tartare - biocViews: ExperimentData, MassSpectrometryData

[cpanse]

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[bioc-issue-bot]

Hi @cpanse

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: tartare
Type: Package
Title: Raw ground spectra recorded on Thermo Fisher Scientific mass
    spectrometers
Version: 0.0.1
Authors@R: c(person(given = "Christian", family = "Panse",
    email = "cp@fgcz.ethz.ch", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-1975-3064")),
    person(given = "Tobias", family = "Kockmann",
    email = "Tobias.Kockmann@fgcz.ethz.ch", role = "aut", 
    comment = c(ORCID = "0000-0002-1847-885X")))
Depends: R (>= 3.6),
    AnnotationHub (>= 2.16),
    ExperimentHub (>= 1.0)
Imports:
    utils
Suggests:
    knitr,
    testthat
Description: provides raw files (size=215MBytes)recorded on different Liquid
  Chromatography Mass Spectrometry (LC-MS) instruments. All included MS
  instruments are manufactured by Thermo Fisher Scientific and belong to the
  Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their
  common origin and shared hardware components (e.g. Orbitrap mass analyser),
  the above instruments tend to write data in different "dialects" in a shared
  binary file format (.raw). The intention behind tartare is to provide complex
  but slim real-world files that can be used to make code robust with respect
  to this diversity. In other words, it is intended for enhanced unit testing.
  The package is considered to be used with the
  rawDiag package (Trachsel, 2018 <doi:10.1021/acs.jproteome.8b00173>) and the
  Spectra MsBackends.
URL: https://github.com/cpanse/tartare
BugReports: https://github.com/cpanse/tartare/issues
Encoding: UTF-8
NeedsCompilation: no
biocViews: ExperimentData, MassSpectrometryData
RoxygenNote: 6.1.1
License: GPL-3
VignetteBuilder: knitr
Collate: 
    'zzz.R'

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[bioc-issue-bot]

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

8e60133 Update DESCRIPTION Adding a Web Hook

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

374f0f5 Update DESCRIPTION * ERROR: Maintainer must regis...

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

48f94fe Update DESCRIPTION managed to subscribe to https:...

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

fc7c9f3 fix md5
7cdaa85 Merge branch 'master' of github.com:cpanse/tartare
67adcc8 version inc

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

de00e18 vignette cosmetics

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

918a7e2 Update DESCRIPTION

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[cpanse]

@lshep, I continue once all metadata are available through ExperimentHub(). Am I on the right track?

R> library(ExperimentHub)
R> eh <- ExperimentHub(); 
snapshotDate(): 2019-09-25
R> query(eh, "tartare")
ExperimentHub with 0 records
# snapshotDate(): 2019-09-25 
R> 

[bioc-issue-bot]

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

1b1d814 version pump

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Dear Package contributor,

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[bioc-issue-bot]

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

222e4c7 initial tartar.R
a5e5357 version inc

[bioc-issue-bot]

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, ERROR".
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Or it may mean that there is a problem with the build system itself.

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

b62e77b version inc

[bioc-issue-bot]

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".
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[cpanse]

Hopefully that fixed that issue - In an effort to try and get this package into this release please see the other comments concerning your package. Hopefully they can be fixed so this package can be added and released with Bioc 3.9

yes it fixed the md5 issue. thanks!

README

* [x]  (optional) include Bioconductor installation instructions.

DONE

vignette

* [ ]  Perhaps most of this seems like data preparation and should be in the
  `inst/scripts` desribing how the data was made. Please move this file to
  `inst/scripts`

most of the things are instrument configurations

* [ ]  I recommend still having an official vignette `tartare.Rmd` It is much
  more intuitive for a user to do `vignette("tartare")` that shows the
  ExperimentHub commands to download and access data

fully agree the instrument setups are the most important part.

R / man

* [x ]  I think you should be very explicit that running the getFilename will
  download the files associate with the package. So the users are aware there will
  be a download.

done

* [x ]  Please create a different R file to contain package code `zzz.R` file is
  generally only associated with code for `onLoad/onAttach`.

right; done

general

As it could affect vignette and R/man

* [ ]  Would there be a usecase to show the file names associated with this
  without downloading?

the package is meant to be used together with the Spectra and MsBackendRawfilereader.
I added a picture in the README @jorainer presented today on the #SWEMSA conference.

exec

* [x]  Please remove and then `.gitignore` this directory. Important for you but
  not for anyone else.

DONE

Cheers

Iam going to fix the warnings later today.

best wishes,C

[lshep]

Awesome. I'll wait for the final corrections of the warnings but I don't see anything else preventing acceptance.

[bioc-issue-bot]

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

60bb902 version inc
d0aded6 eliminate warnings

[lshep]

Hang tight - we are experiencing some delay with the builder. We are in the process of fixing it.

[bioc-issue-bot]

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, 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]

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

434709c windows warnings and version inc

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

[cpanse]

Awesome. I'll wait for the final corrections of the warnings but I don't see anything else preventing acceptance.

DONE. no more warnings. thanks.
C

[bioc-issue-bot]

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]

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/cpanse.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

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

https://bioconductor.org/checkResults/

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

https://bioconductor.org/packages/tartare

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.