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bigomics / omicsplayground

Visual self-service analytics platform for big omics data.
http://www.bigomics.ch
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Install docs need update: Issues installing omicsplayground #401

Closed phisanti closed 1 year ago

phisanti commented 1 year ago

Hi, first of all, congratulations on the great app. However, today I tried to install the omicsplayground from the repo and noticed that some of the instructions might need to be updated.

  1. Pre-requisites I noticed that the omicsplayground relies on GLIBC 2.33 or higher. In Windows, it can be automatically installed with WSL Ubuntu 22.04 or manually. Therefore including a line such as: 
    
ldd --version

ldd (Ubuntu GLIBC 2.35-0ubuntu3.1) 2.35

Copyright (C) 2022 Free Software Foundation, Inc.

This is free software; see the source for copying conditions. There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Written by Roland McGrath and Ulrich Drepper.

cat /etc/os-release

PRETTY_NAME="Ubuntu 22.04.2 LTS"

NAME="Ubuntu"

VERSION_ID="22.04"

VERSION="22.04.2 LTS (Jammy Jellyfish)"

VERSION_CODENAME=jammy

ID=ubuntu

ID_LIKE=debian

HOME_URL="https://www.ubuntu.com/"

SUPPORT_URL="https://help.ubuntu.com/"

BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"

PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"

UBUNTU_CODENAME=jammy


2. Installing `requiremets.R`
The file `requirements.R` is not located in `R/` but in `dev/`.

3. Include extra dependencies
I noticed that `omicsplayground` has been split into separate projects but is not included in the `requirements.R` file. These are: `playbase`, `bigLoaders`, `bigdash` and `firebase`, `reticulate` and `miniconda`.

```r
remotes::install_github("bigomics/playbase")
remotes::install_github("bigomics/bigLoaders")
remotes::install_github("bigomics/bigdash")
install.packages("firebase")
install.packages("reticulate")
reticulate::install_miniconda()
  1. Run the app locally I noticed that in order to run the app, the command R -e "shiny::runApp(launch.browser=TRUE)" throws the following error: 
    Loading required package: shiny
Error in `shinyAppDir()`:
! App dir must contain either app.R or server.R.
Backtrace:
▆
1. └─shiny::runApp(launch.browser = TRUE)
2.   ├─shiny::as.shiny.appobj(appDir)
3.   └─shiny:::as.shiny.appobj.character(appDir)
4.     └─shiny::shinyAppDir(x)
5.       └─rlang::abort(...)
Execution halted

    Also, running the command Rscript dev/05_run.R (the method to run Golem Shiny apps) gives another error:

    ℹ Using R 4.3.0 (lockfile was generated with R 4.2.2)
Error in sass::sass_file("inst/app/www/custom.sass") :
Could not find file: 'inst/app/www/custom.sass' in dir: /mnt/c/Users/tisal/OneDrive/Playground/omicsplayground
Calls: <Anonymous> ... is_sass_bundle_like -> is_sass_bundle -> <Anonymous>
Execution halted

    It is however possible to run the app via runApp('components/app/R').

I hope this can be of some help. Here is a snapshot of my session:

> devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United Kingdom.utf8
 ctype    English_United Kingdom.utf8
 tz       Europe/London
 date     2023-05-19
 rstudio  2023.03.1+446 Cherry Blossom (desktop)
 pandoc   NA

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package      * version    date (UTC) lib source
 P askpass        1.1        2019-01-13 [?] CRAN (R 4.2.2)
 P base64enc      0.1-3      2015-07-28 [?] CRAN (R 4.2.0)
   bigdash        0.0.0.9003 2023-05-18 [1] Github (bigomics/bigdash@049de26)
   bigLoaders     0.0.2      2023-05-18 [1] Github (bigomics/bigLoaders@7efb55b)
 P BiocManager    1.30.20    2023-02-24 [?] RSPM (R 4.2.0)
   bitops         1.0-7      2021-04-24 [1] RSPM (R 4.2.0)
 P bslib          0.4.2      2022-12-16 [?] CRAN (R 4.2.2)
 P cachem         1.0.8      2023-05-01 [?] RSPM (R 4.2.0)
 P callr          3.7.3      2022-11-02 [?] CRAN (R 4.2.2)
 P cli            3.6.1      2023-03-23 [?] RSPM (R 4.2.0)
 P codetools      0.2-18     2020-11-04 [?] CRAN (R 4.2.2)
   colorspace     2.1-0      2023-01-23 [1] RSPM (R 4.2.0)
 P crayon         1.5.2      2022-09-29 [?] CRAN (R 4.2.2)
   crosstalk      1.2.0      2021-11-04 [1] RSPM (R 4.2.0)
 P curl           5.0.0      2023-01-12 [?] CRAN (R 4.2.2)
   data.table     1.14.8     2023-02-17 [1] RSPM (R 4.2.0)
 P desc           1.4.2      2022-09-08 [?] CRAN (R 4.2.2)
 P devtools       2.4.5      2022-10-11 [?] CRAN (R 4.2.2)
 P digest         0.6.31     2022-12-11 [?] CRAN (R 4.2.2)
   doParallel     1.0.17     2022-02-07 [1] RSPM (R 4.2.0)
   dplyr          1.1.2      2023-04-20 [1] RSPM (R 4.2.0)
   DT             0.27       2023-01-17 [1] RSPM (R 4.2.0)
 P ellipsis       0.3.2      2021-04-29 [?] CRAN (R 4.2.2)
 P fansi          1.0.4      2023-01-22 [?] CRAN (R 4.2.2)
 P fastmap        1.1.1      2023-02-24 [?] CRAN (R 4.2.2)
 P firebase       1.0.1      2022-02-08 [?] CRAN (R 4.2.1)
 P fontawesome    0.5.1      2023-04-18 [?] RSPM (R 4.2.0)
   foreach        1.5.2      2022-02-02 [1] RSPM (R 4.2.0)
 P fs             1.6.2      2023-04-25 [?] RSPM (R 4.2.0)
   generics       0.1.3      2022-07-05 [1] RSPM (R 4.2.0)
   ggplot2        3.4.2      2023-04-03 [1] RSPM (R 4.2.0)
 P glue           1.6.2      2022-02-24 [?] CRAN (R 4.2.2)
   gtable         0.3.3      2023-03-21 [1] RSPM (R 4.2.0)
 P htmltools      0.5.5      2023-03-23 [?] RSPM (R 4.2.0)
 P htmlwidgets    1.6.2      2023-03-17 [?] RSPM (R 4.2.0)
 P httpuv         1.6.11     2023-05-11 [?] RSPM (R 4.2.0)
 P httr           1.4.6      2023-05-08 [?] RSPM (R 4.2.0)
   iterators      1.0.14     2022-02-05 [1] RSPM (R 4.2.0)
 P jose           1.2.0      2021-11-06 [?] CRAN (R 4.2.3)
 P jquerylib      0.1.4      2021-04-26 [?] CRAN (R 4.2.2)
 P jsonlite       1.8.4      2022-12-06 [?] CRAN (R 4.2.2)
 P knitr          1.42       2023-01-25 [?] CRAN (R 4.2.2)
 P later          1.3.1      2023-05-02 [?] RSPM (R 4.2.0)
 P lattice        0.20-45    2021-09-22 [?] CRAN (R 4.2.2)
   lazyeval       0.2.2      2019-03-15 [1] RSPM (R 4.2.0)
 P lifecycle      1.0.3      2022-10-07 [?] CRAN (R 4.2.2)
 P magrittr     * 2.0.3      2022-03-30 [?] CRAN (R 4.2.2)
 P Matrix         1.5-1      2022-09-13 [?] CRAN (R 4.2.2)
 P memoise        2.0.1      2021-11-26 [?] CRAN (R 4.2.2)
 P mime           0.12       2021-09-28 [?] CRAN (R 4.2.0)
 P miniUI         0.1.1.1    2018-05-18 [?] CRAN (R 4.2.2)
   munsell        0.5.0      2018-06-12 [1] RSPM (R 4.2.0)
 P openssl        2.0.6      2023-03-09 [?] CRAN (R 4.2.2)
 P pillar         1.9.0      2023-03-22 [?] RSPM (R 4.2.0)
 P pkgbuild       1.4.0      2022-11-27 [?] CRAN (R 4.2.2)
 P pkgconfig      2.0.3      2019-09-22 [?] CRAN (R 4.2.2)
 P pkgload        1.3.2      2022-11-16 [?] CRAN (R 4.2.2)
   playbase       0.1.0      2023-05-18 [1] Github (bigomics/playbase@112ab73)
   plotly         4.10.1     2022-11-07 [1] RSPM (R 4.2.0)
   png            0.1-8      2022-11-29 [1] RSPM (R 4.2.0)
 P prettyunits    1.1.1      2020-01-24 [?] CRAN (R 4.2.2)
 P processx       3.8.1      2023-04-18 [?] RSPM (R 4.2.0)
 P profvis        0.3.8      2023-05-02 [?] RSPM (R 4.2.0)
 P promises       1.2.0.1    2021-02-11 [?] CRAN (R 4.2.2)
 P ps             1.7.5      2023-04-18 [?] RSPM (R 4.2.0)
 P purrr          1.0.1      2023-01-10 [?] CRAN (R 4.2.2)
 P R6             2.5.1      2021-08-19 [?] CRAN (R 4.2.2)
 P rappdirs       0.3.3      2021-01-31 [?] CRAN (R 4.2.2)
 P Rcpp           1.0.10     2023-01-22 [?] CRAN (R 4.2.2)
   RCurl          1.98-1.12  2023-03-27 [1] RSPM (R 4.2.0)
 P remotes        2.4.2      2021-11-30 [?] CRAN (R 4.2.2)
   renv           0.17.3     2023-04-06 [1] RSPM (R 4.2.0)
   reticulate     1.28       2023-01-27 [1] RSPM (R 4.2.0)
 P rlang          1.1.1      2023-04-28 [?] RSPM (R 4.2.0)
 P rprojroot      2.0.3      2022-04-02 [?] CRAN (R 4.2.2)
 P rstudioapi     0.14       2022-08-22 [?] CRAN (R 4.2.2)
 P sass           0.4.6      2023-05-03 [?] RSPM (R 4.2.0)
   scales         1.2.1      2022-08-20 [1] RSPM (R 4.2.0)
 P sessioninfo    1.2.2      2021-12-06 [?] CRAN (R 4.2.2)
   sever          0.0.7      2021-07-14 [1] RSPM (R 4.2.0)
 P shiny        * 1.7.4      2022-12-15 [?] CRAN (R 4.2.2)
   shinyalert     3.0.0      2021-12-20 [1] RSPM (R 4.2.0)
   shinyBS      * 0.61.1     2022-04-17 [1] RSPM (R 4.2.0)
   shinybusy      0.3.1      2022-05-10 [1] RSPM (R 4.2.0)
   shinyjs        2.1.0      2021-12-23 [1] RSPM (R 4.2.0)
   shinyWidgets   0.7.6      2023-01-08 [1] RSPM (R 4.2.0)
 P stringi        1.7.12     2023-01-11 [?] CRAN (R 4.2.2)
 P stringr        1.5.0      2022-12-02 [?] CRAN (R 4.2.2)
 P tibble         3.2.1      2023-03-20 [?] RSPM (R 4.2.0)
   tidyr          1.3.0      2023-01-24 [1] RSPM (R 4.2.0)
   tidyselect     1.2.0      2022-10-10 [1] RSPM (R 4.2.0)
 P urlchecker     1.0.1      2021-11-30 [?] CRAN (R 4.2.2)
 P usethis        2.1.6      2022-05-25 [?] CRAN (R 4.2.2)
 P utf8           1.2.3      2023-01-31 [?] CRAN (R 4.2.2)
   uuid           1.1-0      2022-04-19 [1] RSPM (R 4.2.0)
 P vctrs          0.6.2      2023-04-19 [?] RSPM (R 4.2.0)
   viridisLite    0.4.2      2023-05-02 [1] RSPM (R 4.2.0)
   waiter         0.2.5      2022-01-03 [1] RSPM (R 4.2.0)
 P withr          2.5.0      2022-03-03 [?] CRAN (R 4.2.2)
 P xfun           0.39       2023-04-20 [?] RSPM (R 4.2.0)
 P xtable         1.8-4      2019-04-21 [?] CRAN (R 4.2.2)
 P yaml           2.3.7      2023-01-23 [?] CRAN (R 4.2.2)

 [1] C:/Users/tisal/OneDrive/Playground/omicsplayground/renv/library/R-4.2/x86_64-w64-mingw32
 [2] C:/Users/tisal/AppData/Local/R/cache/R/renv/sandbox/R-4.2/x86_64-w64-mingw32/30182023

 P ── Loaded and on-disk path mismatch.

─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
mauromiguelm commented 1 year ago

Hi Santiago,

Thanks for the feedback, these are valid points! As you mentioned, we are using different packages to handle different processess in the App. That is due a large migration we did a few weeks ago, where we split Omics Playground into different packages, and we should now focus on documenting all changes.

Thanks again for reporting, we will update documentation in the next days.

Best, Mauro

ivokwee commented 1 year ago

for the sass stuff, you might need to run 'make packer' in the bigdash folder. I remember John saying that whenever you change JS stuff in bigdash.

ivokwee commented 1 year ago

Yes. docs need update. Also the README.rst should be updated. V3 now needs all other repos: bigdash, playdata, playbase, etc. This needs to be documented.

ESCRI11 commented 1 year ago

@phisanti Does PR #648 close this issue?

phisanti commented 1 year ago

@ESCRI11 I think so. I will close it for now, but we can reopen if something changes.