diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 42 | ||||
| -rw-r--r-- | gnu/packages/cran.scm | 27 | ||||
| -rw-r--r-- | gnu/packages/llvm.scm | 10 | ||||
| -rw-r--r-- | gnu/services/desktop.scm | 58 | ||||
| -rw-r--r-- | gnu/services/herd.scm | 36 | ||||
| -rw-r--r-- | guix/scripts/import.scm | 39 |
6 files changed, 170 insertions, 42 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59b921af82..4d3f86bfd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5111,6 +5111,48 @@ includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.") (license license:gpl3))) +(define-public r-scmap + (package + (name "r-scmap") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scmap" version)) + (sha256 + (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (properties `((upstream-name . "scmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dplyr + r-e1071 + r-ggplot2 + r-googlevis + r-matrixstats + r-proxy + r-randomforest + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hemberg-lab/scmap") + (synopsis "Tool for unsupervised projection of single cell RNA-seq data") + (description + "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the +composition of complex tissues since the technology allows researchers to +define cell-types using unsupervised clustering of the transcriptome. +However, due to differences in experimental methods and computational +analyses, it is often challenging to directly compare the cells identified in +two different experiments. @code{scmap} is a method for projecting cells from +a scRNA-seq experiment onto the cell-types or individual cells identified in a +different experiment.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 61a1b055b9..5a8285b342 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -425,6 +425,33 @@ Distance (EMD).") (description "This package lets you manage Google Drive files from R.") (license license:expat))) +(define-public r-googlevis + (package + (name "r-googlevis") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "googleVis" version)) + (sha256 + (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz")))) + (properties `((upstream-name . "googleVis"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite)) + (native-inputs (list r-knitr)) + (home-page "https://mages.github.io/googleVis/") + (synopsis "R interface to Google Charts") + (description + "The @code{googleVis} package provides an interface between R and the Google +Charts API. Google Charts offer interactive charts which can be embedded into +web pages. The functions of the @code{googleVis} package allow the user to +visualise data stored in R data frames with Google Charts without uploading +the data to Google. The output of a @code{googleVis} function is HTML code +that contains the data and references to JavaScript functions hosted by +Google. @code{googleVis} makes use of the internal R HTTP server to display +the output locally.") + (license license:gpl2+))) + (define-public r-guix-install (package (name "r-guix-install") diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index aedf039ff4..d3b16f2759 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -216,7 +216,15 @@ given PATCHES. When TOOLS-EXTRA is given, it must point to the ;; Use a sane default include directory. (string-append "-DC_INCLUDE_DIRS=" (assoc-ref %build-inputs "libc") - "/include")) + "/include") + ,@(if (target-riscv64?) + (list "-DLIBOMP_LIBFLAGS=-latomic" + "-DCMAKE_SHARED_LINKER_FLAGS=-latomic") + `())) + + ,@(if (target-riscv64?) + `(#:make-flags '("LDFLAGS=-latomic")) + '()) ;; Don't use '-g' during the build to save space. #:build-type "Release" diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index 24fd43a207..0499071436 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -1075,10 +1075,60 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks." ("HybridSleepMode" (sleep-list elogind-hybrid-sleep-mode)))) (define (elogind-dbus-service config) - (list (wrapped-dbus-service (elogind-package config) - "libexec/elogind/elogind" - `(("ELOGIND_CONF_FILE" - ,(elogind-configuration-file config)))))) + "Return a @file{org.freedesktop.login1.service} file that tells D-Bus how to +\"start\" elogind. In practice though, our elogind is started when booting by +shepherd. Thus, the @code{Exec} line of this @file{.service} file does not +explain how to start elogind; instead, it spawns a wrapper that waits for the +@code{elogind} shepherd service. This avoids a race condition where both +@command{shepherd} and @command{dbus-daemon} would attempt to start elogind." + ;; For more info on the elogind startup race, see + ;; <https://issues.guix.gnu.org/55444>. + + (define elogind + (elogind-package config)) + + (define wrapper + (program-file "elogind-dbus-shepherd-sync" + (with-imported-modules '((gnu services herd)) + #~(begin + (use-modules (gnu services herd) + (srfi srfi-34)) + + (guard (c ((service-not-found-error? c) + (format (current-error-port) + "no elogind shepherd service~%") + (exit 1)) + ((shepherd-error? c) + (format (current-error-port) + "elogind shepherd service not \ +started~%") + (exit 2))) + (wait-for-service 'elogind)))))) + + (define build + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils) + (ice-9 match)) + + (define service-directory + "/share/dbus-1/system-services") + + (mkdir-p (dirname (string-append #$output service-directory))) + (copy-recursively (string-append #$elogind service-directory) + (string-append #$output service-directory)) + (symlink (string-append #$elogind "/etc") ;for etc/dbus-1 + (string-append #$output "/etc")) + + ;; Replace the "Exec=" line of the 'org.freedesktop.login1.service' + ;; file with one that refers to WRAPPER instead of elogind. + (match (find-files #$output "\\.service$") + ((file) + (substitute* file + (("Exec[[:blank:]]*=.*" _) + (string-append "Exec=" #$wrapper "\n")))))))) + + (list (computed-file "elogind-dbus-service-wrapper" build))) (define (pam-extension-procedure config) "Return an extension for PAM-ROOT-SERVICE-TYPE that ensures that all the PAM diff --git a/gnu/services/herd.scm b/gnu/services/herd.scm index 80d08f849e..a7c845b4b0 100644 --- a/gnu/services/herd.scm +++ b/gnu/services/herd.scm @@ -58,7 +58,8 @@ load-services/safe start-service stop-service - restart-service)) + restart-service + wait-for-service)) ;;; Commentary: ;;; @@ -313,6 +314,39 @@ when passed a service with an already-registered name." (with-shepherd-action name ('restart) result result)) +(define* (wait-for-service name #:key (timeout 20)) + "Wait for the service providing NAME, a symbol, to be up and running, and +return its \"running value\". Give up after TIMEOUT seconds and raise a +'&shepherd-error' exception. Raise a '&service-not-found-error' exception +when NAME is not found." + (define (relevant-service? service) + (memq name (live-service-provision service))) + + (define start + (car (gettimeofday))) + + ;; Note: As of Shepherd 0.9.1, we cannot just call the 'start' method and + ;; wait for it: it would spawn an additional elogind process. Thus, poll. + (let loop ((attempts 0)) + (define services + (current-services)) + + (define now + (car (gettimeofday))) + + (when (>= (- now start) timeout) + (raise (condition (&shepherd-error)))) ;XXX: better exception? + + (match (find relevant-service? services) + (#f + (raise (condition (&service-not-found-error + (service name))))) + (service + (or (live-service-running service) + (begin + (sleep 1) + (loop (+ attempts 1)))))))) + ;; Local Variables: ;; eval: (put 'alist-let* 'scheme-indent-function 2) ;; eval: (put 'with-shepherd 'scheme-indent-function 1) diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm index fa79f3211e..62aa7bdbc5 100644 --- a/guix/scripts/import.scm +++ b/guix/scripts/import.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2020, 2021 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014 David Thompson <davet@gnu.org> ;;; Copyright © 2018 Kyle Meyer <kyle@kyleam.com> -;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2019, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz> ;;; Copyright © 2022 Philip McGrath <philip@philipmcgrath.com> @@ -25,6 +25,7 @@ (define-module (guix scripts import) #:use-module (guix ui) #:use-module (guix scripts) + #:use-module (guix scripts style) #:use-module (guix utils) #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) @@ -32,43 +33,11 @@ #:use-module (srfi srfi-37) #:use-module (ice-9 format) #:use-module (ice-9 match) - #:use-module (ice-9 pretty-print) #:export (%standard-import-options guix-import)) ;;; -;;; Helper. -;;; - -(define (newline-rewriting-port output) - "Return an output port that rewrites strings containing the \\n escape -to an actual newline. This works around the behavior of `pretty-print' -and `write', which output these as \\n instead of actual newlines, -whereas we want the `description' field to contain actual newlines -rather than \\n." - (define (write-string str) - (let loop ((chars (string->list str))) - (match chars - (() - #t) - ((#\\ #\n rest ...) - (newline output) - (loop rest)) - ((chr rest ...) - (write-char chr output) - (loop rest))))) - - (make-soft-port (vector (cut write-char <>) - write-string - (lambda _ #t) ; flush - #f - (lambda _ #t) ; close - #f) - "w")) - - -;;; ;;; Command line options. ;;; @@ -119,9 +88,7 @@ Run IMPORTER with ARGS.\n")) ((importer args ...) (if (member importer importers) (let ((print (lambda (expr) - (pretty-print expr (newline-rewriting-port - (current-output-port)) - #:max-expr-width 80)))) + (pretty-print-with-comments (current-output-port) expr)))) (match (apply (resolve-importer importer) args) ((and expr (or ('package _ ...) ('let _ ...) |