* bug#50483: [R] Package r-shiny: Shiny server logic inactive
@ 2021-09-09 12:35 Todor Kondić via Bug reports for GNU Guix
2021-09-15 16:50 ` zimoun
2021-09-27 12:50 ` zimoun
0 siblings, 2 replies; 9+ messages in thread
From: Todor Kondić via Bug reports for GNU Guix @ 2021-09-09 12:35 UTC (permalink / raw)
To: 50483
Hi,
I started having issues with R Shiny applications with newer Guix distro commits. I have a feeling that this is an issue arising from `r-shiny` dependency clashes and that (some) of those dependencies should be either downgraded, or upgraded.
The problem is that the server logic of a shiny application is never active. The web application UI is displayed correctly, even initialised correctly, but the logic behind it does not work.
Take, for example, a classic shiny demo app [1]. The control with the number of observations is displayed, but the plot depending on it never shows up. This behavior exists on recent Guix builds [2].
However, on one older build from a few months ago [3], the application runs fine.
You will find below the manifest[4] for creating the environment where Shiny programs malfunction and the command[5] to create the environment with the manifest.
By the way, for those of you who are R savvy, comparing sessionInfo() between the running and non-running version did uncover few version changes. I have not yet delved deeper in
what is the root cause, but I think I noticed that this is not
the difference in versions of R itself.
Lastly, if this is really a universal (ie I am not the
only one seeing this), then this is a significant problem
for a lot of people doing scientific computing on Guix.
sessionInfo() for working version:
R version 4.1.0 (2021-05-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Matrix products: default
BLAS/LAPACK: /gnu/store/bs9pl1f805ins80xaf4s3n35a0x2lyq3-openblas-0.3.9/lib/libopenblasp-r0.3.9.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.6.0
loaded via a namespace (and not attached):
[1] compiler_4.1.0 fastmap_1.1.0 ellipsis_0.3.2 magrittr_2.0.1
[5] R6_2.5.0 promises_1.2.0.1 later_1.2.0 tools_4.1.0
[9] htmltools_0.5.1.1 Rcpp_1.0.6 digest_0.6.27 xtable_1.8-4
[13] httpuv_1.6.1 lifecycle_1.0.0 mime_0.10 rlang_0.4.11
sessionInfo for the non-working version:
R version 4.1.1 (2021-08-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
Matrix products: default
BLAS/LAPACK: /gnu/store/bs9pl1f805ins80xaf4s3n35a0x2lyq3-openblas-0.3.9/lib/libopenblasp-r0.3.9.so
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.6.0
loaded via a namespace (and not attached):
[1] compiler_4.1.1 fastmap_1.1.0 ellipsis_0.3.2 magrittr_2.0.1
[5] R6_2.5.1 promises_1.2.0.1 later_1.3.0 htmltools_0.5.1.1
[9] tools_4.1.1 Rcpp_1.0.7 digest_0.6.27 xtable_1.8-4
[13] httpuv_1.6.2 lifecycle_1.0.0 mime_0.11 rlang_0.4.11
Reproducible-ish demo:
1. runme.R
```r
library(ggplot2)
library(shiny)
app <- shinyApp(
ui = bootstrapPage(
numericInput('n', 'Number of obs', 100),
plotOutput('plot')
),
server = function(input, output) {
output$plot <- renderPlot({ hist(runif(input$n)) })
}
)
# Will show a warning, because the browser is not in the manifest, but
# it it will serve the application on a listed port, which means it
# can be accessed by a browser external to the environment.
options(browser="itdoesnotmatter")
shiny::runApp(app)
```
2. for example, guix version: 816d52ba93d262548f5e1139ff6051887f13dd0d
3. for example, guix version:
29745d23b87529275a677ee7962b0405594e84db
4. Manifest for creating the environment:
```scheme
(use-modules (guix packages)
(guix inferior)
(guix channels)
(guix profiles)
(guix utils)
(guix build-system gnu)
(gnu packages)
(gnu packages commencement)
(gnu packages gcc)
(srfi srfi-1)
(ice-9 pretty-print))
(define base-specs '("git"
"rsync"
"make"))
(define font-specs '("unicode-emoji"
"fontconfig"
"font-dejavu"
"font-gnu-freefont"
"font-terminus"
"font-liberation"
"font-inconsolata"
"font-gnu-unifont"
"font-public-sans"
"font-misc-misc"
"font-awesome"
"font-hack"
"font-iosevka"
"font-iosevka-term"
"font-iosevka-term-slab"
"font-iosevka-slab"
"font-iosevka-etoile"
"font-iosevka-aile"
"font-google-noto"))
(define r-specs '("r"
"r-curl"
"r-ellipsis"
"r-future"
"r-rmarkdown"
"r-knitr"
"r-rcolorbrewer"
"r-data-table"
"r-shiny"
"r-cowplot"
"r-pander"
"r-rstatix"
"r-r-utils"))
(define texlive-specs '("texlive"))
(define misc-specs '("sshpass"
"xdg-utils"
"xdg-user-dirs"
"pango"
"libxft"
"cairo"
"gnupg"
"openssl"))
(define java-specs '(;"maven"
"openjdk:out"
"openjdk:jdk"))
(define perl-specs '("perl-yaml-libyaml"))
(define gnu-toolchain-specs '("gcc-toolchain"))
(define specs `(,@base-specs
,@font-specs
,@perl-specs
,@r-specs
,@java-specs
,@gnu-toolchain-specs
,@misc-specs
,@texlive-specs))
(define dev-channels
(list (channel
;; This is custom Environmental Cheminformatics LCSB channel.
(name 'eci-addons)
(url "https://git.sr.ht/~condor/eci-guix")
(branch "master")
(introduction
(make-channel-introduction
"6642600059913e86657242ba369d752c0af2bff5"
(openpgp-fingerprint
"EDC3 9790 A06D 5F72 41D9 70F9 BBEF E71B 7A28 3C6F"))))
(channel
(name 'guix)
(url "https://git.savannah.gnu.org/git/guix.git")
(commit "29745d23b87529275a677ee7962b0405594e84db"))))
(define inferior (inferior-for-channels dev-channels))
(define inferior-mnf-entry-list
(map (lambda (spec)
(let*
((spkgout (string-split spec #\:))
(spkg (car spkgout))
(rest (cdr spkgout))
(sout (if (null? rest)
"out"
(car rest)))
(pkg (first
(lookup-inferior-packages inferior spkg))))
(display (format #f "Commiting ~a to the inferior manifest list.\n" spkg))
(inferior-package->manifest-entry pkg sout)))
specs))
(display "Done building inferior list.\n")
(define default-manifest
(make-manifest '()))
(define all-manifest-entries inferior-mnf-entry-list)
(define manifest (make-manifest all-manifest-entries))
;;; For the fresh version
;;; (define manifest (specifications->manifest specs))
(display "Ready to go.") (newline)
manifest
```
5. Shell command to invoke the environment
```shell
guix environment -m ~/.local/my-scripts/r-manif.scm -c4 --pure -- R
```
After the command is run, just `source('runme.R')`.
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-09 12:35 bug#50483: [R] Package r-shiny: Shiny server logic inactive Todor Kondić via Bug reports for GNU Guix
@ 2021-09-15 16:50 ` zimoun
2021-09-16 5:57 ` Charles via Bug reports for GNU Guix
2021-09-27 12:50 ` zimoun
1 sibling, 1 reply; 9+ messages in thread
From: zimoun @ 2021-09-15 16:50 UTC (permalink / raw)
To: Todor Kondić; +Cc: charles.b.jackson, 50483
Hi,
Thanks for the report.
IIUC, the package uglify-js from gnu/packages/lisp-xyz was previously
used to minify and now replaced by the new uglifyjs package from the new
gnu/packages/uglifyjs. Then something is incompatible.
I propose to revert to the Lisp JavaScript compressor instead of the
Node one. JS people, WDYT?
On jeu., 09 sept. 2021 at 12:35, Todor Kondić <tk.code@protonmail.com> wrote:
> ```r
> library(ggplot2)
> library(shiny)
>
>
> app <- shinyApp(
> ui = bootstrapPage(
> numericInput('n', 'Number of obs', 100),
> plotOutput('plot')
> ),
> server = function(input, output) {
> output$plot <- renderPlot({ hist(runif(input$n)) })
> }
> )
>
>
> # Will show a warning, because the browser is not in the manifest, but
> # it it will serve the application on a listed port, which means it
> # can be accessed by a browser external to the environment.
> options(browser="itdoesnotmatter")
> shiny::runApp(app)
>
> ```
Using the R script above, and running:
guix time-machine --commit=<commit>
-- environment --ad-hoc r r-shiny r-ggplot2
-- R -e 'source("script.r")'
to bisect, the commit introducing a regression is:
--8<---------------cut here---------------start------------->8---
commit 385c485c651c0b1a467bdbbf31fa723dc4cabd9e
Author: Charles <charles.b.jackson@protonmail.com>
Date: Mon Jul 12 22:50:44 2021 -0500
build: Update uglifyjs for minify-build-system.
* guix/build-system/minify.scm (default-uglify-js): Update uglifyjs package used.
* guix/build/minify-build-system.scm (minify): Use updated uglifyjs command name.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
guix/build-system/minify.scm | 4 ++--
guix/build/minify-build-system.scm | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
--8<---------------cut here---------------end--------------->8---
with the Bisect Log (14):
816d52ba93 bad gnu: Add r-megadepth.
29745d23b8 good gnu: Use define-public in (gnu packages xiph).
aa6e6fb2e9 good gnu: Add ytfzf.
c8bcef2598 bad gnu: sameboy: Update to 0.14.4.
d84c24935b bad gnu: icedove: Update to 78.12.0 [security fixes].
026bd0b219 good gnu: r-matrixcalc: Update to 1.0-4.
7da8f66e52 good gnu: password-store: Fix passmenu paths substitution.
a49c5488bd good gnu: Add putty.
b019496fc3 good pack/deb: Add default section and priority fields to the control file.
bfa847dbe0 good gnu: Add node-acorn.
3436d3f801 bad gnu: Add emacs-zmq.
4cda5a4dab bad gnu: git-annex: Update to 8.20210714.
385c485c65 bad build: Update uglifyjs for minify-build-system.
d16148fcfd good gnu: Add node-uglify-js.
385c485c651c0b1a467bdbbf31fa723dc4cabd9e is the first bad commit
Cheers,
simon
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-15 16:50 ` zimoun
@ 2021-09-16 5:57 ` Charles via Bug reports for GNU Guix
2021-09-16 6:32 ` zimoun
0 siblings, 1 reply; 9+ messages in thread
From: Charles via Bug reports for GNU Guix @ 2021-09-16 5:57 UTC (permalink / raw)
To: zimoun; +Cc: 50483, Todor Kondić, efraim
Hello, I am responsible to updating the minify build syste to use the updated uglifyjs (now node-uglify-js found in gnu/packages/uglifyjs.scm). When updating I noticed that some R packages had the input uglify-js (the old lisp one). I chose not mess with them at risk of breaking. What I failed to realize is that some R packages (like r-shiny) actually use the minify build-system to do the minifying, thus trying to call the updated uglifyer, while only importing the new one. Other R package like (r-shinytree) do not use the minify build system and instead directly call uglify-js using open-pipe* (these are the ones I didn't want to break).
I would highly suggest against using the old lisp uglifyer since it is outdated by 6 years, and if anyone decides to write some modern javascript, your package will break. Instead simply update the input to ("node-uglify-js" ,node-uglify-js) and don't forget to use module (gnu packages uglifyjs). For the packages like r-shinytree, I would suggest having them use the minify-build system like r-shiny (and also updating to the newer node-uglify-js). I have tested updaing the input, and it works for the ggplot2 example stated earlier in this thread.
Again I'm really sorry for not catching this. It is very late where I am, so if it isn't clear how to update, I can do it tomorrow.
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-16 5:57 ` Charles via Bug reports for GNU Guix
@ 2021-09-16 6:32 ` zimoun
2021-09-18 5:14 ` Charles via Bug reports for GNU Guix
0 siblings, 1 reply; 9+ messages in thread
From: zimoun @ 2021-09-16 6:32 UTC (permalink / raw)
To: Charles; +Cc: 50483, Todor Kondić
Hi Charles,
On Thu, 16 Sep 2021 at 05:57, Charles <charles.b.jackson@protonmail.com> wrote:
> Hello, I am responsible to updating the minify build syste to use the
> updated uglifyjs (now node-uglify-js found in
> gnu/packages/uglifyjs.scm). When updating I noticed that some R
> packages had the input uglify-js (the old lisp one). I chose not mess
> with them at risk of breaking. What I failed to realize is that some R
> packages (like r-shiny) actually use the minify build-system to do the
> minifying, thus trying to call the updated uglifyer, while only
> importing the new one. Other R package like (r-shinytree) do not use
> the minify build system and instead directly call uglify-js using
> open-pipe* (these are the ones I didn't want to break).
>
> I would highly suggest against using the old lisp uglifyer since it is
> outdated by 6 years, and if anyone decides to write some modern
> javascript, your package will break. Instead simply update the input
> to ("node-uglify-js" ,node-uglify-js) and don't forget to use module
> (gnu packages uglifyjs). For the packages like r-shinytree, I would
> suggest having them use the minify-build system like r-shiny (and also
> updating to the newer node-uglify-js). I have tested updaing the
> input, and it works for the ggplot2 example stated earlier in this
> thread.
Thanks for explaining.
It is “broken” since:
CommitDate: Mon Jul 19 14:46:28 2021 +0300
so I propose to revert now or wait a couple of days for a fix.
Efraim, WDYT?
> Again I'm really sorry for not catching this. It is very late where I
> am, so if it isn't clear how to update, I can do it tomorrow.
Do not worry. That happens. :-) The good is that the situation shows
some limitations and how to improve.
Cheers,
simon
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-16 6:32 ` zimoun
@ 2021-09-18 5:14 ` Charles via Bug reports for GNU Guix
2021-09-20 19:03 ` zimoun
0 siblings, 1 reply; 9+ messages in thread
From: Charles via Bug reports for GNU Guix @ 2021-09-18 5:14 UTC (permalink / raw)
To: zimoun; +Cc: 50483, Todor Kondić, efraim
[-- Attachment #1: Type: text/plain, Size: 2303 bytes --]
Here is a patch to update the packages to use the up to date minifier. Is the the correct thread to put this or should I start a new thread in the patches mailing list?
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Thursday, September 16th, 2021 at 1:32 AM, zimoun <zimon.toutoune@gmail.com> wrote:
> Hi Charles,
>
> On Thu, 16 Sep 2021 at 05:57, Charles charles.b.jackson@protonmail.com wrote:
>
> > Hello, I am responsible to updating the minify build syste to use the
> >
> > updated uglifyjs (now node-uglify-js found in
> >
> > gnu/packages/uglifyjs.scm). When updating I noticed that some R
> >
> > packages had the input uglify-js (the old lisp one). I chose not mess
> >
> > with them at risk of breaking. What I failed to realize is that some R
> >
> > packages (like r-shiny) actually use the minify build-system to do the
> >
> > minifying, thus trying to call the updated uglifyer, while only
> >
> > importing the new one. Other R package like (r-shinytree) do not use
> >
> > the minify build system and instead directly call uglify-js using
> >
> > open-pipe* (these are the ones I didn't want to break).
> >
> > I would highly suggest against using the old lisp uglifyer since it is
> >
> > outdated by 6 years, and if anyone decides to write some modern
> >
> > javascript, your package will break. Instead simply update the input
> >
> > to ("node-uglify-js" ,node-uglify-js) and don't forget to use module
> >
> > (gnu packages uglifyjs). For the packages like r-shinytree, I would
> >
> > suggest having them use the minify-build system like r-shiny (and also
> >
> > updating to the newer node-uglify-js). I have tested updaing the
> >
> > input, and it works for the ggplot2 example stated earlier in this
> >
> > thread.
>
> Thanks for explaining.
>
> It is “broken” since:
>
> CommitDate: Mon Jul 19 14:46:28 2021 +0300
>
> so I propose to revert now or wait a couple of days for a fix.
>
> Efraim, WDYT?
>
> > Again I'm really sorry for not catching this. It is very late where I
> >
> > am, so if it isn't clear how to update, I can do it tomorrow.
>
> Do not worry. That happens. :-) The good is that the situation shows
>
> some limitations and how to improve.
>
> Cheers,
>
> simon
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Update-some-packages-using-old-JavaScript-minifi.patch --]
[-- Type: text/x-patch; name=0001-gnu-Update-some-packages-using-old-JavaScript-minifi.patch, Size: 13971 bytes --]
From 57c3801034e77120e4030d0e5421a02343e9280c Mon Sep 17 00:00:00 2001
From: Charles <charles.b.jackson@protonmail.com>
Date: Sat, 18 Sep 2021 00:05:55 -0500
Subject: [PATCH] gnu: Update some packages using old JavaScript minifier.
* gnu/packages/minetest.scm (minetest-basic-trains): New variable.
* gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input.
* gnu/packages/ci.scm (laminar): Update uglifyjs input.
* gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker
r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input.
* gnu/packages/javascript.scm (): Update uglifyjs input.
---
gnu/packages/bioinformatics.scm | 6 +++---
gnu/packages/ci.scm | 8 ++++----
gnu/packages/cran.scm | 32 ++++++++++++++++----------------
gnu/packages/javascript.scm | 11 +++++------
4 files changed, 28 insertions(+), 29 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ee85ab1a06..4f6d7d384a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -105,7 +105,6 @@
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages jupyter)
#:use-module (gnu packages linux)
- #:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages logging)
#:use-module (gnu packages lsof)
#:use-module (gnu packages machine-learning)
@@ -147,6 +146,7 @@
#:use-module (gnu packages textutils)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
+ #:use-module (gnu packages uglifyjs)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
@@ -9284,7 +9284,7 @@ Browser.")
(lambda* (#:key inputs #:allow-other-keys)
(let* ((file (assoc-ref inputs "plotly.js"))
(installed "plotly/plotly.js"))
- (let ((minified (open-pipe* OPEN_READ "uglify-js" file)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" file)))
(call-with-output-file installed
(cut dump-port minified <>))))
#t))
@@ -9342,7 +9342,7 @@ Browser.")
"v1.39.4/dist/plotly.js"))
(sha256
(base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
- ("uglify-js" ,uglify-js)))
+ ("uglifyjs" ,node-uglify-js)))
(home-page "https://www.bioinformatics.babraham.ac.uk/projects/bismark/")
(synopsis "Map bisulfite treated sequence reads and analyze methylation")
(description "Bismark is a program to map bisulfite treated sequencing
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index b7ea77ca31..a6d296923f 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -38,7 +38,7 @@
#:use-module (gnu packages guile)
#:use-module (gnu packages guile-xyz)
#:use-module (gnu packages gnupg)
- #:use-module (gnu packages lisp-xyz)
+ #:use-module (gnu packages uglifyjs)
#:use-module (gnu packages mail)
#:use-module (gnu packages package-management)
#:use-module (gnu packages perl)
@@ -252,7 +252,7 @@ intended as a replacement for Hydra.")
(let* ((file
(assoc-ref inputs (string-append name ".js")))
(port
- (open-pipe* OPEN_READ "uglify-js" file))
+ (open-pipe* OPEN_READ "uglifyjs" file))
(destination
(string-append
"../build/js/" name ".min.js")))
@@ -263,7 +263,7 @@ intended as a replacement for Hydra.")
(let ((exit (close-pipe port)))
(unless (zero? exit)
- (error "uglify-js failed" exit)))))
+ (error "uglifyjs failed" exit)))))
'("vue"
"vue-router"
@@ -282,7 +282,7 @@ intended as a replacement for Hydra.")
("zlib" ,zlib)))
(native-inputs
`(("googletest" ,googletest)
- ("uglify-js" ,uglify-js)
+ ("uglifyjs" ,node-uglify-js)
("vue.js"
,(origin (method url-fetch)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f80256c901..81dd78ac94 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -84,7 +84,7 @@
#:use-module (gnu packages java)
#:use-module (gnu packages javascript)
#:use-module (gnu packages libevent)
- #:use-module (gnu packages lisp-xyz)
+ #:use-module (gnu packages uglifyjs)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
@@ -2084,7 +2084,7 @@ previewing themes in real time.")
("js-strftime" ,js-strftime)
("js-highlight" ,js-highlight)))
(native-inputs
- `(("uglify-js" ,uglify-js)
+ `(("uglifyjs" ,node-uglify-js)
("gfortran" ,gfortran)
("js-bootstrap-accessibility"
,(origin
@@ -2151,7 +2151,7 @@ responsive, and powerful applications with minimal effort.")
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
source target)
- (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
@@ -2166,7 +2166,7 @@ responsive, and powerful applications with minimal effort.")
(inputs
`(("js-requirejs" ,js-requirejs)))
(native-inputs
- `(("uglify-js" ,uglify-js)
+ `(("uglifyjs" ,node-uglify-js)
("js-jquery"
,(origin
(method url-fetch)
@@ -2204,7 +2204,7 @@ supports interactive trees, to enable rich, editable trees in Shiny.")
(lambda _
(with-directory-excursion "inst/AdminLTE"
(delete-file "app.min.js")
- (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" "app.js")))
(call-with-output-file "app.min.js"
(lambda (port)
(dump-port minified port))))))))))
@@ -2213,7 +2213,7 @@ supports interactive trees, to enable rich, editable trees in Shiny.")
("r-promises" ,r-promises)
("r-shiny" ,r-shiny)))
(native-inputs
- `(("uglify-js" ,uglify-js)))
+ `(("uglifyjs" ,node-uglify-js)))
(home-page "https://rstudio.github.io/shinydashboard/")
(synopsis "Create dashboards with shiny")
(description "This package provides an extension to the Shiny web
@@ -15397,7 +15397,7 @@ to easily call your own custom JavaScript functions from R.")
(format #t "Processing ~a --> ~a~%"
source target)
(delete-file target)
- (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
@@ -15413,7 +15413,7 @@ to easily call your own custom JavaScript functions from R.")
("r-shinyjs" ,r-shinyjs)))
(native-inputs
`(("r-knitr" ,r-knitr)
- ("uglify-js" ,uglify-js)
+ ("uglifyjs" ,node-uglify-js)
("js-jquery"
,(origin
(method url-fetch)
@@ -17903,7 +17903,7 @@ and Learning to Rank measures (LambdaMart).")
(format #t "Processing ~a --> ~a~%"
source target)
(delete-file target)
- (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
@@ -17915,7 +17915,7 @@ and Learning to Rank measures (LambdaMart).")
("r-htmlwidgets" ,r-htmlwidgets)
("r-igraph" ,r-igraph)))
(native-inputs
- `(("uglify-js" ,uglify-js)
+ `(("uglifyjs" ,node-uglify-js)
("js-jquery"
,(origin
(method url-fetch)
@@ -18175,7 +18175,7 @@ etc.). Text boxes with automatic word wrap are also supported.")
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
source target)
- (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
@@ -18189,7 +18189,7 @@ etc.). Text boxes with automatic word wrap are also supported.")
("r-rmarkdown" ,r-rmarkdown)
("r-shiny" ,r-shiny)))
(native-inputs
- `(("uglify-js" ,uglify-js)
+ `(("uglifyjs" ,node-uglify-js)
("js-raphael"
,(origin
(method url-fetch)
@@ -20187,14 +20187,14 @@ tools for help in data interpretation.")
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
source target)
- (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
sources targets))))
#t)))))
(native-inputs
- `(("uglify-js" ,uglify-js)
+ `(("uglifyjs" ,node-uglify-js)
;; NOTE: Make sure that this version of d3 is still valid when
;; upgrading the package.
("d3.v4.js"
@@ -24540,14 +24540,14 @@ documents, Shiny applications, Plumber APIs, plots, and static web content.")
(for-each (lambda (source target)
(format #t "Processing ~a --> ~a~%"
source target)
- (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
(call-with-output-file target
(lambda (port)
(dump-port minified port)))))
sources targets))))
#t)))))
(native-inputs
- `(("uglify-js" ,uglify-js)
+ `(("uglifyjs" ,node-uglify-js)
;; They actually use version 1.11.1, but this more recent version
;; should be just fine.
("js-jquery"
diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm
index 81de5b67a6..e107dd6126 100644
--- a/gnu/packages/javascript.scm
+++ b/gnu/packages/javascript.scm
@@ -26,7 +26,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
- #:use-module (gnu packages lisp-xyz)
+ #:use-module (gnu packages uglifyjs)
#:use-module (gnu packages readline)
#:use-module (gnu packages web)
#:use-module (guix packages)
@@ -163,14 +163,14 @@ context menu in TypeScript.")
(cond
((string-match "\\.js$" file)
(mkdir-p (dirname installed))
- (let ((minified (open-pipe* OPEN_READ "uglify-js" file)))
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" file)))
(call-with-output-file installed
(lambda (port)
(dump-port minified port)))
(let ((exit (close-pipe minified)))
(unless (zero? exit)
- (error "dear, uglify-js failed" exit)))))
+ (error "dear, uglifyjs failed" exit)))))
(else
(install-file file (dirname installed))))))
(find-files "."))
@@ -179,7 +179,7 @@ context menu in TypeScript.")
(native-inputs
`(("font-mathjax" ,font-mathjax)
("glibc-utf8-locales" ,glibc-utf8-locales)
- ("uglify-js" ,uglify-js)
+ ("uglifyjs" ,node-uglify-js)
,@(package-native-inputs font-mathjax)))
(synopsis "JavaScript display engine for LaTeX, MathML, and AsciiMath")
(description "MathJax is a JavaScript display engine for LaTeX, MathML,
@@ -527,8 +527,7 @@ means that these shams cause many ES5 methods to silently fail.")
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-uglification
- ;; Remove "export" keyword which prevents the file from being
- ;; uglified by uglify-js. Moreover, that keyword is not present in
+ ;; Remove "export" keyword. That keyword is not present in
;; the minified version of the library some projects are using,
;; e.g.,
;; <https://github.com/jmoenig/Snap--Build-Your-Own-Blocks/blob/master/FileSaver.min.js>
--
2.32.0
^ permalink raw reply related [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-18 5:14 ` Charles via Bug reports for GNU Guix
@ 2021-09-20 19:03 ` zimoun
2021-09-20 19:30 ` Charles via Bug reports for GNU Guix
0 siblings, 1 reply; 9+ messages in thread
From: zimoun @ 2021-09-20 19:03 UTC (permalink / raw)
To: Charles; +Cc: 50483, Todor Kondić
Hi Charles,
Thanks for the patch.
On Sat, 18 Sep 2021 at 05:14, Charles <charles.b.jackson@protonmail.com> wrote:
> Here is a patch to update the packages to use the up to date
> minifier. Is the the correct thread to put this or should I start a
> new thread in the patches mailing list?
I think the bestis to send this patch to guix-patches@gnu.org. See
commit message and suggestions below.
> From 57c3801034e77120e4030d0e5421a02343e9280c Mon Sep 17 00:00:00 2001
> From: Charles <charles.b.jackson@protonmail.com>
> Date: Sat, 18 Sep 2021 00:05:55 -0500
> Subject: [PATCH] gnu: Update some packages using old JavaScript minifier.
Subject: [PATCH] gnu: Switch to (gnu package uglifyjs) minifier.
Fixes <https://bugs.gnu.org/50483>
> * gnu/packages/minetest.scm (minetest-basic-trains): New variable.
> * gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input.
> * gnu/packages/ci.scm (laminar): Update uglifyjs input.
> * gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker
> r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input.
> * gnu/packages/javascript.scm (): Update uglifyjs input.
Missing package --^
I have not compiled, so I assume this removal:
> - #:use-module (gnu packages lisp-xyz)
does not trigger warning when compiling Guix, right?
> diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
> index b7ea77ca31..a6d296923f 100644
> --- a/gnu/packages/ci.scm
> +++ b/gnu/packages/ci.scm
> @@ -38,7 +38,7 @@
> #:use-module (gnu packages guile)
> #:use-module (gnu packages guile-xyz)
> #:use-module (gnu packages gnupg)
> - #:use-module (gnu packages lisp-xyz)
> + #:use-module (gnu packages uglifyjs)
It seems the module are sorted by alphabetic order.
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index f80256c901..81dd78ac94 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -84,7 +84,7 @@
> #:use-module (gnu packages java)
> #:use-module (gnu packages javascript)
> #:use-module (gnu packages libevent)
> - #:use-module (gnu packages lisp-xyz)
> + #:use-module (gnu packages uglifyjs)
Idem.
> diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm
> index 81de5b67a6..e107dd6126 100644
> --- a/gnu/packages/javascript.scm
> +++ b/gnu/packages/javascript.scm
> @@ -26,7 +26,7 @@
> #:use-module (gnu packages)
> #:use-module (gnu packages base)
> #:use-module (gnu packages compression)
> - #:use-module (gnu packages lisp-xyz)
> + #:use-module (gnu packages uglifyjs)
Idem.
Otherwise, LGTM. Thanks.
Cheers,
simon
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-20 19:03 ` zimoun
@ 2021-09-20 19:30 ` Charles via Bug reports for GNU Guix
2021-09-26 12:26 ` Todor Kondić via Bug reports for GNU Guix
0 siblings, 1 reply; 9+ messages in thread
From: Charles via Bug reports for GNU Guix @ 2021-09-20 19:30 UTC (permalink / raw)
To: zimoun; +Cc: 50483, Todor Kondić, efraim
Thanks simon, I will take into account your suggestions and submit to patches.
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-20 19:30 ` Charles via Bug reports for GNU Guix
@ 2021-09-26 12:26 ` Todor Kondić via Bug reports for GNU Guix
0 siblings, 0 replies; 9+ messages in thread
From: Todor Kondić via Bug reports for GNU Guix @ 2021-09-26 12:26 UTC (permalink / raw)
Cc: 50483
On Monday, September 20th, 2021 at 7:30 PM, Charles <charles.b.jackson@protonmail.com> wrote:
> Thanks simon, I will take into account your suggestions and submit to patches.
Thanks for your efforts!
^ permalink raw reply [flat|nested] 9+ messages in thread
* bug#50483: [R] Package r-shiny: Shiny server logic inactive
2021-09-09 12:35 bug#50483: [R] Package r-shiny: Shiny server logic inactive Todor Kondić via Bug reports for GNU Guix
2021-09-15 16:50 ` zimoun
@ 2021-09-27 12:50 ` zimoun
1 sibling, 0 replies; 9+ messages in thread
From: zimoun @ 2021-09-27 12:50 UTC (permalink / raw)
To: Todor Kondić; +Cc: 50483-done
Hi,
On Thu, 9 Sept 2021 at 14:46, Todor Kondić via Bug reports for GNU
Guix <bug-guix@gnu.org> wrote:
> I started having issues with R Shiny applications with newer Guix distro commits.
I think it is fixed by f36b789f788ffe3ebdaaeac1d3a05534acaa909c.
Closing.
All the best,
simon
^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2021-09-27 12:53 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2021-09-09 12:35 bug#50483: [R] Package r-shiny: Shiny server logic inactive Todor Kondić via Bug reports for GNU Guix
2021-09-15 16:50 ` zimoun
2021-09-16 5:57 ` Charles via Bug reports for GNU Guix
2021-09-16 6:32 ` zimoun
2021-09-18 5:14 ` Charles via Bug reports for GNU Guix
2021-09-20 19:03 ` zimoun
2021-09-20 19:30 ` Charles via Bug reports for GNU Guix
2021-09-26 12:26 ` Todor Kondić via Bug reports for GNU Guix
2021-09-27 12:50 ` zimoun
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