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(inactive) massconverter #2482

Closed jaspershen closed 2 years ago

jaspershen commented 2 years ago

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bioc-issue-bot commented 2 years ago

Hi @jaspershen

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: massconverter
Title: Convert mass spectrometry raw data to othter format data
Version: 0.99.1
Date: 2022-01-08
Authors@R: 
    person(given = "Xiaotao",
 family = "Shen",
 role = c("aut", "cre"),
 email = "shenxt1990@outlook.com",
 comment = c(ORCID = "0000-0002-9608-9964"))
Description: Convert mass spectrometry raw data to othter format data. Now it is
   based on the docker for msconvert. So the users need to install 
   docker and run docker first.
URL: https://github.com/tidymass/massconverter
BugReports: https://github.com/tidymass/massconverter/issues
Depends: R (>= 4.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Imports: 
    magrittr,
    rstudioapi,
    crayon,
    purrr,
    tools,
    leaflet,
    stevedore,
    methods
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    RUnit,
    BiocGenerics,
    tidyverse,
    testthat (>= 3.0.0)
Note:
biocViews: Metabolomics, MassSpectrometry
vjcitn commented 2 years ago

Should depend on R >= 4.2. No vignettes folder. Seems to be a pkgdown site source. Please read developer guidelines.

jaspershen commented 2 years ago

Hi. Just added vignettes. For the R version, I am using R 4.1, so I am wondering if I can keep 4.1 in my depends? Thanks!

jaspershen commented 2 years ago

Hi. Just changed R > 4.2 and ran well. Thanks.

vjcitn commented 2 years ago
-- re-building ‘convert_data.Rmd’ using rmarkdown
Warning in normalizePath(input_path) :
  path[1]="demo_data/raw_data": No such file or directory
Warning in normalizePath(output_path) :
  path[1]="demo_data/mzxml": No such file or directory

Is something missing?

jaspershen commented 2 years ago

Thanks @vjcitn . Just fixed the bug in one function and now the warnings have gone! Thank you!

lgatto commented 2 years ago

Hi @jaspershen - I am reviewing your packages and wanted to make sure I don't miss any. I'm aware of massconverter and masstools (issue #2481); anything else?

jaspershen commented 2 years ago

Thanks so much, Laurent! That’s all. No other packages. Thank you!


Xiaotao Shen, PhD
 Postdoctoral Research Fellow Prof. Michael Snyder’s labhttp://med.stanford.edu/snyderlab.html Stanford University School of Medicine Co-chair | SCPAhttps://scpa.netlify.app/ Biomedical Innovations Building, 240 Pasteur @.,-122.1795782,17z/data=!4m5!3m4!1s0x808fa52ba51d58eb:0xe8daaea65a01418c!8m2!3d37.4329555!4d-122.1773895> Stanford, CA 94305 
 @.,-122.1795782,17z/data=!4m5!3m4!1s0x808fa52ba51d58eb:0xe8daaea65a01418c!8m2!3d37.4329555!4d-122.1773895> Personal website: shenxt.infohttps://www.shenxt.info/ Phone: +1 571 267 9283

From: Laurent Gatto @.> Date: Tuesday, January 25, 2022 at 05:24 To: Bioconductor/Contributions @.> Cc: Xiaotao Shen @.>, Mention @.> Subject: Re: [Bioconductor/Contributions] massconverter (Issue #2482)

Hi @jaspershenhttps://github.com/jaspershen - I am reviewing your packages and wanted to make sure I don't miss any. I'm aware of massconverter and masstools (issue #2481https://github.com/Bioconductor/Contributions/issues/2481); anything else?

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/2482#issuecomment-1021179259, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADEJWWNOJCMOJT44PKFXNTDUX2P77ANCNFSM5LQPZRJQ. You are receiving this because you were mentioned.Message ID: @.***>

vjcitn commented 2 years ago

The vignettes of massconverter are seemingly designed for pkgdown. I find it difficult to navigate them through help.start(). It is specifically unclear whether the user HAS TO use docker with this package. Please write an overview.Rmd that explains concisely what the package does and what the user must do to use the package. Note that the vast majority of packages in Bioconductor do not require docker client usage. If it is in fact mandatory for your package we need to discuss this further.

vjcitn commented 2 years ago

This is all nice but not relevant for a Bioconductor submission:

massc

Review cannot begin until the vignettes are more consistent with the Bioconductor guidelines. Thanks.

vjcitn commented 2 years ago

Please add prefixes to your vignette titles so they are ordered meaningfully in the page generated by help.start()

bioc-issue-bot commented 2 years ago

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bioc-issue-bot commented 2 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, 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. This link will be 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/massconverter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lgatto commented 2 years ago

Hi @jaspershen - here are a few comments to consider before going to a detailed review:

  1. The vignettes need to be amended to fit a Bioconductor package rather than a pkgdown webpage. This is also true for masstools.
  2. There needs to be an example that is actually run. Currently, the code in the vignette that is supposed to convert raw data isn't evaluated (even though there's a RAW file in the data), and actually fails. It isn't clear if the data files need to be in a specific directory (looks like based on the error message), but it wasn't obvious to me and I couldn't find the relevant info in the manual page.
  3. Finally, and most importantly, I am not convinced that massconverter is a good fit for Bioconductor. That doesn't mean that the package isn't useful, of course; it is an interface to pull and run docker container to convert raw MS data directly from R, but it doesn't really address any goal of the Bioconductor project (analysis and comprehension of biological data). Tagging @lshep and @vjcitn to see what they think.
vjcitn commented 2 years ago

Sorry to have missed this. I would tend to agree that software that requires docker is out of scope for Bioconductor at present. I will look more closely at massconverter and comment further.

vjcitn commented 2 years ago

Is massconverter per se essential to other packages in the tidymass ecosystem? I think its reliance on docker client separates it from all other bioconductor packages to date. I don't want to be technologically restrictive but I think reliance on something like https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses is very unappealing.

vjcitn commented 2 years ago

@jaspershen will you be responding on these review issues? @lshep

jaspershen commented 2 years ago

Hi@vjcitn. Thank you for the noticement. I will respond very this week. Sorry for the late reply! Thank you!

bioc-issue-bot commented 2 years ago

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.