* [bug#55615] [PATCH] gnu: Add r-pscbs. @ 2022-05-24 18:08 zimoun 2022-05-24 21:29 ` bug#55615: " Ricardo Wurmus 0 siblings, 1 reply; 5+ messages in thread From: zimoun @ 2022-05-24 18:08 UTC (permalink / raw) To: 55615; +Cc: zimoun, rekado * gnu/packages/bioconductor.scm (r-pscbs): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80cf28c954..7fed1aa18b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4560,6 +4560,48 @@ (define-public r-pcamethods structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-aroma-light, r-dnacopy.. +(define-public r-pscbs + (package + (name "r-pscbs") + (version "0.66.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PSCBS" version)) + (sha256 + (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (properties `((upstream-name . "PSCBS"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-aroma-light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r-cache + r-r-methodss3 + r-r-oo + r-r-utils)) + (native-inputs + (list r-r-rsp ;used to build vignettes + r-r-devices)) + (home-page "https://github.com/HenrikBengtsson/PSCBS") + (synopsis "Analysis of Parent-Specific DNA Copy Numbers") + (description + "Segmentation of allele-specific DNA copy number data and detection of +regions with abnormal copy number within each parental chromosome. Both +tumor-normal paired and tumor-only analyses are supported.") + (license license:gpl2+))) + (define-public r-protgenerics (package (name "r-protgenerics") base-commit: 01793ed03e8aa0960bff7adc21fd270e1527e68e -- 2.36.0 ^ permalink raw reply related [flat|nested] 5+ messages in thread
* bug#55615: [PATCH] gnu: Add r-pscbs. 2022-05-24 18:08 [bug#55615] [PATCH] gnu: Add r-pscbs zimoun @ 2022-05-24 21:29 ` Ricardo Wurmus 2022-05-25 7:31 ` [bug#55615] " zimoun 0 siblings, 1 reply; 5+ messages in thread From: Ricardo Wurmus @ 2022-05-24 21:29 UTC (permalink / raw) To: zimoun; +Cc: 55615-done zimoun <zimon.toutoune@gmail.com> writes: > * gnu/packages/bioconductor.scm (r-pscbs): New variable. Applied with formatting changes. Thanks! -- Ricardo ^ permalink raw reply [flat|nested] 5+ messages in thread
* [bug#55615] [PATCH] gnu: Add r-pscbs. 2022-05-24 21:29 ` bug#55615: " Ricardo Wurmus @ 2022-05-25 7:31 ` zimoun 2022-05-27 8:12 ` Ricardo Wurmus 0 siblings, 1 reply; 5+ messages in thread From: zimoun @ 2022-05-25 7:31 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: 55615-done Hi, On Tue, 24 May 2022 at 23:30, Ricardo Wurmus <rekado@elephly.net> wrote: > Applied with formatting changes. Thanks! Indeed, sorry. I reformatted the output of "guix import" but then I forgot to reformat again the phase modification (my bad!). And I ran "guix lint" which reported nothing. But "guix style" reformats; which I do not use (yet). Well, it is many manual error-prone steps. My questions are : 1. Could we adapted "guix import cran" to output something using the format of "guix style"? 2. Could we add a checker in "guix lint" using "guix style" and warn? Cheers, simon ^ permalink raw reply [flat|nested] 5+ messages in thread
* [bug#55615] [PATCH] gnu: Add r-pscbs. 2022-05-25 7:31 ` [bug#55615] " zimoun @ 2022-05-27 8:12 ` Ricardo Wurmus 2022-06-01 9:02 ` zimoun 0 siblings, 1 reply; 5+ messages in thread From: Ricardo Wurmus @ 2022-05-27 8:12 UTC (permalink / raw) To: zimoun; +Cc: 55615-done [-- Attachment #1: Type: text/plain, Size: 600 bytes --] zimoun <zimon.toutoune@gmail.com> writes: > Hi, > > On Tue, 24 May 2022 at 23:30, Ricardo Wurmus <rekado@elephly.net> wrote: > >> Applied with formatting changes. Thanks! > > Indeed, sorry. I reformatted the output of "guix import" but then I > forgot to reformat again the phase modification (my bad!). And I ran > "guix lint" which reported nothing. But "guix style" reformats; > which I do not use (yet). > > Well, it is many manual error-prone steps. My questions are : > > 1. Could we adapted "guix import cran" to output something using the > format of "guix style"? How about this: [-- Attachment #2: 0001-scripts-import-Use-pretty-printer-from-guix-scripts-.patch --] [-- Type: text/x-patch, Size: 3312 bytes --] From a10afc4c60ce734941c3c080cf13ec6636f0be33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <rekado@elephly.net> Date: Fri, 27 May 2022 10:07:26 +0200 Subject: [PATCH] scripts/import: Use pretty printer from (guix scripts style). * guix/scripts/import.scm (guix-import): Use pretty-print-with-comments. (newline-rewriting-port): Remove procedure. --- guix/scripts/import.scm | 39 +++------------------------------------ 1 file changed, 3 insertions(+), 36 deletions(-) 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) @@ -32,41 +33,9 @@ (define-module (guix scripts import) #: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)) -\f -;;; -;;; 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")) - \f ;;; ;;; Command line options. @@ -119,9 +88,7 @@ (define-command (guix-import . args) ((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 _ ...) -- 2.36.1 [-- Attachment #3: Type: text/plain, Size: 13 bytes --] -- Ricardo ^ permalink raw reply related [flat|nested] 5+ messages in thread
* [bug#55615] [PATCH] gnu: Add r-pscbs. 2022-05-27 8:12 ` Ricardo Wurmus @ 2022-06-01 9:02 ` zimoun 0 siblings, 0 replies; 5+ messages in thread From: zimoun @ 2022-06-01 9:02 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: 55615-done Hi Ricardo, On Fri, 27 May 2022 at 10:13, Ricardo Wurmus <rekado@elephly.net> wrote: > How about this: I am late and you already applied it. Cool! :-) Thanks, simon ^ permalink raw reply [flat|nested] 5+ messages in thread
end of thread, other threads:[~2022-06-01 9:08 UTC | newest] Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2022-05-24 18:08 [bug#55615] [PATCH] gnu: Add r-pscbs zimoun 2022-05-24 21:29 ` bug#55615: " Ricardo Wurmus 2022-05-25 7:31 ` [bug#55615] " zimoun 2022-05-27 8:12 ` Ricardo Wurmus 2022-06-01 9:02 ` zimoun
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