geyser

[davemcg]

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• Repository: https://github.com/davemcg/geyser

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[bioc-issue-bot]

Hi @davemcg

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: geyser
Title: Gene Expression displaYer of SummerizedExperiment in R
Version: 0.99.0
Authors@R: 
    person(given = "David",
 family = "McGaughey",
 role = c("aut", "cre"),
 email = "mcgaughey@gmail.com",
 comment=c(ORCID="0000-0002-9224-2888"))
Description: Lightweight Gene Expression displaYer (plotter / viewer) of SummarizedExperiment object. This package provides a quick and easy that uses Shiny-based GUI to empower a user to use a SummarizedExperiment object and then view gene expression grouped from the sample metadata columns (in the `colData` slot). Gene expression can either be viewed with a box plot or a heatmap. 
License: LICENSE
LazyData: true
biocViews: Software, ShinyApps, GUI
Imports:
  bslib (>= 0.5.0),
  ComplexHeatmap,
  dplyr,
  DT,
  ggbeeswarm,
  ggplot2,
  htmltools,
  shiny,
  SummarizedExperiment,
  tibble,
  tidyr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: 
    airway,
    knitr,
    DESeq2,
    recount3,
    rmarkdown,
    stringr,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "ERROR, skipped". 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 Bioconductor Build System: 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 git@git.bioconductor.org:packages/geyser 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: 5e27d2762851adf1d54916a8c3f0f61fb7d43398

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: geyser_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): geyser_0.99.1.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 git@git.bioconductor.org:packages/geyser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[davemcg]

I believe the only error now is because I haven't set up a watch tag. Which I cannot do as I am locked out of my bioc account. I have contacted bioc-devel@r-project.org and they are looking into it.

The only other issue is because I work for the US Government and I cannot use a standard license.

[vjcitn]

Is the LICENSE text required to mention "third party software"? What are the "third-party packages" mentioned there?

[davemcg]

I believe that third party packages are anything not me (so other libraries/packages). Is there better language I should use?

[vjcitn]

You aren't redistributing any other libraries or packages. I think you could take that clause out? You are using names of functions in other packages or calling such functions, but does that behavior need to be regulated by license text?

[davemcg]

I've tweaked the text (the first block is just for line formatting and a missing space) of the LICENSE. I've simplified the language of the last paragraph. I'm a bit nervous about removing it entirely as l believe lawyers had some role in crafting this.

https://github.com/davemcg/geyser/commit/c2747ad0ea1aef68948b36c3fa43671c046057de

I can increment the version if this edit is helpful (I'm still awaiting a response on getting access to my bioconductor account so I can add the watch. )

[vjcitn]

@HelenaLC please proceed with review of this package as your time permits. @lshep I think we can proceed with the license given.

[HelenaLC]

Please see my comments below and come back with any questions you might have, as well as what has/not been addressed when ready; thanks!

code

• [ ] avoid T/F variables; if logical, use TRUE/FALSE (exp_plot.R line 42)

• [ ] avoid using = for assignment and use <- instead

documentation

• [ ] please provide source information on how example data was generated and/or a corresponding script in inst/scripts (namely, tiny_rse is undocumented at the moment)

• [ ] just a reminder to remove the comment hashtags in lines 24+ of the vignette

• [ ] we encourage use of BiocStyle for formatting with html_document as rendering target (see here)

• [ ] I think the visual demo of the app's different panels in the vignette is nice and clear, but there's very little text/description if any

• [ ] also, I am missing an introduction section that puts the package into context and outlines it's main purpose and functionalists, potentially related frameworks etc. (e.g., there are other frameworks within Bioc that you mention at the end; this could also be part of the intro, or the section referred to and kept as is (see here for details)

other

• [ ] in the README, please provide Bioc installation instructions using BiocManager::install()

• [ ] importing entire packages (@import) should be avoided in favor of selective imports (@importFrom) (see here for details)

• [ ] consider adding URL: and BugReports: fields in the DESCRIPTION that link to https://github.com/davemcg/geyser and .../issues, respectively

• [ ] in the DESCRIPTION, LazyData: should be set to false or removed (see here)

• [ ] appreciate unit testing (!), though coverage is fairly low and might be worth improving on (44% according to devtools::test_coverage() without any testing on 2 scripts)

[federicomarini]

Hy @davemcg, I tried to run the vignette also with the interactive chunks of code to launch the app.

At this point https://github.com/davemcg/geyser/blob/c2747ad0ea1aef68948b36c3fa43671c046057de/vignettes/Gene_Expression_Plotting_GUI.Rmd#L157 I am encountering an error crashing the app

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'sort': error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'x' in selecting a method for function 'colData': object 'SummarizedExperiment(ddsSE)' not found

This can be because the "conversion" step you introduce does drop the info you need?

You can compare the two objects here:

> ddsSE
class: DESeqDataSet 
dim: 63677 8 
metadata(2): '' version
assays(1): counts
rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
  ENSG00000273493
rowData names(10): gene_id gene_name ... seq_coord_system symbol
colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
colData names(9): SampleName cell ... Sample BioSample
> SummarizedExperiment(ddsSE)
class: SummarizedExperiment 
dim: 63677 8 
metadata(0):
assays(1): ''
rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
  ENSG00000273493
rowData names(0):
colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
colData names(0):

Actually, an even better (IMO) selling point is that you can simply pass the ddsSE object to geyser(). Like this

geyser(ddsSE)

... which captures the full extent of relevant colData

HTH, Federico (couldn't skip on following this one closer since you mentioned iSEE in it 😉 )

[lshep]

@davemcg just wanted to check in that you saw the comments from above and are working on updates?

[davemcg]

I have! Appreciate all the comments - I've been trying to address other work and haven't had time to come back to this. Hoping to address these soon.

[davemcg]

0.99.2 pushed which I hope addresses all of the comments (and doesn't create new issues). Happy end of 2023 everyone.

[lshep]

it doesn't look like a push was made to git.bioconductor.org as that still has 0.99.1 Please push to git.bioconductor.org to trigger a new build.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f9b7f99a9e46749b48070425b874e4ec32cdb4e3

[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: "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: macOS 12.7.1 Monterey: geyser_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): geyser_0.99.2.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 git@git.bioconductor.org:packages/geyser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[davemcg]

Hmm, missed an "=" that should have been a "<-". Will fix that for the next release. The testing works on my computer....that said the error thrown is a warning for me? Hmm I just updated my bslib to 0.6.1 and now and throwing an error. I'll look into that.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5ed732cb1f9bf3fc8353b48b5cbd4af452b40091

[davemcg]

OK, fixed some small things (assignment <-, removed ds_store, removed trailing comma that was throwing an error). Hopefully this will build.

[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: "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: macOS 12.7.1 Monterey: geyser_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): geyser_0.99.3.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 git@git.bioconductor.org:packages/geyser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[davemcg]

Great - the only error is my inability to add "geyser" to the watch list (as I cannot reset my password on the bioc support forum to log in).

[lshep]

I just tested the password reset on the support site and it works for me. Are you not getting the reset email at all (have you checked your spam folder?) ? or do you try to set it and then you still cannot login?

[davemcg]

I don't get the reset email at all...nothing in my junk folder either....

[lshep]

I will email you off list with a few options and some follow up questions.

[davemcg]

Lori Kern (couldn't find github profile) reset my account. I've created a new account and added geyser to my watch list. I re-ran BiocCheck::BiocCheck() and now I'm at zero errors. Should I bump the version increment to re-run the server testing?

[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: Linux (Ubuntu 22.04.3 LTS): geyser_0.99.3.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 git@git.bioconductor.org:packages/geyser to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

I‘d like to sincerely apologize, this totally slipped my radar as I usually wait for build/check reports to clear, and then lost track :/ …could you please address the warning regarding the license and any other easily fixable report notes? I‘ll then try and wrap up the review hopefully asap. Thanks & again: My apologies for the huge delay.