tidySpatialExperiment

[william-hutchison]

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[bioc-issue-bot]

Hi @william-hutchison

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: tidySpatialExperiment
Title: Brings SpatialExperiment to the tidyverse 
Version: 0.99.0
Authors@R: c(
    person("William", "Hutchison", email = "[email protected]", role = c("aut", "cre")),
    person("Stefano", "Mangiola", email = "[email protected]", role = "aut")
  )
Description: tidySpatialExperiment is an adapter that abstracts the SpatialExperiment container 
    in the form of a tibble and allows data manipulation, plotting and nesting using functions from
    the tidyverse ecosystem.
License: GPL-3
Depends:
    R (>= 4.3.0),
    SingleCellExperiment,
    SpatialExperiment,
    tidySingleCellExperiment,
Imports:
    ttservice,
    SummarizedExperiment,
    BiocGenerics,
    dplyr,
    tibble,
    tidyr,
    ggplot2,
    plotly,
    magrittr,
    rlang,
    purrr,
    lifecycle,
    methods,
    utils,
    S4Vectors,
    tidyselect,
    ellipsis,
    vctrs,
    pillar,
    stringr,
    cli,
    fansi,
    Matrix,
    pkgconfig
Suggests:
    BiocStyle,
    testthat,
    knitr,
    markdown,
    SingleCellSignalR,
    SingleR,
    scater,
    scran,
    tidyHeatmap,
    igraph,
    GGally,
    uwot,
    celldex,
    dittoSeq,
    EnsDb.Hsapiens.v86,
    cowplot, 
    microbenchmark
VignetteBuilder: 
    knitr
Biarch: true
biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
URL: https://github.com/william-hutchison/tidySpatialExperiment
BugReports: https://github.com/william-hutchison/tidySpatialExperiment/issues

[vjcitn]

you need DropletUtils in Suggests, or R_CHECK_SUGGESTS_ONLY will lead to error

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The following are build products from R CMD build on the Bioconductor Build
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Linux (Ubuntu 22.04.2 LTS): tidySpatialExperiment_0.99.2.tar.gz
macOS 12.6.5 Monterey: tidySpatialExperiment_0.99.2.tar.gz

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[william-hutchison]

Hello, thank you for your feedback. I have addressed all warnings and errors produced during the automated test process. Let me know if you have any further suggestions

[hpages]

Thanks @william-hutchison. Please consider addressing the following NOTEs:

R CMD check NOTEs:

1.  * checking dependencies in R code ... NOTE
    Packages in Depends field not imported from:
      ‘SpatialExperiment’ ‘tidySingleCellExperiment’
      These packages need to be imported from (in the NAMESPACE file)
      for when this namespace is loaded but not attached.
   

2.  Consider adding
      importFrom("methods", "callNextMethod", "getMethod", "is")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
   

   Note that for the above note we actually recommend to import the full methods namespace with import(methods) instead of the suggested selective import.

   Fixing the imports should get rid of most "no visible binding for global variable" and "no visible global function definition" messages. Any remaining one will need to be assessed to determine whether it's a false positive or not.

3.  * checking Rd files ... NOTE
    prepare_Rd: group_by.Rd:70-72: Dropping empty section \seealso
   

BiocCheck() NOTEs:

4.  * Checking for recommended biocViews...
        * NOTE: Consider adding these automatically suggested biocViews:
          Spatial, Transcriptomics, SingleCell, ImmunoOncology, DataImport
   

   Maybe not all the terms above are relevant but maybe some of them are?

5.  * Checking vignette directory...
        * NOTE: 'sessionInfo' not found in vignette(s)
   

6.  * Checking coding practice...
        * NOTE: Avoid using '=' for assignment and use '<-' instead
   

Let me know if you have any questions.

Thanks,
H.

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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/tidySpatialExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: 05b0a894b63e5033aa35b6776c39845a1db8c0df

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Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): tidySpatialExperiment_0.99.4.tar.gz
macOS 12.6.5 Monterey: tidySpatialExperiment_0.99.4.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/tidySpatialExperiment to trigger a new build.
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[william-hutchison]

Hi @hpages, thank you for your feedback.

I had removed the plot_ly() generic from tidySummarizedExperiment in our development version but did not push these changes to Bioconductor. Sorry about that, I will address this now.

Kind regards,
William

[william-hutchison]

Hi @hpages. The updated tidySummarizedExperiment has been pushed the devel branch of Bioconductor. Thanks again.

[hpages]

Great, thanks!

Last thing on the list: since in the end the plot_ly() generic is defined in the ttservice package, do you really need to list tidySummarizedExperiment in Depends? What is tidySummarizedExperiment used for in tidySpatialExperiment?

If you do need to depend on tidySummarizedExperiment, then make sure to import the package in your NAMESPACE like you did for tidySingleCellExperiment. This issue is actually reported by R CMD check:

* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘tidySummarizedExperiment’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

If you don't need to depend on tidySummarizedExperiment then remove it from Depends.

Maybe the same applies to tidySingleCellExperiment? Do you really need to depend on it?

Thanks again,
H.

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Received a valid push on git.bioconductor.org; starting a build for commit id: f04ba04b09eaf91519ec6dd3b3d2ff88022e67f7

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ERROR before build products produced.

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Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: b6fd6bf220ecea2b49a6646e72bea3f380f226c1

[bioc-issue-bot]

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,
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[email protected]:packages/tidySpatialExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 7d76d7947d5fb1bbb04d6d84a099a2a399c94d49

[bioc-issue-bot]

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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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.2 LTS): tidySpatialExperiment_0.99.15.tar.gz

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Remember: if you submitted your package after July 7th, 2020,
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Received a valid push on git.bioconductor.org; starting a build for commit id: 68c204b4f8382d2e6d9caabdf5d276cd69272674

[bioc-issue-bot]

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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The following are build products from R CMD build on the Single Package Builder:
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[william-hutchison]

Hi @hpages, thank you for your suggestions.

I have moved tidySummarizedExperiment to Suggests. I believe tidySingleCellExperiment should remain in Depends to attach functions which are not exported by tidySpatialExperiment and are instead called directly from tidySingleCellExperiment e.g count().

Unfortunately I am now encountering an error with the macOS build:

ERROR: dependency SpatialExperiment is not available for package tidySpatialExperiment

All works well on Ubuntu and I am not sure what could be causing this, as SpatialExperiment has always been listed in Depends. I will continue to investigate, but let me know if you have any ideas. Maybe it could be a problem with the build process?

Thanks again

[hpages]

Maybe it was just bad timing. We updated R to the latest R-devel on all our devel build machines a couple of days ago. It could be that the SPB got triggered before all the BioC packages got reinstalled on merida1. Can you please trigger a new build by bumping the version again? Thanks

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Received a valid push on git.bioconductor.org; starting a build for commit id: 96365815bb3f5b9b0b7a4874693d8f82a3bca1fe

[bioc-issue-bot]

Dear Package contributor,

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

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[hpages]

Thanks. Let's ignore the warning on merida1. R CMD check took a little bit more than 10 min there (11 minutes 43.62 seconds), not a big deal.

3 minor things left and the package will be good to go:

1. This R CMD build note:

* checking for empty or unneeded directories
Omitted LazyData from DESCRIPTION

(just remove the LazyData: false line)

2. This R CMD check note:

* checking Rd line widths ... NOTE
Rd file 'rectangle.Rd':
  \examples lines wider than 100 characters:
         mutate(in_rectangle = rectangle(array_col, array_row, center = c(50, 50), height = 20, width = 10))

3. This R CMD BiocCheck note:

* Checking coding practice...
    * NOTE: Avoid using '=' for assignment and use '<-' instead

Almost there.

Thanks again.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 17747da50095e662e483dbafc5dbf2e5711dfc1f

[bioc-issue-bot]

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:
macOS 12.7.1 Monterey: tidySpatialExperiment_0.99.19.tar.gz
Linux (Ubuntu 22.04.2 LTS): tidySpatialExperiment_0.99.19.tar.gz

Links above active for 21 days.

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[william-hutchison]

Hi @hpages, I have addressed the three notes you raised. Thank you for helping me improve tidySpatialExperiment.

[hpages]

Great, thanks!

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