed3955c739874ae8620533aadda11679fd77 (diff)
downloadguix-b962e908a0a3a88d01ea5d30d26641139d64a1f1.tar.gz
guix-b962e908a0a3a88d01ea5d30d26641139d64a1f1.zip
gnu: r-keggrest: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.40.0.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioconductor.scm4
1 files changed, 2 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9559a20149..027f4922ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7214,14 +7214,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc"))))
+ "1zmsk5w8i3cq0983nx1d24a6awrbq7aj2wrapsnizq9gvrsrhbbb"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
> 2023-12-11gnu: cross-gcc: Handle AVR inputs....* gnu/packages/cross-base.scm (cross-gcc)[native-inputs]: Add case to handle AVR. Change-Id: I1ac38b721ed807302747cecb5fb1f6075694a01a Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jean-Pierre De Jesus DIAZ 2023-12-11gnu: cross-libc: Add AVR Libc support....* gnu/packages/avr.scm (make-avr-libc/implementation)[arguments]: Add avr target parameter and disable implicit cross inputs. [native-inputs]: Rename avr-gcc and avr-binutils to cross-gcc and cross-binutils to keep consistency with gnu-build-system. * gnu/packages/cross-base.scm (cross-libc): Add case for avr. Change-Id: I6b087946d1287a82fac61c48c513e7f2d2184794 Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jean-Pierre De Jesus DIAZ 2023-12-11gnu: cross-gcc: Handle target include paths....* gnu/packages/cross-base.scm (cross-gcc-search-paths): New procedure. (cross-gcc)[search-paths]: Convert to and use cross-gcc-search-paths procedure. Change-Id: Id306782eaf928d05cd005b9539087ed631506b5b Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jean-Pierre De Jesus DIAZ 2023-12-11gnu: cross-gcc: Enable multilib for AVR....* gnu/build/cross-toolchain.scm (patch-multilib-shebang): New procedure. * gnu/packages/avr.scm (make-avr-gcc): Remove uneeded phases and flags for multilib. * gnu/packages/cross-base (cross-gcc-arguments) <#:configure-flags> [target-avr?]: Remove --disable-multilib and add --enable-multilib. Change-Id: Id68d803057ac898f0a670f10487b08bf0891ab0b Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jean-Pierre De Jesus DIAZ 2023-12-11gnu: cross-libc: Return #f if no libc available....* gnu/packages/cross-base.scm (cross-libc): Return #f if no libc is available for the given TARGET. Change-Id: I17d19716373dd5704bb70d805437738fd29bd96b Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jean-Pierre De Jesus DIAZ 2023-07-13gnu: hurd-minimal: Include libshouldbeinlibc and libstore....* gnu/packages/hurd.scm (hurd-minimal)[inputs]: Add gnumach-headers. [arguments]: Rewrite to include libshouldbeinlibc and libstore. * gnu/packages/cross-base.scm (cross-kernel-headers*): Update xhurd-minimal accordingly: Add xgnumach-headers, add them to cpath, use gexps for modify-phases, add delete-shared-target phase. Signed-off-by: Josselin Poiret <dev@jpoiret.xyz> Janneke Nieuwenhuizen 2023-07-13gnu: Add libc-for-target and glibc/hurd....* gnu/packages/patches/glibc-2.37-hurd-clock_t_centiseconds.patch * gnu/packages/patches/glibc-2.37-hurd-local-clock_gettime_MONOTONIC.patch * gnu/packages/patches/glibc-2.37-versioned-locpath.patch: New patches. * gnu/local.mk (dist_patch_DATA): Register them. * gnu/packages/base.scm (glibc/hurd, libc-for-target): New variables. (glibc/hurd-headers): Use glibc/hurd. * gnu/packages/commencement.scm (glibc-final-with-bootstrap-bash)[outputs, source, arguments] (glibc-final)[source]: Use libc-for-target instead of glibc. * gnu/packages/cross-base.scm (cross-libc/deprecated, cross-libc*): Use libc-for-target. This part fixes https://issues.guix.gnu.org/63641#25 * gnu/packages/commencement.scm (%final-inputs): Change to memoized lambda taking "system". * gnu/packages/commencement.scm (canonical-package): Likewise, and update user, passing (%current-system). (make-gcc-toolchain): Update user, passing (%current-system). * gnu/packages/base.scm (%final-inputs): Likewise. * guix/scripts/refresh.scm (options->update-specs): Likewise. * guix/build-system/gnu.scm (standard-packages): Add optional "system" parameter. (lower): Update caller. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Co-authored-by: Janneke Nieuwenhuizen <janneke@gnu.org> Josselin Poiret 2023-07-13gnu: gnumach-headers: Cross-build without relying on x86....* gnu/packages/hurd.scm (gnumach-headers): Remove configure flags where we say the builder is running x86. * gnu/packages/cross-base.scm (cross-gnumach-headers): Work around limitation of build system, by manually changing the target host_cpu without relying on --host, because we don't have a working cross-compiler yet. Josselin Poiret 2023-07-13gnu: glibc/hurd-headers: Properly cross-build....* gnu/packages/base.scm (glibc/hurd-headers): Rely on cross-mig, and remove hardcoded configure flag `--host=i586-pc-gnu`. * gnu/packages/cross-base.scm (cross-kernel-headers*): Add `--host` and `--build` configure flags. Josselin Poiret 2023-03-30gnu: cross-base: Removed useless inputs to xhurd-core-headers....* gnu/packages/cross-base.scm (cross-kernel-headers*): Remove them. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret 2023-03-30gnu: cross-base: Add cross arguments to hurd derivatives....* gnu/packages/cross-base.scm (cross-kernel-headers*): Add --build and --host to xhurd-headers and xhurd-minimal. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret 2023-03-30gnu: cross-base: Factor out cross-mig....* gnu/packages/cross-base.scm (cross-mig): New exported procedure. (cross-gnumach-headers): New procedure. (cross-kernel-headers*): Factor them out. (cross-libc*): Use them there. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret 2023-03-30gnu: cross-base: Use gexps for 'cross-gcc-arguments'....* gnu/packages/cross-base.scm (cross-gcc-arguments): Switch to gexps. Ludovic Courtès 2023-03-30gnu: glibc: Work around broken GNU Mach header detection....* gnu/packages/base.scm (%glibc/hurd-configure-flags): New variable. (glibc)[arguments]: Use it. (glibc/hurd-headers)[arguments]: likewise. * gnu/packages/cross-base.scm (cross-libc*): Likewise. Co-authored-by: Josselin Poiret <dev@jpoiret.xyz> Ludovic Courtès 2023-03-04gnu: cross-base: Inherit arguments from 'mig'....That way, 'xmig' inherits the 'avoid-perl-dependency' build phase. * gnu/packages/hurd.scm (mig)[arguments]: In 'avoid-perl-dependency', use 'find-files' to locate the "mig" executable(s). * gnu/packages/cross-base.scm (cross-kernel-headers*)[xmig]: Use 'substitute-keyword-arguments'. Ludovic Courtès 2023-03-04gnu: cross-base: Remove input labels for GNU Mach and MiG....* gnu/packages/cross-base.scm (cross-kernel-headers*)[xgnumach-headers] [xmig]: Remove input labels; use gexps and 'modify-inputs'. [xgnumach-headers-name]: New variable. Ludovic Courtès 2023-02-16gnu: Remove unneeded module imports....* gnu/packages/abiword.scm, * gnu/packages/ada.scm, * gnu/packages/agda.scm, * gnu/packages/backup.scm, * gnu/packages/barrier.scm, * gnu/packages/bioinformatics.scm, * gnu/packages/bootstrap.scm, * gnu/packages/bqn.scm, * gnu/packages/c.scm, * gnu/packages/chemistry.scm, * gnu/packages/coq.scm, * gnu/packages/cross-base.scm, * gnu/packages/databases.scm, * gnu/packages/emacs-xyz.scm, * gnu/packages/enlightenment.scm, * gnu/packages/games.scm, * gnu/packages/geo.scm, * gnu/packages/ghostscript.scm, * gnu/packages/gl.scm, * gnu/packages/golang.scm, * gnu/packages/jami.scm, * gnu/packages/java-maths.scm, * gnu/packages/kde-frameworks.scm, * gnu/packages/kde-plasma.scm, * gnu/packages/language.scm, * gnu/packages/libreoffice.scm, * gnu/packages/linphone.scm, * gnu/packages/lisp.scm, * gnu/packages/llvm.scm, * gnu/packages/machine-learning.scm, * gnu/packages/minetest.scm, * gnu/packages/monitoring.scm, * gnu/packages/nfs.scm, * gnu/packages/ocr.scm, * gnu/packages/opencl.scm, * gnu/packages/pdf.scm, * gnu/packages/python-xyz.scm, * gnu/packages/racket.scm, * gnu/packages/rust.scm, * gnu/packages/syncthing.scm, * gnu/packages/syndication.scm, * gnu/packages/telegram.scm, * gnu/packages/vulkan.scm, * gnu/packages/web-browsers.scm, * gnu/packages/web.scm, * gnu/packages/webkit.scm: Remove some unecessary module imports. Efraim Flashner 2023-01-03gnu: cross-base: Standardize API to use keyword arguments....This makes it possible to invoke the procedures with a single or fewer optional arguments. * gnu/packages/cross-base.scm (contains-keyword?): New procedure. (cross-binutils): Dispatch to either... (cross-binutils/deprecated): ... this renamed procedure or ... (cross-binutils*): ... this new procedure. (cross-kernel-headers, cross-libc/deprecated): Likewise. Maxim Cournoyer