chevreul #3332

whtns · 2024-03-12T15:54:23Z

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bioc-issue-bot · 2024-03-12T15:54:26Z

Hi @whtns

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:

Type: Package
Package: chevreul
Title: Tools for managing SingleCellExperiment objects as projects
Version: 0.99.0
Authors@R: c(
    person("Kevin", "Stachelek", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2085-695X")),
    person("Bhavana", "Bhat", , "[email protected]", role = "aut")
  )
Description: Tools for managing SingleCellExperiment objects as projects. 
  Includes functions for analysis and visualization of single-cell data. 
  Also included is a shiny app for visualization of pre-processed scRNA data.
License: MIT + file LICENSE
URL: https://github.com/whtns/chevreul,
    https://whtns.github.io/chevreul/
Date: 2024-03-05
BugReports: https://github.com/cobriniklab/chevreul/issues
Depends:
    R (>= 4.4.0),
    SingleCellExperiment,
    scater,
    shiny (>= 1.6.0),
    shinydashboard
Imports:
    SummarizedExperiment,
    annotables (>= 0.1.91),
    clustree,
    ComplexHeatmap (>= 2.5.4),
    DataEditR (>= 0.0.9),
    DBI,
    dplyr,
    DT,
    ensembldb,
    fs,
    future,
    glue,
    ggplotify,
    ggpubr,
    httr,
    janitor,
    magrittr,
    megadepth,
    methods,
    patchwork,
    plotly,
    rlang,
    RSQLite,
    shinyFiles,
    shinyhelper,
    shinyjs,
    shinyWidgets,
    tidyr,
    unglue,
    waiter,
    wiggleplotr (>= 1.13.1),
    purrr,
    batchelor,
    stringr,
    tibble,
    ggplot2,
    scran,
    AnnotationDbi,
    EnhancedVolcano,
    EnrichmentBrowser,
    harmony,
    scuttle,
    grDevices,
    graphics,
    stats,
    utils,
    pillar,
    cluster,
    circlize,
    bluster,
    EnsDb.Hsapiens.v86,
    EnsDb.Mmusculus.v79,
    scales,
    readr,
    velociraptor,
    LoomExperiment,
    chevreuldata,
    S4Vectors,
    base,
    grid,
    forcats
Suggests:
    BiocStyle,
    knitr,
    monocle3 (>= 0.2.1),
    RefManageR,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder:
    knitr
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
biocViews: Coverage, RNASeq, Sequencing, Visualization, GeneExpression, Transcription, SingleCell
Config/testthat/edition: 3

lshep · 2024-03-21T15:20:13Z

All package dependencies must be on CRAN or Bioconductor. annotables is currently not on CRAN or Bioconductor and must not be used or referenced in the package.

I assume chevreuldata will be submitted once this issue can accept additional packages. I glanced at that github repo. All Bioconductor packages must include a vignette.

whtns · 2024-03-25T17:38:12Z

Thank you for taking a look at these packages. I removed the annotables dependency in chevreul and added a vignette in chevreuldata. I'd greatly appreciate further review.

whtns · 2024-03-25T17:40:27Z

adding an explicit reference to accompanying data package chevreuldata

AdditionalPackage: https://github.com/whtns/chevreuldata

bioc-issue-bot · 2024-03-25T17:40:28Z

Can't build unless issue is open and past pre-review stage, or issue is closed and 'TESTING' label is present.

lshep · 2024-03-28T15:33:04Z

A few questions:

Can default for saving or writing files be a tempdir() unless specified by a user?

Insteading of defining ~/.cache/ which isn't necessarily a default for all operating systems can you use tools::R_user_dir(which="cache") or rappdirs::user_cache_dir which would grab an appropriate path for a given OS.

Why is a chmod explicit set_permission_call necessary?

It looks like you import httr::GET but is it utilized anywhere?

whtns · 2024-04-24T23:09:16Z

Thank you for continuing to share feedback/shortcomings. I addressed the points you raised above in my last commit.

Can default for saving or writing files be a tempdir() unless specified by a user?
I've removed any hardcoded filepaths previously used for saving

Insteading of defining ~/.cache/ which isn't necessarily a default for all operating systems can you use tools::R_user_dir(which="cache") or rappdirs::user_cache_dir which would grab an appropriate path for a given OS.
I've replaced references to caches with rappdirs::user_cache_dir

Why is a chmod explicit set_permission_call necessary?
removed

It looks like you import httr::GET but is it utilized anywhere?
removed

lshep · 2024-05-17T14:48:02Z

When I try to run R CMD build I'm getting the following

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

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

Quitting from lines  at lines 71-77 [unnamed-chunk-2] (integration.Rmd)
Error: processing vignette 'integration.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘integration.Rmd’

--- re-building ‘preprocessing.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘preprocessing.Rmd’

--- re-building ‘shiny_app.Rmd’ using rmarkdown
--- finished re-building ‘shiny_app.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page

Quitting from lines  at lines 144-145 [unnamed-chunk-5] (visualization.Rmd)
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘visualization.Rmd’

SUMMARY: processing the following files failed:
  ‘integration.Rmd’ ‘visualization.Rmd’

Error: Vignette re-building failed.

It looks like you are hard linking to a file on your system that would not exist for a user.

whtns · 2024-05-31T20:48:28Z

I'm sorry I can't identify the source of the errors listed above in my current branch. I incremented the package version. Can you confirm that the check and build is run against the devel branch?
thanks,

lshep · 2024-06-03T15:06:49Z

Yes it is

lorikern@jbcj433:~/PkgReview/PreReview/chevreul(devel)$ git remote -v
origin	https://github.com/whtns/chevreul/ (fetch)
origin	https://github.com/whtns/chevreul/ (push)


lorikern@jbcj433:~/PkgReview/PreReview/chevreul(devel)$ git pull
remote: Enumerating objects: 7, done.
remote: Counting objects: 100% (7/7), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 7 (delta 5), reused 7 (delta 5), pack-reused 0
Unpacking objects: 100% (7/7), 620 bytes | 38.00 KiB/s, done.
From https://github.com/whtns/chevreul
   e4d2858..da02a9c  sce        -> origin/sce
Already up to date.


lorikern@jbcj433:~/PkgReview/PreReview/chevreul(devel)$ cd ..
lorikern@jbcj433:~/PkgReview/PreReview$ R CMD build chevreul
* checking for file 'chevreul/DESCRIPTION' ... OK
* preparing 'chevreul':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘chevreul.Rmd’ using rmarkdown
--- finished re-building ‘chevreul.Rmd’

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

Quitting from lines 71-77 [unnamed-chunk-2] (integration.Rmd)
Error: processing vignette 'integration.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘integration.Rmd’

--- re-building ‘preprocessing.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘preprocessing.Rmd’

--- re-building ‘shiny_app.Rmd’ using rmarkdown
--- finished re-building ‘shiny_app.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page

Quitting from lines 144-145 [unnamed-chunk-5] (visualization.Rmd)
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘visualization.Rmd’

SUMMARY: processing the following files failed:
  ‘integration.Rmd’ ‘visualization.Rmd’

Error: Vignette re-building failed.
Execution halted

whtns · 2024-06-03T17:24:07Z

Ah, thank you very much. I had a mismatch between local and remote branches. The branch you are pulling is origin/sce in the above snippet. I've updated the local and remote branches and incremented version again. Can you try building again? Sorry for the trouble.

skevin@cobrinik-srt:~/rpkgs/chevreul$ git status
On branch devel
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        deleted:    docs/articles/Heatmap2.0.PNG
        deleted:    docs/articles/PlotCoverage2.0.PNG
        deleted:    docs/articles/violinPlot.PNG

skevin@cobrinik-srt:~/rpkgs/chevreul$ ..
skevin@cobrinik-srt:~/rpkgs$ R CMD build chevreul
* checking for file 'chevreul/DESCRIPTION' ... OK
* preparing 'chevreul':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'chevreul_0.99.2.tar.gz'

lshep · 2024-06-07T12:41:24Z

Same

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

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

Quitting from lines 71-77 [unnamed-chunk-2] (integration.Rmd)
Error: processing vignette 'integration.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘integration.Rmd’

--- re-building ‘preprocessing.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘preprocessing.Rmd’

--- re-building ‘shiny_app.Rmd’ using rmarkdown
--- finished re-building ‘shiny_app.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page

Quitting from lines 144-145 [unnamed-chunk-5] (visualization.Rmd)
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘visualization.Rmd’

SUMMARY: processing the following files failed:
  ‘integration.Rmd’ ‘visualization.Rmd’

Error: Vignette re-building failed.
Execution halted

In the vignette this seems to have to do with the plot_violin function. For what its worth it is also reproducible if I use devtools to load the package and just try to run that example as well

> load_all(".")
ℹ Loading chevreul
> chevreul_sce <- chevreuldata::human_gene_transcript_sce()
snapshotDate(): 2024-05-28
see ?chevreuldata and browseVignettes('chevreuldata') for documentation
loading from cache
> plot_violin(chevreul_sce, plot_var = "batch", features = "NRL")
Error in .Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE = "HDF5Array") : 
  file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist

whtns · 2024-06-13T22:10:13Z

Ok, I think I've resolved this problem. The example dataset (in accompanying experimenthub package chevreuldata) includes a SingleCellLoomExperiment assay for use with the velociraptor package. Because the source loom file is inaccessible on any other system even unrelated functions break. Because I don't know best practices to share loom files in this manner I've removed that assay from the dataset and excluded those functions from vignettes and examples.

lshep · 2024-06-14T13:48:11Z

You should not disable these examples and vignettes. If the data isn't loading, you should check out LoomExperiment where this class is defined and figure out the proper way. Exported functions need to be run/tested somewhere in the code base.

whtns · 2024-06-14T17:49:36Z

Ok thanks, I recognize the submission requirement to have included functions documented with examples. I've removed any dependency on LoomExperiment or velociraptor from the package

lshep · 2024-06-25T14:22:33Z

monocle3 does not appear to be on CRAN or Bioconductor. Bioconductor packages require all dependencies to be on CRAN or Bioconductor. You must remove the dependency from your package or request the monocle3 maintainers to officially submit the package.

whtns · 2024-07-05T21:36:44Z

Thank you, we've removed all references to monocle3 and dropped the package dependency in DESCRIPTION

bioc-issue-bot · 2024-07-16T13:19:09Z

Your package has been added to git.bioconductor.org to continue the
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bioc-issue-bot · 2024-07-16T13:20:36Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "skipped, ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
ERROR before build products produced.

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreul to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-11-19T19:38:46Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreuldata_0.99.21.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-11-19T21:26:49Z

Received a valid push on git.bioconductor.org; starting a build for commit id: ed4e257b82d06540b3427c348ab8e17a8f453bc6

bioc-issue-bot · 2024-11-19T21:44:18Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "TIMEOUT".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreuldata_0.99.22.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

whtns · 2024-11-19T22:14:04Z

Hi Marcel @LiNk-NY and Lori @lshep

Three packages referenced in this issue have passed R CMD check without WARNING or ERROR:

chevreulProcess
chevreulPlot
chevreulShiny

Two other packages chevreuldata and chevreul have not passed.
The ERROR in chevreuldata is due to TIMEOUT during example checking. I'd like to drop this package from the issue and will drop any reference in package vignettes
The WARNING in chevreul is due to. "No Bioconductor dependencies detected..." I don't know how to resolve this WARNING as this is a metapackage and should have dependencies only on the three passing packages listed above.

Could you let me know how to proceed? Thank you!

bioc-issue-bot · 2024-12-06T18:13:28Z

Received a valid push on git.bioconductor.org; starting a build for commit id: c309c60287a91b5d66756c42fa5ff4ab2d3aaf8e

bioc-issue-bot · 2024-12-06T18:30:51Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "TIMEOUT".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreuldata_0.99.23.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-12-06T18:36:38Z

Received a valid push on git.bioconductor.org; starting a build for commit id: e438954375815b48d649ae7366e8c8d64ad41c2b

bioc-issue-bot · 2024-12-06T18:53:54Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreuldata_0.99.24.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-12-06T18:57:59Z

Received a valid push on git.bioconductor.org; starting a build for commit id: c9380612e642d3093b2421d3db4176abfd01a963

bioc-issue-bot · 2024-12-06T19:15:14Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "TIMEOUT".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreuldata_0.99.25.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY · 2024-12-13T14:22:17Z

Hi Kevin, @whtns
Sorry for the delay. I was out of town.
Can you please bump the version of the relevant packages?
Thank you!

bioc-issue-bot · 2024-12-15T18:48:41Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 174869aac9381bf721b557dba70bcd104669318f

bioc-issue-bot · 2024-12-15T18:49:29Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 30edca0cf8365876601bb3af10686a30645d2939

bioc-issue-bot · 2024-12-15T18:50:33Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 30ed939524c07a48894273ddc51f4e0edf83c81a

bioc-issue-bot · 2024-12-15T19:01:58Z

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Your package has been built on the Bioconductor Single Package Builder.

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreulProcess_0.99.23.tar.gz

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bioc-issue-bot · 2024-12-15T19:03:17Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
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The following are build products from R CMD build on the Single Package Builder:
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-12-15T19:04:16Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreulShiny_0.99.19.tar.gz

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Remember: if you submitted your package after July 7th, 2020,
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bioc-issue-bot · 2024-12-15T23:12:35Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 091ae893b30afc0f4ddec8b1f16a631443f04fad

bioc-issue-bot · 2024-12-15T23:14:15Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 81ef2d758cd6f3f77b479af6b444f6ce05bb59ef

bioc-issue-bot · 2024-12-15T23:30:31Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreulPlot_0.99.25.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreulPlot to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-12-15T23:31:10Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreulShiny_0.99.20.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreulShiny to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-12-15T23:44:39Z

Received a valid push on git.bioconductor.org; starting a build for commit id: d2c0954ac9ab2159c35235108eb2ed64b1db1cf3

whtns · 2024-12-15T23:54:23Z

Hi Marcel, @LiNk-NY. I updated package versions for the three separate packages that you suggested, but no longer meet minimum checktime requirements. Could this be due to changes in minimum R and Bioconductor versions? Do you have information on documentation to meet the 10 min threshold?

bioc-issue-bot · 2024-12-16T00:00:10Z

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): chevreulShiny_0.99.21.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/chevreulShiny to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Mar 12, 2024

whtns changed the title ~~chevreuldata~~ chevreul Mar 12, 2024

lshep added the 3e. pending pre-review changes review has indicated blocking concern that needs attention label Mar 21, 2024

lshep added pre-check passed pre-review performed and ready to be added to git and removed 3e. pending pre-review changes review has indicated blocking concern that needs attention labels Jul 16, 2024

bioc-issue-bot added the ERROR label Jul 16, 2024

This was referenced Jul 18, 2024

(inactive) chevreuldata #3490

Closed

chevreuldata #3491

Closed

bioc-issue-bot added TIMEOUT and removed ERROR labels Nov 19, 2024

bioc-issue-bot added the WARNINGS label Dec 15, 2024

bioc-issue-bot removed OK TIMEOUT labels Dec 15, 2024

bioc-issue-bot added the ERROR label Dec 16, 2024

chevreul #3332

chevreul #3332

Comments

whtns commented Mar 12, 2024

bioc-issue-bot commented Mar 12, 2024

lshep commented Mar 21, 2024

whtns commented Mar 25, 2024

whtns commented Mar 25, 2024

bioc-issue-bot commented Mar 25, 2024

lshep commented Mar 28, 2024

whtns commented Apr 24, 2024

lshep commented May 17, 2024

whtns commented May 31, 2024

lshep commented Jun 3, 2024

whtns commented Jun 3, 2024 • edited Loading

lshep commented Jun 7, 2024

whtns commented Jun 13, 2024

lshep commented Jun 14, 2024

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lshep commented Jun 25, 2024

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whtns commented Jun 3, 2024 •

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