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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=protonmail.com header.s=protonmail header.b="mOw6v/w5"; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Spam-Score: -2.91 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=protonmail.com header.s=protonmail header.b="mOw6v/w5"; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Queue-Id: B2C6AE96E X-Spam-Score: -2.91 X-Migadu-Scanner: scn1.migadu.com X-TUID: KqUD28ZeRguX Hi, I started having issues with R Shiny applications with newer Guix distro co= mmits. I have a feeling that this is an issue arising from `r-shiny` depend= ency clashes and that (some) of those dependencies should be either downgra= ded, 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 numbe= r 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 Shin= y programs malfunction and the command[5] to create the environment with th= e manifest. By the way, for those of you who are R savvy, comparing sessionInfo() betwe= en the running and non-running version did uncover few version changes. I h= ave 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=3Den_GB.utf8 LC_NUMERIC=3DC [3] LC_TIME=3Den_GB.utf8 LC_COLLATE=3Den_GB.utf8 [5] LC_MONETARY=3Den_GB.utf8 LC_MESSAGES=3Den_GB.utf8 [7] LC_PAPER=3Den_GB.utf8 LC_NAME=3DC [9] LC_ADDRESS=3DC LC_TELEPHONE=3DC [11] LC_MEASUREMENT=3Den_GB.utf8 LC_IDENTIFICATION=3DC 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 =3D bootstrapPage( numericInput('n', 'Number of obs', 100), plotOutput('plot') ), server =3D 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=3D"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) =09 (guix inferior) =09 (guix channels) =09 (guix profiles) =09 (guix utils) =09 (guix build-system gnu) =09 (gnu packages) =09 (gnu packages commencement) =09 (gnu packages gcc) (srfi srfi-1) =09 (ice-9 pretty-print)) (define base-specs '("git" =09=09 "rsync" "make")) (define font-specs '("unicode-emoji" =09=09 "fontconfig" =09=09 "font-dejavu" =09=09 "font-gnu-freefont" =09=09 "font-terminus" =09=09 "font-liberation" =09=09 "font-inconsolata" =09=09 "font-gnu-unifont" =09=09 "font-public-sans" =09=09 "font-misc-misc" =09=09 "font-awesome" =09=09 "font-hack" =09=09 "font-iosevka" =09=09 "font-iosevka-term" =09=09 "font-iosevka-term-slab" =09=09 "font-iosevka-slab" =09=09 "font-iosevka-etoile" =09=09 "font-iosevka-aile" =09=09 "font-google-noto")) (define r-specs '("r" =09=09 "r-curl" =09=09 "r-ellipsis" =09=09 "r-future" =09=09 "r-rmarkdown" =09=09 "r-knitr" =09=09 "r-rcolorbrewer" =09=09 "r-data-table" =09=09 "r-shiny" =09=09 "r-cowplot" =09=09 "r-pander" =09=09 "r-rstatix" "r-r-utils")) (define texlive-specs '("texlive")) (define misc-specs '("sshpass" =09=09 "xdg-utils" =09=09 "xdg-user-dirs" =09=09 "pango" =09=09 "libxft" =09=09 "cairo" =09=09 "gnupg" "openssl")) (define java-specs '(;"maven" =09=09 "openjdk:out" =09=09 "openjdk:jdk")) (define perl-specs '("perl-yaml-libyaml")) (define gnu-toolchain-specs '("gcc-toolchain")) (define specs `(,@base-specs =09=09,@font-specs =09=09,@perl-specs =09=09,@r-specs =09=09,@java-specs =09=09,@gnu-toolchain-specs =09=09,@misc-specs ,@texlive-specs)) (define dev-channels (list (channel =09 ;; This is custom Environmental Cheminformatics LCSB channel. (name 'eci-addons) (url "https://git.sr.ht/~condor/eci-guix") =09(branch "master") (introduction =09 (make-channel-introduction =09 "6642600059913e86657242ba369d752c0af2bff5" =09 (openpgp-fingerprint =09 "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) =09 (let* =09 ((spkgout (string-split spec #\:)) =09 (spkg (car spkgout)) =09 (rest (cdr spkgout)) =09 (sout (if (null? rest) =09=09=09"out" =09=09=09(car rest))) =09 (pkg (first =09=09 (lookup-inferior-packages inferior spkg)))) =09 (display (format #f "Commiting ~a to the inferior manifest list.\n" s= pkg)) =09 (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')`.