Demographic table example error message
Closed this issue · 2 comments
@pawelru using the latest CRAN installations of all packages in our posit cloud workspace I get the following when running the R code from https://github.com/pharmaverse/examples/blob/main/tlg/demographic.qmd:
> result <- build_table(lyt, adsl)
Error: Error applying analysis function (var - SEX): Assertion on 'x' failed: Must have at least 1 levels.
occured at (row) path: root
Please can you update the example as needed.
I checked the code and it all should be good.
I went ahead to Posit Cloud and noticed that you might be using outdated version. Did git pull and that's the outcome:
/cloud/project$ git pull
remote: Enumerating objects: 599, done.
remote: Counting objects: 100% (353/353), done.
remote: Compressing objects: 100% (116/116), done.
remote: Total 599 (delta 279), reused 294 (delta 231), pack-reused 246
Receiving objects: 100% (599/599), 496.18 KiB | 26.11 MiB/s, done.
Resolving deltas: 100% (406/406), completed with 26 local objects.
From https://github.com/pharmaverse/examples
0b1f7c7..483a3da main -> origin/main
abcbf59..eda927d gh-pages -> origin/gh-pages
* [new branch] teal -> origin/teal
Updating 0b1f7c7..483a3da
error: Your local changes to the following files would be overwritten by merge:
tlg/demographic.qmd
Please commit your changes or stash them before you merge.
Aborting
/cloud/project$ git reset --hard
HEAD is now at 0b1f7c7 Merge pull request #60 from pharmaverse/enhance_gha
/cloud/project$ git pull
Updating 0b1f7c7..483a3da
Fast-forward
DESCRIPTION | 4 +-
README.md | 138 +++++----
_quarto.yml | 2 +
adam/adpc.R | 465 ++++++++++++++++++++++++++++
adam/adpc.qmd | 25 +-
adam/adppk.R | 435 ++++++++++++++++++++++++++
adam/adppk.qmd | 21 +-
adam/adsl.R | 142 +++++++++
adam/adsl.qmd | 41 +--
index.qmd | 7 +-
logging/index.qmd | 3 +
logging/logging.qmd | 915 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
logging/script.R | 14 +
{adam => metadata}/pk_spec.xlsx | Bin
tlg/adverse_events.R | 60 ++++
tlg/adverse_events.qmd | 6 +
tlg/demographic.R | 49 +++
tlg/demographic.qmd | 6 +
18 files changed, 2239 insertions(+), 94 deletions(-)
create mode 100644 adam/adpc.R
create mode 100644 adam/adppk.R
create mode 100644 adam/adsl.R
create mode 100644 logging/index.qmd
create mode 100644 logging/logging.qmd
create mode 100644 logging/script.R
rename {adam => metadata}/pk_spec.xlsx (100%)
create mode 100644 tlg/adverse_events.R
create mode 100644 tlg/demographic.R
/cloud/project$ git status
On branch main
Your branch is up to date with 'origin/main'.
nothing to commit, working tree clean
After this I was able to render the article:
/cloud/project$ quarto render tlg/demographic.qmd
processing file: demographic.qmd
output file: demographic.knit.md
pandoc
to: html
output-file: demographic.html
standalone: true
title-prefix: pharmaverse examples
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
css:
- ../assets/css/style.scss
number-sections: false
metadata
document-css: false
link-citations: true
date-format: long
lang: en-US
search: true
theme:
light:
- flatly
dark:
- darkly
anchor-sections: true
smooth-scroll: true
code-copy: true
code-block-bg: true
code-block-border-left: '#1482FA'
page-layout: full
title: Demographic Table
order: 1
Warning message:
The downlit and xml2 packages are required for code linking
Output created: ../_site/tlg/demographic.html
Now I'm just not so sure if git pull executed on my account also refreshes the "golden" environment that all the others are probably based on. My best guess is that it is not. I did refresh the page and the problem appeared again. Do you know how to "globally" and persistently run git pull?
ah of course, my mistake! i just repeated it on my side (think it has to be me as its my workspace) and all fine now, thanks!