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PloidyPeaks #3567

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MicroStatsLab opened this issue Sep 18, 2024 · 15 comments
Open

PloidyPeaks #3567

MicroStatsLab opened this issue Sep 18, 2024 · 15 comments
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ERROR pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean

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@MicroStatsLab
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Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

  • [ x] I understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
    general public.

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    instructions. My package is consistent with the Bioconductor
    Package Guidelines.

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    Bioconductor may retain use of package name.

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    is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS.
    Passing these checks does not result in automatic acceptance. The
    package will then undergo a formal review and recommendations for
    acceptance regarding other Bioconductor standards will be addressed.

  • [ x] My package addresses statistical or bioinformatic issues related
    to the analysis and comprehension of high throughput genomic data.

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@bioc-issue-bot
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Hi @MicroStatsLab

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: PloidyPeaks
Title: Peak Detection Algorithm For Flow Cytometry Data
Version: 0.99.0
Authors@R: c(
    person("Margot", "Henry", email="[email protected]", role = c("aut", "cre")),
    person("Aleeza", "Gerstein", email="[email protected]", role=c("aut", "ths")),
    person("Maxime", "Turgeon", email="[email protected]", role="ctb"),
    person("Caitlin", "Kostna", email="[email protected]", role="ctb"),
    person("Leanne", "Von Giese", role="ctb"))
Description: PloidyPeaks is a package to quantify population-level genome size variation from flow cytometry data without requiring user input.
	The package uses peak detection algorithms and flow cytometry population definitions to quantify sub-populations.
	The workflow is separated into three parts: 1) gating and 2) peak detection, 3) dataset output.
	Built-in visualizations options are included throughout.
biocViews: FlowCytometry, PeakDetection, Visualization
Imports: AzureRMR,
    AzureStor,
    BiocFileCache,
    cowplot,
    data.table,
    dplyr,
    flowCore,
    flowTime,
    ggcyto,
    ggplot2,
    gridExtra,
    here,
    htmltools,
    kableExtra,
    magrittr,
    moments,
    patchwork,
    purrr,
    scorepeak,
    sqldf,
    tcltk,
    tidyr,
    tidyverse,
    tools,
    vctrs,
    xpectr,
    zoo
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Suggests: 
    rmarkdown,
    knitr,
    testthat
VignetteBuilder: knitr

@bioc-issue-bot bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Sep 18, 2024
@lshep lshep added the pre-check passed pre-review performed and ready to be added to git label Sep 23, 2024
@bioc-issue-bot
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Your package has been added to git.bioconductor.org to continue the
pre-review process. A build report will be posted shortly. Please
fix any ERROR and WARNING in the build report before a reviewer is
assigned or provide a justification on why you feel the ERROR or
WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting
up remotes to push to git.bioconductor.org. All changes should be
pushed to git.bioconductor.org moving forward. It is required to push a
version bump to git.bioconductor.org to trigger a new build report.

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

@bioc-issue-bot bioc-issue-bot added pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean and removed 1. awaiting moderation submitted and waiting clearance to access resources pre-check passed pre-review performed and ready to be added to git labels Sep 24, 2024
@bioc-issue-bot
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Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): PloidyPeaks_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/PloidyPeaks to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@MicroStatsLab
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MicroStatsLab commented Sep 28, 2024 via email

@lshep
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lshep commented Sep 30, 2024 •
edited
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I also cannot reproduce. I will kick off a new build manually to see if it clears up. But yes there is internet when running the builds

@bioc-issue-bot
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Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): PloidyPeaks_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/PloidyPeaks to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@MicroStatsLab
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MicroStatsLab commented Sep 30, 2024 via email

@lshep
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lshep commented Sep 30, 2024

I just checked and the listed maintainer email [email protected] does not appear to be registered on [email protected]. I'm not sure off hand what could be going on with the file recognition but will try to investigate further in the next few days.

@MicroStatsLab
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MicroStatsLab commented Sep 30, 2024 via email

@lshep
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lshep commented Sep 30, 2024

There seems to be a PloidyPeaks-Ex.timings that gets copied/created in the raw_data folder. I'm not sure why this file would get created here even if it was the last example to run. @jwokaty / @hpages any ideas on this one?

@lshep
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lshep commented Oct 7, 2024

@MicroStatsLab the email is hidden for privacy when you type so I don't know what you are comparing too but the DESCRIPTION maintainer (as designated with the 'cre') is checked for mailing list and support site.

We are still investigating my comment above which is causing the ERROR on the builder

@jwokaty
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jwokaty commented Oct 7, 2024 •
edited
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@MicroStatsLab I'm able to produce the error on my laptop by adding the --timing check on the binary: R CMD check --timings PloidyPeaks_0.99.0.tar.gz . When running R CMD check, I see messages that the working directory is being changed. I wonder if that's how PloidyPeaks-Ex.timings gets in raw_data. It might be better to avoid changing the working directory to prevent side effects even if it's not the cause. I would defer to @lshep for advice. Maybe @MicroStatsLab you can use this to troubleshoot?

@MicroStatsLab
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MicroStatsLab commented Oct 8, 2024 via email

@lshep
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lshep commented Oct 11, 2024

@MicroStatsLab Just wanted to make sure you saw @jwokaty comment above about the issue going on. perhaps copying needed files to a user specified (and in the cases of vignette/examples) temporary directory might be a better approach. Perhaps tracking what the working directory is before changing directory with a getwd and resetting at the end might also help

@MicroStatsLab
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MicroStatsLab commented Oct 11, 2024 via email

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@jwokaty @bioc-issue-bot @lshep @MicroStatsLab