Spaniel

[RachelQueen1]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/RachelQueen1/Spaniel

Confirm the following by editing each check box to '[x]'

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @RachelQueen1

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: Spaniel
Type: Package
Title: Spatial Transcriptomics Analysis
Version: 0.99.0
Author: Rachel Queen <rachel.queen@newcastle.ac.uk>
Maintainer: Rachel Queen <rachel.queen@newcastle.ac.uk>
Description: A collection of tools for  analysing  Spatial Transcriptomics Data.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0),
         Seurat,
         SingleCellExperiment,
         dplyr
Imports: methods,
         ggplot2,
         scater, 
         shiny,
         jpeg,
         magrittr, 
         SummarizedExperiment,
         utils,
         S4Vectors
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    devtools
VignetteBuilder: knitr
RoxygenNote: 6.1.1.9000
Collate: 
    'utilities.R'
    'addClusterCols.R'
    'parseImage.R'
    'readData.R'
    'removeSpots.R'
    'spaniel_plot_internals.R'
    'spatialPlot.R'
    'shinySpaniel.R'
biocViews: SingleCell, RNASeq, QualityControl, 
  Preprocessing, Normalization, Visualization, Transcriptomics, 
  GeneExpression, Sequencing, Software, DataImport,
  DataRepresentation, Infrastructure, Coverage, Clustering

Add SSH keys to your GitHub account. SSH keys will are used to control access to accepted Bioconductor packages. See these instructions to add SSH keys to your GitHub account.

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[RachelQueen1]

Hi, Just wondered if there is anything I need to do as I haven't had an update for a while? Thanks in advance

[nturaga]

Hi @RachelQueen1 ,

I will review your package and post a review in a few days time. You need to set up the build reports for your package, so it can build and check. Please see the comments issued by the bot above.

https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook

Best,

Nitesh

[RachelQueen1]

Great, thank you :)

Rachel

[nturaga]

Great, thank you :)

Rachel

Please take a look at the edits in my previous comment.

[RachelQueen1]

Thanks, I have added the web hook.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

00c23ec Update version

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

891cdca remove supress messages and update version

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

0da4aab fix typo and update version

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

a8f8c83 change calculateQCMetrics to addQCPerCell

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

a9ecd6d update version

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details.

[nturaga]

Spaniel Review

R CMD build

ok

R CMD check

ok

DESCRIPTION

• Description is not enough. Please think of this as an abstract to a paper. It needs to give the user information about exactly what the tool does.

NAMESPACE

• ok

vignette

I cannot get the vignette to run, (Note, there is also an incomplete function call in this.

    sce <- scater::addQCPerCell(
        sce, 
    )

The package scater doesn't have the function addQCPerCell.

Error: processing vignette 'spaniel-vignette.Rmd' failed with diagnostics:
'addQCPerCell' is not an exported object from 'namespace:scater'

R

• Dead code,

    if(removeTmpFile){
    }

Please correct these basic issues before a more in depth review.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

4de2b51 remove dead code, update description and add versi...

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ABNORMAL". 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

fd528c1 fix typo

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ABNORMAL". 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.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ABNORMAL". 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

b709d10 version bump

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

7588d1d Version bump

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

1569645 remove remove tmp file option from example

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details.

[RachelQueen1]

Hi Nitesh,

Thanks for starting the review process. I have now addressed the problem with the Description and removed the dead code. addQCPerCell is exported from the development version of Scater: https://bioconductor.org/packages/devel/bioc/html/scater.html. The function replaces calculateQCMetrics and I was getting a warning message to say that that function would soon be depreciated. Is it the right thing to do to use the development version of scater or should I stick with the current version in Bioconductor?

Thanks in advance,

Rachel

[lshep]

New packages and packages being submitted should use the development version of Bioconductor (and therefore the devel version of packages). So this is the right version to be developing against https://bioconductor.org/packages/devel/bioc/html/scater.html . Cheers.

[nturaga]

Update

• Variable naming is not consistent. MetaData vs whichCols, use only one type of casing. Use either, "UpperCamelCase" or "lowerCamelCase"(recommended). Just make sure your variable names are consistent across.

• Add the Bioconductor way of installing the package in the vigneette BiocManager::install('Spaniel').

• readSeurat() and readSCE() are not very descriptive of "creating" seurat or SCE objects. The function name should probably be createSeurat and createSCE()

• It would also help if you used markdown formatting features to annotate your vignette to make it more readable. Function calls can be functionCall(), and important points can be marked as important. This allows greater readability.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

4e527b3 Add the Bioconductor way of installing the package... d8a5e9d change function names to from readSeurat and readS... b9abfd4 version bump

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

87fc110 change ST_plot to spanielPlot

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

cfaa56d revert to devtools way of installation

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

2323a14 revert to devtools way of installation

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

35ef0b5 version bump

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

58f4553 change parameter names in removeSpots function

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

282152c correct example in removeSpots

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

22acc4d fix example for remove spots documentation

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

6dada98 Add the Bioconductor way of installing the package...

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details.