Closed jaspershen closed 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
Should depend on R >= 4.2. No vignettes folder. Seems to be a pkgdown site source. Please read developer guidelines.
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!
Hi. Just changed R > 4.2 and ran well. Thanks.
-- 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?
Thanks @vjcitn . Just fixed the bug in one function and now the warnings have gone! Thank you!
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?
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: @.***>
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.
This is all nice but not relevant for a Bioconductor submission:
Review cannot begin until the vignettes are more consistent with the Bioconductor guidelines. Thanks.
Please add prefixes to your vignette titles so they are ordered meaningfully in the page generated by help.start()
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
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.
Hi @jaspershen - here are a few comments to consider before going to a detailed review:
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. 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.
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.
@jaspershen will you be responding on these review issues? @lshep
Hi@vjcitn. Thank you for the noticement. I will respond very this week. Sorry for the late reply! Thank you!
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.
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