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CytoTree #1501

Closed ytdai closed 4 years ago

ytdai commented 4 years ago

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bioc-issue-bot commented 4 years ago

Hi @ytdai

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: CytoTree
Type: Package
Title: A Toolkit for Flow And Mass Cytometry Data
Version: 0.99.1
Date: 2020-05-10
Authors@R: person("Yuting", "Dai", role = c("aut", "cre"), email = "forlynna@sjtu.edu.cn")
Description: A trajectory inference toolkit for flow and mass 
    cytometry data. CytoTree is a valuable tool to build a 
    tree-shaped trajectory using flow and mass cytometry data. 
    The application of CytoTree ranges from clustering 
    and dimensionality reduction to trajectory reconstruction 
    and pseudotime estimation. It offers complete analyzing 
    workflow for flow and mass cytometry data. 
Depends: R (>= 3.6), igraph
Imports: FlowSOM, Rtsne, ggplot2, destiny, gmodels,
        flowUtils, Biobase, Matrix, flowCore, sva,
        matrixStats, methods, mclust, prettydoc, 
        RANN(>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors,
        cluster, pheatmap, scatterpie, umap, scatterplot3d,
        limma, stringr, grDevices, grid, stats
Suggests: BiocGenerics, knitr, RColorBrewer,
        rmarkdown, testthat, BiocStyle
biocViews: CellBiology, Clustering, Visualization, 
        Software, CellBasedAssays, FlowCytometry,
        NetworkInference, Network
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
BugReports: https://github.com/JhuangLab/CytoTree/issues
git_url: https://github.com/JhuangLab/CytoTree
URL: http://www.r-project.org, https://github.com/JhuangLab/CytoTree
git_last_commit: 
git_last_commit_date: 
Date/Publication: 
LinkingTo: Rcpp
Packaged:

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bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 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.

bioc-issue-bot commented 4 years ago

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

2d6ff58 update R version

bioc-issue-bot commented 4 years ago

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LiNk-NY commented 4 years ago

Hi Yuting, @ytdai Thank you for your submission. I will review your package today. Best, Marcel

ytdai commented 4 years ago

Hi Yuting, @ytdai Thank you for your submission. I will review your package today. Best, Marcel

Dear Marcel:

Thank you. The CytoTree package is the updated version of the flowSpy package in Bioconductor (https://bioconductor.org/packages/flowSpy/). For some reason, we had to change the package name of flowSpy to CytoTree. Most functions and workflow in CytoTree are the same as flowSpy. After discussed with the Bioc team, I submitted CytoTree as a new package to GitHub for traditional review. The update of flowSpy will continue until the end of 3.11. And for the 3.12 devel, flowSpy will be deprecated.

Thank you for reviewing my package.

Best,

Yuting Dai

bioc-issue-bot commented 4 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: "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.

LiNk-NY commented 4 years ago

Hi Yuting, @ytdai

Thank you for your submission. Please see the review below.

If you have any questions, feel free to post them here.

Best, Marcel

CytoTree #1501

DESCRIPTION

vignettes

R

bioc-issue-bot commented 4 years ago

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

c7b3244 update version 0.99.3

bioc-issue-bot commented 4 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: "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 commented 4 years ago

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

a9e0352 update v0.99.4

bioc-issue-bot commented 4 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: "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.

ytdai commented 4 years ago

Hi Marcel, @LiNk-NY

Thank you very much for reviewing the package.

According to your comments, I have changed the code of the package. The newest version of CytoTree is 0.99.4. The response and modifications were attached below.

As for the ERROR message on the build bin of CytoTree on macOS, I didn't meet this error when I was running R CMD install on my MacBook. Could you please help me to fix it?

The link is http://bioconductor.org/spb_reports/CytoTree_buildreport_20200604141703.html

Thank you very much.

Best,

Yuting Dai 2020-06-05

DESCRIPTION

[A] The empty fields were removed.

vignettes

[A] For the first question, if the detailed tutorial was included in the package, the size of the package will be so large. So I chose to put the tutorial on the website.

For the second question, I have continuous integration set up for the tutorials. The update of the tutorials was controlled by another GitHub project (https://github.com/JhuangLab/CytoTree-dataset). I used Rmarkdown to control the entire workflow to generate tutorials of this package. Once the package is modified, I will also update the tutorials on the website.

And for the third and fourth questions, I can ensure to keep synchronous updates for both the package and tutorial.

R

[A] Yes, I agree it is redundant to use 'ERROR', 'WARNING' and 'INFO'. These habits come from the writing style of Perl packages. In fact, these massage tags do not affect the function. With the message tags, I think the output information are more eye-catching. So I decided to keep it.

For the second question, I have deleted the %in% generic in BiocGenerics. %in% generic was not used in this package.

For the third question, the workflow of this package was in series. For example, if users want to run function E, they must run functions A, B, C, D step by step in advance. So it is hard to provide a small example of a dataset for testing. I have added an example file in extdata, and all if (FALSE) were removed.

For the fourth question, all 1:ncol(x) were changed to seq_along(x) or seq_len(x).

For the fifth question, the name was changed.

ytdai commented 4 years ago

Hi Marcel, @LiNk-NY

Last week, I have modified the code of CytoTree and submitted the novel version of CytoTree package to Bioconductor/Contributions. The answers to your comments were also added to the link https://github.com/Bioconductor/Contributions/issues/1501. Could you have time to take a look?

As for the ERROR message on the build bin of CytoTree on macOS, I didn't meet this error when I was running R CMD install on my MacBook. Could you please help me to fix it?

Thank you very much.

Yuting Dai 2020-06-11

ytdai commented 4 years ago

Hi Marcel,

Last week, I have modified the code of CytoTree and submitted the novel version of CytoTree package to Bioconductor/Contributions. The answers to your comments were also added to the link https://github.com/Bioconductor/Contributions/issues/1501. Could you have time to take a look?

As for the ERROR message on the build bin of CytoTree on macOS, I didn't meet this error when I was running R CMD install on my MacBook. Could you please help me to fix it?

Thank you very much.

Yuting Dai 2020-06-11

------------------ 原始邮件 ------------------ 发件人: "Marcel Ramos"<notifications@github.com>; 发送时间: 2020年6月2日(星期二) 晚上10:02 收件人: "Bioconductor/Contributions"<Contributions@noreply.github.com>; 抄送: "代雨婷"<809449456@qq.com>;"Mention"<mention@noreply.github.com>; 主题: Re: [Bioconductor/Contributions] CytoTree (#1501)

Hi Yuting, @ytdai

Thank you for your submission. Please see the review below.

If you have any questions, feel free to post them here.

Best, Marcel

CytoTree #1501

Example code in examples, vignettes, unit tests, are meant to guarantee that a package is working for the users. The absence of this code in your package does not look favorable for users who would like to replicate a workflow. Please include working examples and a substantial vignette for users who do not want to access your online resources or who have limited internet connectivity on their servers.

DESCRIPTION

Looks good

Remove empty fields from the file

vignettes

Is there a reason why you link to the website instead of providing a vignette that is built nightly with other packages?

Do you have continuous integration set up on tutorial documents?

My concern is that content like this will become stale because it is not regularly updated and checked as it would if it were a vignette in the package.

An alternative to consider is to have the vignettes from the linked website built from the package and served to github.io using something like the pkgdown package

R

It is redundant to use 'ERROR', 'WARNING', etc. tags with the appropriate functions. stop already returns an explicit error message.

Why not use the %in% generic in BiocGenerics?

Avoid using if (FALSE) in the examples. This creates stale code, provide code that users can run if they need to test a function. If you data is large provide a small example dataset for testing and use within the examples.

Avoid using 1:ncol(x) sequence generation use seq_along(x) or seq_len(ncol(x))

Rename R files so that they match with the function (e.g., subsetCYT() in subsetFSPY.R)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

LiNk-NY commented 4 years ago

Hi Yuting, @ytdai Sorry for the delay in getting back to you. I will have take a look at your package today. Thank you for your patience.

LiNk-NY commented 4 years ago

Can you try bumping the version to re-build the package? Thanks

ytdai commented 4 years ago

Can you try bumping the version to re-build the package? Thanks

Okay, I am re-building this package now.

bioc-issue-bot commented 4 years ago

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

a465c27 update v0.99.5

bioc-issue-bot commented 4 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: "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.

LiNk-NY commented 4 years ago

Hi Yuting, @ytdai

I had a look at your response. We would prefer that you use a vignette that has a smaller example dataset that fits inside the package, rather than having a large example hosted elsewhere. You are free to host these vignettes independent of the package but in this instance, those websites are replacing the functionality of the vignettes that we require.

We recommend that you use a "toy" example dataset to demonstrate the functionality of the package. If you would like to publish a more drawn out example, you are welcome to submit a workflow package. We don't really accept vignettes that link to other websites.

For the third question, the workflow of this package was in series. For example, if users want to run function E, they must run functions A, B, C, D step by step in advance. So it is hard to provide a small example of a dataset for testing. I have added an example file in extdata, and all if (FALSE) were removed.

If your functionality is to show function E, why not take the results of step D and add a small dataset of D in the package?

Consider this example for removing redundant keywords from similar functions. There is no added value to repeating the "ERROR"/"WARNING" word etc.

stop("ERROR: The function is not working")
# Error: ERROR: The function is not working

Thank you. -Marcel

bioc-issue-bot commented 4 years ago

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

e54bf2c update v 0.99.6

ytdai commented 4 years ago

Hi Marcel, @LiNk-NY

Thank you very much.

For the vignettes, I have added a vignette included in the package and remove the link of the vignette on the website.

For the examples, I have added a small example data. So all the examples included in the function are runnable.

And for the redundant keywords, they were all removed.

I hope to get your reply soon, thank you.

Best,

Yuting Dai 2020-06-19

bioc-issue-bot commented 4 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: "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.

LiNk-NY commented 4 years ago

Hi Yuting, @ytdai Thanks for making those changes! Your package has been accepted. Best regards, Marcel

bioc-issue-bot commented 4 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!

mtmorgan commented 4 years ago

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

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/ytdai.keys is not empty), then no further steps are required. Otherwise, do the following:

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  2. Submit your SSH key to Bioconductor

See further instructions at

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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("CytoTree"). The package 'landing page' will be created at

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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.