[PATCH] gnu: Add r-pscbs.

DoneSubmitted by zimoun.
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2 participants
  • Ricardo Wurmus
  • zimoun
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Z
Z
zimoun wrote on 24 May 20:08 +0200
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20220524180850.3381234-1-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-pscbs): New variable.
---
gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)

Toggle diff (57 lines)
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
R
R
Ricardo Wurmus wrote on 24 May 23:29 +0200
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 55615-done@debbugs.gnu.org)
87wneahb5b.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (2 lines)
> * gnu/packages/bioconductor.scm (r-pscbs): New variable.

Applied with formatting changes. Thanks!

--
Ricardo
Closed
Z
Z
zimoun wrote on 25 May 09:31 +0200
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 55615-done@debbugs.gnu.org)
CAJ3okZ2a=_hbzvZTkdMZ9PK_pXgis8NTvg1P4dXrCKS=1bth1w@mail.gmail.com
Hi,

On Tue, 24 May 2022 at 23:30, Ricardo Wurmus <rekado@elephly.net> wrote:

Toggle quote (2 lines)
> 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
Closed
R
R
Ricardo Wurmus wrote on 27 May 10:12 +0200
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 55615-done@debbugs.gnu.org)
87zgj3cs09.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (16 lines)
> 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:
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(-)

Toggle diff (76 lines)
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))
 
-
-;;;
-;;; 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 @@ (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
--
Ricardo
Closed
Z
Z
zimoun wrote on 1 Jun 11:02 +0200
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 55615-done@debbugs.gnu.org)
CAJ3okZ3Y17i=5=nguFRg0=W50JK3J-QaSiQy3qyXKYPuZC=z7w@mail.gmail.com
Hi Ricardo,

On Fri, 27 May 2022 at 10:13, Ricardo Wurmus <rekado@elephly.net> wrote:

Toggle quote (2 lines)
> How about this:

I am late and you already applied it. Cool! :-)

Thanks,
simon
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