seahtrue

[vcjdeboer]

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• Repository: https://github.com/vcjdeboer/seahtrue

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[bioc-issue-bot]

Hi @vcjdeboer

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: seahtrue
Type: Package
Title: Seahtrue revives XF data for structured data analysis
Version: 0.99.0
Authors@R: c(
person("Vincent", "de Boer", 
  email = "vincent.deboer@wur.nl", 
  role = c("cre", "aut"),
  comment=c(ORCID="0000-0001-9928-1698")),
person("Gerwin", "Smits", role = c("aut")),
person("Xiang", "Zhang", role = c("aut"))
)
Description:
    Seahtrue organizes oxygen consumption and extracellular acidification 
    analysis data from experiments performed on an XF analyzer 
    into structured nested tibbles.This allows for detailed processing of 
    raw data and advanced data visualization and statistics. Seahtrue introduces 
    an open and reproducible way to analyze these XF experiments. 
    It uses file paths to .xlsx files. These .xlsx files are supplied by the 
    userand are generated by the user in the Wave software from Agilent from the
    assay result files (.asyr). The .xlsx file contains different sheets of 
    important data for the experiment;
    1. Assay Information - Details about how the experiment was set up.
    2. Rate Data - Information about the OCR and ECAR rates.
    3. Raw Data - The original raw data collected during the experiment.
    4. Calibration Data - Data related to calibrating the instrument.
    Seahtrue focuses on getting the specific data needed for analysis. 
    Once this data is extracted, it is prepared for calculations through 
    preprocessing. To make sure everything is accurate, both the initial data 
    and the preprocessed data go through thorough checks.
biocViews: CellBasedAssays, FunctionalPrediction, DataRepresentation, 
  DataImport, CellBiology, Cheminformatics, 
  Metabolomics, MicrotitrePlateAssay, Visualization, 
  QualityControl, BatchEffect, ExperimentalDesign, 
  Preprocessing, GO
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
Suggests:
    rmarkdown,
    testthat (>= 3.0.0),
Imports:
    dplyr (>= 1.1.2),
    readxl (>= 1.4.1),
    logger (>= 0.2.2),
    tidyxl (>= 1.0.8),
    knitr (>= 1.40),
    purrr (>= 0.3.5),
    tidyr (>= 1.3.0),
    lubridate (>= 1.8.0),
    stringr (>= 1.4.1),
    tibble (>= 3.1.8),
    validate (>= 1.1.1),
    rlang (>= 1.0.0),
    glue (>= 1.6.2),
    cli (>= 3.4.1),
    janitor (>= 2.2.0),
    ggplot2 (>= 3.5.0),
    RColorBrewer (>= 1.1.3),
    colorspace (>= 2.1.0),
    forcats (>= 1.0.0),
    ggridges (>= 0.5.6),
    readr (>= 2.1.5),
    scales (>= 1.3.0),
    sessioninfo (>= 1.2.2),
    details (>= 0.3.0),
    knitr (>= 1.46.0)
RoxygenNote: 7.3.1
Depends:
    R (>= 4.2.0) 
VignetteBuilder: knitr
StagedInstall: no
URL: https://vcjdeboer.github.io/seahtrue/
BugReports: https://vcjdeboer.github.io/seahtrue/issues

[lshep]

I'm getting the following ERROR when trying to build your package

R CMD build seahtrue 
* checking for file 'seahtrue/DESCRIPTION' ... OK
* preparing 'seahtrue':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘inspect.Rmd’ using rmarkdown

Quitting from lines  at lines 163-170 [unnamed-chunk-13] (inspect.Rmd)
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘inspect.Rmd’

--- re-building ‘plot.Rmd’ using rmarkdown
INFO [2024-05-20 09:05:00] Start reviving
INFO [2024-05-20 09:05:10] Finished reviving
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
  semi-transparency is not supported on this device: reported only once per page
INFO [2024-05-20 09:05:12] Start glueing
INFO [2024-05-20 09:05:12] Start reviving
INFO [2024-05-20 09:05:22] Finished reviving
INFO [2024-05-20 09:05:22] Start reviving
INFO [2024-05-20 09:05:31] Finished reviving
INFO [2024-05-20 09:05:31] Start reviving
INFO [2024-05-20 09:05:40] Finished reviving
INFO [2024-05-20 09:05:40] Finished glueing
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
  semi-transparency is not supported on this device: reported only once per page

Quitting from lines  at lines 280-285 [unnamed-chunk-18] (plot.Rmd)
Error: processing vignette 'plot.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘plot.Rmd’

--- re-building ‘revive.Rmd’ using rmarkdown
INFO [2024-05-20 09:05:42] Start reviving
INFO [2024-05-20 09:05:51] Finished reviving

Quitting from lines  at lines 75-80 [unnamed-chunk-2] (revive.Rmd)
Error: processing vignette 'revive.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘revive.Rmd’

--- re-building ‘seahtrue.Rmd’ using rmarkdown

Quitting from lines  at lines 48-53 [unnamed-chunk-2] (seahtrue.Rmd)
Error: processing vignette 'seahtrue.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘seahtrue.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘plot.Rmd’ ‘revive.Rmd’ ‘seahtrue.Rmd’

Error: Vignette re-building failed.
Execution halted

[lshep]

I will also mention, I have a .Rprofile that sets certain settings such as options(useFancyQuotes=FALSE) . It appears that when trying to build your package my settings are being overwritten. Changing user settings is not allowed and should be corrected.

[vcjdeboer]

thank you for trying to build the package! I updated the vignettes to use the BiocStyle and removed the vignettes that were initially created for a pkgdown site that was deployed on github. Also, I deleted the .Rprofile file from the package.