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* [bug#59911] [PATCH] gnu: Add r-logging, r-shinycustomloader, r-anytime, r-shinywidgets, r-attempt, r-golem and r-wpm.
@ 2022-12-08 21:10 MadalinIonel.Patrascu
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
  0 siblings, 1 reply; 11+ messages in thread
From: MadalinIonel.Patrascu @ 2022-12-08 21:10 UTC (permalink / raw)
  To: 59911

[-- Attachment #1: Type: text/plain, Size: 410 bytes --]

* gnu/packages/bioconductor.scm (r-wpm): New variable.
* gnu/packages/cran.scm (r-logging, r-shinycustomloader, r-anytime, r-shinywidgets,
r-attempt, r-golem): New variables.




All the best!

Mădălin Ionel Patrașcu

System Administrator
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center (MDC)
Hannoversche Straße 28
House 101, room 1.89
10115 Berlin, Germany

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^ permalink raw reply	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 1/7] gnu: Add r-logging.
  2022-12-08 21:10 [bug#59911] [PATCH] gnu: Add r-logging, r-shinycustomloader, r-anytime, r-shinywidgets, r-attempt, r-golem and r-wpm MadalinIonel.Patrascu
@ 2022-12-08 21:13 ` Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 2/7] gnu: Add r-shinycustomloader Mădălin Ionel Patrașcu
                     ` (6 more replies)
  0 siblings, 7 replies; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/cran.scm (r-logging): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5c5258d6e0..553c53887c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16814,6 +16814,26 @@ (define-public r-locfdr
 discovery rates.")
     (license license:gpl2)))
 
+(define-public r-logging
+  (package
+    (name "r-logging")
+    (version "0.10-108")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "logging" version))
+              (sha256
+               (base32
+                "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5"))))
+    (properties `((upstream-name . "logging")))
+    (build-system r-build-system)
+    (home-page "https://github.com/WLOGSolutions/r-logging")
+    (synopsis "R logging implementation of log4j")
+    (description
+     "This package implements the R version of the @code{log4j} package.  It offers
+hierarchic loggers, multiple handlers per logger, level based filtering, space
+handling in messages and custom formatting.")
+    (license license:gpl3)))
+
 (define-public r-longitudinal
   (package
     (name "r-longitudinal")

base-commit: 81191e3410cc00c6438f532599dd0b96d521982f
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 2/7] gnu: Add r-shinycustomloader.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
@ 2022-12-08 21:13   ` Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 3/7] gnu: Add r-anytime Mădălin Ionel Patrașcu
                     ` (5 subsequent siblings)
  6 siblings, 0 replies; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/cran.scm (r-shinycustomloader): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 553c53887c..1a5bef3cdb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -17465,6 +17465,29 @@ (define-public r-upsetr
 several common set, element and attribute related tasks.")
     (license license:expat)))
 
+(define-public r-shinycustomloader
+  (package
+    (name "r-shinycustomloader")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "shinycustomloader" version))
+              (sha256
+               (base32
+                "1klx71vr26g0gjf6hbiia1qidqii5d467i1sdjvlrg1hxdcggqff"))))
+    (properties `((upstream-name . "shinycustomloader")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-glue
+           r-shiny))
+    (home-page "https://cran.r-project.org/package=shinycustomloader")
+    (synopsis "Custom loader for Shiny outputs")
+    (description
+     "This package provides a custom @code{CSS/HTML} or @code{GIF/image} file
+for the loading screen in R @code{Shiny}.  It also can use the marquee to have
+a custom text loading screen.")
+    (license license:gpl3)))
+
 ;; This package includes a JavaScript file, which is not minified.  When
 ;; upgrading please check that there are no new minified JavaScript files.
 (define-public r-shinybs
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 3/7] gnu: Add r-anytime.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 2/7] gnu: Add r-shinycustomloader Mădălin Ionel Patrașcu
@ 2022-12-08 21:13   ` Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 4/7] gnu: Add r-shinywidgets Mădălin Ionel Patrașcu
                     ` (4 subsequent siblings)
  6 siblings, 0 replies; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/cran.scm (r-anytime): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1a5bef3cdb..b9d5757795 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -25484,6 +25484,30 @@ (define-public r-anthropometry
 statistical shape analysis and archetypal analysis.")
     (license license:gpl2+)))
 
+(define-public r-anytime
+  (package
+    (name "r-anytime")
+    (version "0.3.9")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "anytime" version))
+              (sha256
+               (base32
+                "0jjpqynai5nd7mfy1smb44356f3d5bmpxhs1i9x9jw5c959c35hh"))))
+    (properties `((upstream-name . "anytime")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bh
+           r-rcpp))
+    (home-page "http://dirk.eddelbuettel.com/code/anytime.html")
+    (synopsis "Converter of input to POSIXct or Date")
+    (description
+     "The package converts the input in any one of character, integer, numeric,
+factor, or an ordered type into @code{POSIXct} (or @code{Date}) objects, using
+one of a number of predefined formats, and relying on Boost facilities for date
+and time parsing.")
+    (license license:gpl2+)))
+
 (define-public r-anndata
   (package
     (name "r-anndata")
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 4/7] gnu: Add r-shinywidgets.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 2/7] gnu: Add r-shinycustomloader Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 3/7] gnu: Add r-anytime Mădălin Ionel Patrașcu
@ 2022-12-08 21:13   ` Mădălin Ionel Patrașcu
  2022-12-12 17:49     ` Ricardo Wurmus
  2022-12-08 21:13   ` [bug#59911] [PATCH 5/7] gnu: Add r-attempt Mădălin Ionel Patrașcu
                     ` (3 subsequent siblings)
  6 siblings, 1 reply; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/cran.scm (r-shinywidgets): New variable.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b9d5757795..9cfca2f4ca 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -25810,6 +25810,33 @@ (define-public r-shinycssloaders
 automatically show a loader when the output is (re)calculating.")
     (license license:gpl3)))
 
+(define-public r-shinywidgets
+  (package
+    (name "r-shinywidgets")
+    (version "0.7.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "shinyWidgets" version))
+              (sha256
+               (base32
+                "1ls28r6dbvi4pml1mxakn327dzl0l71pkaw5rm9n80jd5npq9vmz"))))
+    (properties `((upstream-name . "shinyWidgets")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-anytime
+           r-bslib
+           r-htmltools
+           r-jsonlite
+           r-rlang
+           r-sass
+           r-shiny))
+    (home-page "https://github.com/dreamRs/shinyWidgets")
+    (synopsis "Custom input widgets for Shiny")
+    (description
+     "The package offers a collection of custom input controls and user interface
+components for Shiny applications.")
+    (license license:gpl3)))
+
 (define-public r-rsvg
   (package
     (name "r-rsvg")
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 5/7] gnu: Add r-attempt.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
                     ` (2 preceding siblings ...)
  2022-12-08 21:13   ` [bug#59911] [PATCH 4/7] gnu: Add r-shinywidgets Mădălin Ionel Patrașcu
@ 2022-12-08 21:13   ` Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 6/7] gnu: Add r-golem Mădălin Ionel Patrașcu
                     ` (2 subsequent siblings)
  6 siblings, 0 replies; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/cran.scm (r-attempt): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9cfca2f4ca..cb67edd338 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7235,6 +7235,31 @@ (define-public r-aricode
 variation information} (NVI) and entropy.")
     (license license:gpl3+)))
 
+(define-public r-attempt
+  (package
+    (name "r-attempt")
+    (version "0.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "attempt" version))
+              (sha256
+               (base32
+                "1ylgg7jcp8wqmxgf1mydnvh26k0mr8jyjla4hw06730r40yrs58m"))))
+    (properties `((upstream-name . "attempt")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rlang))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ColinFay/attempt")
+    (synopsis "Tools for defensive programming")
+    (description
+     "This package provides tools for defensive programming.  It is inspired by
+@code{purrr} mappers and based on @code{rlang}.  @code{Attempt} extends and
+facilitates defensive programming by providing a consistent grammar, and a set
+of functions for common tests and conditions.  @code{Attempt} only depends on
+@code{rlang}, and focuses on speed, so it can be integrated with other functions
+and used in the data analysis.")
+    (license license:expat)))
+
 (define-public r-debugme
   (package
     (name "r-debugme")
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 6/7] gnu: Add r-golem.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
                     ` (3 preceding siblings ...)
  2022-12-08 21:13   ` [bug#59911] [PATCH 5/7] gnu: Add r-attempt Mădălin Ionel Patrașcu
@ 2022-12-08 21:13   ` Mădălin Ionel Patrașcu
  2022-12-08 21:13   ` [bug#59911] [PATCH 7/7] gnu: Add r-wpm Mădălin Ionel Patrașcu
  2022-12-12 18:03   ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Ricardo Wurmus
  6 siblings, 0 replies; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/cran.scm (r-golem): New variable.
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cb67edd338..95c3672b78 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11126,6 +11126,43 @@ (define-public r-biasedurn
 distribution).")
     (license license:gpl3)))
 
+(define-public r-golem
+  (package
+    (name "r-golem")
+    (version "0.3.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "golem" version))
+              (sha256
+               (base32
+                "0rjkl1r83h0hcn30zssx64qm07sdx3g4v5rdxn56gbzfghw7ddcl"))))
+    (properties `((upstream-name . "golem")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-attempt
+           r-cli
+           r-config
+           r-crayon
+           r-desc
+           r-fs
+           r-here
+           r-htmltools
+           r-pkgload
+           r-roxygen2
+           r-rstudioapi
+           r-shiny
+           r-usethis
+           r-yaml))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ThinkR-open/golem")
+    (synopsis "Framework for robust shiny applications")
+    (description
+     "This package implements an opinionated framework for building a production-
+ready @code{Shiny} application.  @code{Golem} contains a series of tools like
+dependency management, version management, easy installation and deployment or
+documentation management.")
+    (license license:expat)))
+
 (define-public r-goplot
   (package
     (name "r-goplot")
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 7/7] gnu: Add r-wpm.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
                     ` (4 preceding siblings ...)
  2022-12-08 21:13   ` [bug#59911] [PATCH 6/7] gnu: Add r-golem Mădălin Ionel Patrașcu
@ 2022-12-08 21:13   ` Mădălin Ionel Patrașcu
  2022-12-12 18:03   ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Ricardo Wurmus
  6 siblings, 0 replies; 11+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-12-08 21:13 UTC (permalink / raw)
  To: 59911; +Cc: rekado

* gnu/packages/bioconductor.scm (r-wpm): 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 c62c5970b8..21b69cab01 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12244,6 +12244,48 @@ (define-public r-wppi
 scores and a path search algorithm.")
     (license license:expat)))
 
+(define-public r-wpm
+  (package
+    (name "r-wpm")
+    (version "1.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "wpm" version))
+              (sha256
+               (base32
+                "05zpj0i4741xn1g0yhkq3mg9zjppfryrfc47pxnys9bjfij0az52"))))
+    (properties `((upstream-name . "wpm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-cli
+           r-config
+           r-dplyr
+           r-dt
+           r-ggplot2
+           r-golem
+           r-logging
+           r-rcolorbrewer
+           r-rlang
+           r-shiny
+           r-shinycustomloader
+           r-shinydashboard
+           r-shinywidgets
+           r-stringr
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/HelBor/wpm")
+    (synopsis "Generating well plate maker")
+    (description
+     "The @acronym{WPM, Well-Plate Maker} is a Shiny application deployed as an
+R package.  Functions for a command-line/script use are available.  The WPM allows
+users to generate well plate maps to carry out their experiments while improving
+the handling of batch effects.  In particular, it helps controlling the \"plate
+effect\" thanks to its ability to randomize samples over multiple well plates.
+The algorithm for placing the samples is inspired by the backtracking algorithm:
+the samples are placed at random while respecting specific spatial constraints.")
+    (license license:artistic2.0)))
+
 (define-public r-wrench
   (package
     (name "r-wrench")
-- 
2.38.1





^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 4/7] gnu: Add r-shinywidgets.
  2022-12-08 21:13   ` [bug#59911] [PATCH 4/7] gnu: Add r-shinywidgets Mădălin Ionel Patrașcu
@ 2022-12-12 17:49     ` Ricardo Wurmus
  0 siblings, 0 replies; 11+ messages in thread
From: Ricardo Wurmus @ 2022-12-12 17:49 UTC (permalink / raw)
  To: Mădălin Ionel Patrașcu; +Cc: 59911


Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-shinywidgets): New variable.

This cannot be added as is.  We have had this package in the Guix
Science channel for a while now because it contains massive amounts of
minified JavaScript, sometimes without an obvious source.

Have you perhaps taken a look at some of these JavaScript files yet?

-- 
Ricardo




^ permalink raw reply	[flat|nested] 11+ messages in thread

* [bug#59911] [PATCH 1/7] gnu: Add r-logging.
  2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
                     ` (5 preceding siblings ...)
  2022-12-08 21:13   ` [bug#59911] [PATCH 7/7] gnu: Add r-wpm Mădălin Ionel Patrașcu
@ 2022-12-12 18:03   ` Ricardo Wurmus
  2023-09-02  4:41     ` [bug#59911] Add r-shinywidgets, r-wpm Vagrant Cascadian
  6 siblings, 1 reply; 11+ messages in thread
From: Ricardo Wurmus @ 2022-12-12 18:03 UTC (permalink / raw)
  To: Mădălin Ionel Patrașcu; +Cc: 59911

I applied five of these seven patches.  As I wrote earlier
r-shinywidgets contains minified JavaScript that would need to be
compiled from source instead.  Consequently, r-wpm cannot be accepted
because it depends on r-shinywidgets.

Could you please look into compiling the JavaScript from shinywidgets
from source?  We have a couple of other R packages that come with
minified JavaScript, and we modify them to remove the minified
JavaScript in a snippet, add the sources as native inputs, and then use
a build phase to compile them with esbuild.

-- 
Ricardo




^ permalink raw reply	[flat|nested] 11+ messages in thread

* [bug#59911] Add r-shinywidgets, r-wpm
  2022-12-12 18:03   ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Ricardo Wurmus
@ 2023-09-02  4:41     ` Vagrant Cascadian
  0 siblings, 0 replies; 11+ messages in thread
From: Vagrant Cascadian @ 2023-09-02  4:41 UTC (permalink / raw)
  To: Ricardo Wurmus, Mădălin Ionel Patrașcu; +Cc: 59911, control

[-- Attachment #1: Type: text/plain, Size: 383 bytes --]

retitle 59911 Add r-shinywidgets, r-wpm
thanks

On 2022-12-12, Ricardo Wurmus wrote:
> I applied five of these seven patches.  As I wrote earlier
> r-shinywidgets contains minified JavaScript that would need to be
> compiled from source instead.  Consequently, r-wpm cannot be accepted
> because it depends on r-shinywidgets.

Updating bug title appropriately.

live well,
  vagrant

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 227 bytes --]

^ permalink raw reply	[flat|nested] 11+ messages in thread

end of thread, other threads:[~2023-09-02  5:38 UTC | newest]

Thread overview: 11+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2022-12-08 21:10 [bug#59911] [PATCH] gnu: Add r-logging, r-shinycustomloader, r-anytime, r-shinywidgets, r-attempt, r-golem and r-wpm MadalinIonel.Patrascu
2022-12-08 21:13 ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Mădălin Ionel Patrașcu
2022-12-08 21:13   ` [bug#59911] [PATCH 2/7] gnu: Add r-shinycustomloader Mădălin Ionel Patrașcu
2022-12-08 21:13   ` [bug#59911] [PATCH 3/7] gnu: Add r-anytime Mădălin Ionel Patrașcu
2022-12-08 21:13   ` [bug#59911] [PATCH 4/7] gnu: Add r-shinywidgets Mădălin Ionel Patrașcu
2022-12-12 17:49     ` Ricardo Wurmus
2022-12-08 21:13   ` [bug#59911] [PATCH 5/7] gnu: Add r-attempt Mădălin Ionel Patrașcu
2022-12-08 21:13   ` [bug#59911] [PATCH 6/7] gnu: Add r-golem Mădălin Ionel Patrașcu
2022-12-08 21:13   ` [bug#59911] [PATCH 7/7] gnu: Add r-wpm Mădălin Ionel Patrașcu
2022-12-12 18:03   ` [bug#59911] [PATCH 1/7] gnu: Add r-logging Ricardo Wurmus
2023-09-02  4:41     ` [bug#59911] Add r-shinywidgets, r-wpm Vagrant Cascadian

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