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HCAData #937

Closed federicomarini closed 5 years ago

federicomarini commented 5 years ago

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bioc-issue-bot commented 5 years ago

Hi @federicomarini

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: HCAData
Type: Package
Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor
Version: 0.99.0
Authors@R: c(
    person("Federico","Marini", role=c("aut","cre"), email="marinif@uni-mainz.de",
    comment = c(ORCID = '0000-0003-3252-7758')))
Maintainer: Federico Marini <marinif@uni-mainz.de>
Description: This package allows a direct access to the dataset generated by the 
    Human Cell Atlas project for further processing in R and Bioconductor
    (available in other formats here: http://preview.data.humancellatlas.org/).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews: RNASeqData, SingleCellData, ExperimentData, ExpressionData, ExperimentHub
Depends: R (>= 3.5)
Imports: ExperimentHub,
    AnnotationHub,
    SingleCellExperiment,
    HDF5Array,
    utils
Suggests: knitr,
    rmarkdown,
    BiocStyle,
    scran,
    scater,
    igraph,
    iSEE,
    testthat
VignetteBuilder: knitr
RoxygenNote: 6.1.1
federicomarini commented 5 years ago

As a note of interest, which I touched upon with Lori in a discussion on the bioc-community Slack channel:

I have seen that, for the recent hca application, Martin and Daniel are planning an HCABrowser package. Now, I don’t know the timeline for that, or what the full capabilities for this future package would be. In the meanwhile I think it is still worth having “as a standalone solution”, as I was also planning to have the datasets in this format as a playground to the iSEE package.

I'm not calling them out explicitly for the review, but I'm happy to hear from @mtmorgan and @dvantwisk

bioc-issue-bot commented 5 years ago

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.

bioc-issue-bot commented 5 years ago

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 commented 5 years ago

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

df073ec added Date field to DESCRIPTION and bumped version...

bioc-issue-bot commented 5 years ago

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 commented 5 years ago

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.

federicomarini commented 5 years ago

It worked @lshep, thank you! Still, I can't find out the reason of the warning message (only in R CMD build), which is namely WARNING: directory 'HCAData/build' is empty - since I am not using any such directory.

lshep commented 5 years ago

Not sure but I'd ignore it for now. Let me know if you see any more abnormals

federicomarini commented 5 years ago

Ok, I'll let then the reviewers do their job 😉

bioc-issue-bot commented 5 years ago

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

c594caa added details in the scran suggests dependency, po... 3b664f4 Version bump - 0.99.2

bioc-issue-bot commented 5 years ago

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, 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 commented 5 years ago

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.

Liubuntu commented 5 years ago

Hi @federicomarini ,

Thank you for your contribution to Bioconductor. This package is well-written and could be very useful. There are some minor issues from the technical review. Please seek to address most of them and comment back with any question or when ready for a 2nd look. Thanks!

DESCRIPTION

R/

HCAData.R

man/

HCAData.md

vignette

Cheers, Qian

federicomarini commented 5 years ago

Hi Qian,

thank you a lot for the detailed review!

I'll work on the points you mentioned, and get back to you once all are addressed.

Federico

federicomarini commented 5 years ago

(out of curiosity: did you find out how the HCAData/build folder gets created and raises that warning in R CMD build?)

bioc-issue-bot commented 5 years ago

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

579f894 removed Date field 3891382 removed LazyData: true ca23783 updated detailed description of package, and added... c9c2d8c removed explicit calls to library(SingleCellExperi... 25e5c90 removed explicit calls to load SingleCellExperimen... aef991b replacing double check with tidier if-else 24a3aa9 changed style in variable naming, making it more e... 5cd05b5 Added an intro section in the vignette, Introducin... 4381443 Edited section names when saving the object after ... acc10c3 better phrasing in the vignette as suggested 747f225 couple of edits in the vignette 7cf15b4 edits and cleanups in the vignette e76bf3d breaking up the monster chunk in the vignette, and... 9bff542 Version bump - 0.99.3, addressing first round of c...

bioc-issue-bot commented 5 years ago

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.

federicomarini commented 5 years ago

Qian,

I am done with the first round. I addressed all points you mentioned, and I will go through them in detail in the following lines.

DESCRIPTION

  • Please remove lazyData: true, This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data.

I removed the line from the DESCRIPTION file

Please remove the Date: field.

Same as above

Description field: Since the data returned by calling HCAData() is a SingleCellExperiment object, it would be helpful to add it into description field.

Good point, I added that in the Description

For the same reason as above, you may want to Depends: SingleCellExperiment instead of just importing it, so that user could get automatic loading of that package and use functions directly without a manual library(SingleCellExperiment). The package itself is light-weight and wouldn't make loading process heavy.

True, one will anyway have to play with these functions once the object is there, there is no point to explicitly have the user load it.

R/

HCAData.R

Use if(!is.null(dataset)) {...} else { to avoid checking is.null(dataset) twice.

Nice catch. Edited accordingly

SUGGESTED: This is more coding style thing but I just want to bring it into attention for a better tracking and maintenance of the code. Seems that you have been using rdatapath all through for rowData, colData and h5file. To reuse an R object, you may want to rename it as datapath to be more general, or use rdatapath/cdatapath/h5datapath separately.

Edited as in your suggestion.

man/

HCAData.md

Please remove library(SingleCellExperiment) from example if you Depends: SingleCellExperiment in DESCRIPTION file.

I do now Depend, so this is gone. This is also gone in the unit tests.

vignette

Add a major section of Introduction (before Installation) to briefly introduce this package. You can use a relatively more detailed version of Description field inside DESCRIPTION file.

I added an intro section in the vignette, "Introducing the HCAData package"

Avoid a big chunk of code without enough explanation. In the section of Processing a subset of the HCA bone marrow data, as an example case study, please break it into smaller chunks with proper explanation for each processing step.

I did break up the monster chunk in the vignette, and gave proper bits of explanation for each step.

The section Saving computations is not actually about "computation". You may want to rename it.

Now it is called ## Saving the processed object, more appropriately reflecting the content of the section.

some sentences are not smooth in reading. E.g., you may want to modify "instead storing the counts on disk..." as "instead, it stores ... and loads ...".

Thank you for spotting this, sometimes my phrasing just gets overcomplicated. I edited that sentence, and also cleaned up some leftover commented lines throughout the vignette.

To sum up, thank you for the helpful suggestions. I am happy to proceed with the next round. Side note: I see the build warning is still persisting, but could not track down why that is happening.

Cheers, Federico

Liubuntu commented 5 years ago

Hi @federicomarini ,

Thank you for the prompt update! Now everything looks good for acceptance. For the warning, we'll just ignore it because it comes from R CMD build, there is nothing wrong on our end and nothing you could do to the package itself. We'll continue monitoring to see if it could pass someday later.

Best, Qian

bioc-issue-bot commented 5 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

federicomarini commented 5 years ago

Thank you for the good news! Happy to contribute further to this project & community 👍

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("HCAData"). The package 'landing page' will be created at

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