(inactive) granulator

[BioVinci]

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• Repository: https://github.com/Novartis/granulator

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[bioc-issue-bot]

Hi @BioVinci

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: granulator
Type: Package
Title: A Framework for joint application of deconvolution methods 
Version: 0.99.0
Author: Vincent Kuettel [aut, cre],
    Sabina Pfister [aut]
    Enrico Ferrero [aut]
Maintainer: Vincent Kuettel <vinc.kuettel@gmail.com>
Description: granulator is an R package that provides a unified testing interface
    to rapidly run and benchmark multiple state-of-the-art deconvolution methods
    simultaneously.
Depends: R (>= 3.6.0),
    Biobase,
    BiocManager,
    broom,
    checkmate,
    DeconRNASeq,
    devtools,
    dplyr,
    dtangle,
    epiR,
    e1071,
    ggplot2,
    limSolve,
    magrittr,
    MASS,
    methods,
    nnls,
    parallel,
    pheatmap,
    purrr,
    readr,
    rlang,
    scales,
    stats,
    SummarizedExperiment,
    tibble,
    tidyr,
    utils,
    viridis,
    xbioc
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
biocViews: RNASeq, GeneExpression, DifferentialExpression, Transcriptomics, StatisticalMethod, Regression
Imports:

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[BioVinci]

Hi, I opened the issue a while ago but the package is still awaiting moderation. SSH keys webhooks were added to the Github account. Looking forward to your response.

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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: "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.

[lshep]

Bioconductor only allows dependencies to be from CRAN/Bioconductor. It does not appear that xbioc is on CRAN or Bioconductor. You will either need to remove this dependency or have the maintainers of that package put it in CRAN or Bioconductor.

[BioVinci]

xbioc was taken out from the package. Package can now be build without errors or warnings

[lshep]

Please make sure your webhook is initialized https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook

Then please bump the version in your DESCRIPTION to trigger a new build report.

[bioc-issue-bot]

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

a880db3 fixed error in plt_corr_boxplot.R 144f5d4 increased version to 0.99.1

[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: "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:

2491d18 version 0.99.2: fixed vignette warning

[bioc-issue-bot]

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

449e2bf fixed error due to Rproj file

[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: "skipped, 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]

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: "skipped, 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:

c1946b1 adress vignette error

[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: "skipped, 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:

3f5f2f6 version 0.99.5

[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: "skipped, 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.

[lshep]

Assume the Bioconductor builders already have the package installed. Don't try to install the package.
This

library(devtools)
devtools::install('C:/Users/admin/Documents/Novartis/granulator_github_Novartis/pkg/granulator')
#roxygen2::roxygenise()

Should be removed completely.

[bioc-issue-bot]

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

403f4cc removed package installation from README

[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". 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:

4cbcf74 bump

[BioVinci]

thanks! I wasn't aware of that.

When using the command check() I still receive the following warning: Vignettes with missing or empty \VignetteIndexEntry: vignette.Rmd However, the command build_vignettes() runs sucessfully and creates the directories doc/ and inst/. doc and Meta were added to .Rbuildignore as indicated in the description. What am I missing here?

[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". 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.

[BioVinci]

When using the command check() I still receive the following warning: Vignettes with missing or empty \VignetteIndexEntry: vignette.Rmd However, the command build_vignettes() runs sucessfully and creates the directories doc/ and inst/. doc and Meta were added to .Rbuildignore as indicated in the description. Is there a standard way to fix this warning?

[hpages]

Hi @BioVinci,

I think the problem is that your \VignetteIndexEntry spans more than 1 line:

  %\VignetteIndexEntry{granulator: rapid prototyping and benchmarking of methods for *in silico* deconvolution
  of bulk RNA-seq data}

Try this instead:

  %\VignetteIndexEntry{granulator: rapid prototyping and benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data}

Cheers, H.

[bioc-issue-bot]

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

3d95375 removed warnings

[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". 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:

340b316 update R dependency according to warining

[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.

[hpages]

Looks good. Should I start reviewing?

[BioVinci]

Yes please, that would be great.

[BioVinci]

Looks good. Should I start reviewing?

Have you had a chance to review the package?

[hpages]

Will do ASAP. Sorry for the delay.

[BioVinci]

Will do ASAP. Sorry for the delay.

Thanks a lot!

[hpages]

Hi,

• A major issue with the package is that the central function deconvolute() is actually never called or tested. This makes the software very fragile and unreliable.

• Running the granulator::deconvolute() call that is shown in the vignette generates more than 50 warnings. If that is indeed expected, some explanation needs to be provided. Otherwise, the user might get the impression that something went wrong.

• The following R CMD check NOTEs should not be ignored:

  * checking dependencies in R code ... NOTE
  Packages in Depends field not imported from:
    ‘Biobase’ ‘BiocManager’ ‘SummarizedExperiment’ ‘checkmate’ ‘devtools’
    ‘methods’ ‘readr’
    These packages need to be imported from (in the NAMESPACE file)
    for when this namespace is loaded but not attached.

  Consider adding
    importFrom("grDevices", "colorRampPalette")
  to your NAMESPACE file.

• R CMD BiocCheck produces 10 notes. That's a lot! Please take care of as many of them as you can.

• About the Depends field: I see many packages there (and R CMD check gives you a NOTE about this) but it's not clear to me that you need them all. For example I see that you depend on SummarizedExperiment but I can't figure out where you use it and for what. It's important that you depend only on packages that you actually use in your package. Also please note that packages that you only use in the vignettes or examples (e.g. BiocManager) should be in Suggests rather than Depends.

• Table 1 doesn't render properly in the HTML version of the vignette.

• The signature matrix and bulk RNA-seq data are both conceptually matrices. Any reason you store them in a data.frame instead of a matrix? In addition to the satisfaction of using the right container for the right concept, an immediate and very concrete benefit of using a matrix here is that it allows the user to use matrix summarization functions like rowSums() or colMeans() directly on it.

• Please use the left arrow (<-) instead of = for assignments.

Thanks!

[hpages]

Hi @BioVinci , do you intend to follow up on this submission? Thanks!

[BioVinci]

Hi @hpages

Thanks for following up. Yes, I am actually working on the package right now and will push soon.

[BioVinci]

Hi @hpages ,

I adressed the errors, warnings and notes. I was able to adress most of them, however the following remains:

no visible binding for global variable

Hope this issue won't matter. Best regards

[lshep]

Please make sure to do a version bump so that there is a new build report for review

[BioVinci]

I was inconsistent with the version numbering. The last version was 0.99.9.1, and now I used 0.99.99 However, the version bump label was not removed. Is there a way to reset the version label?

[lshep]

I'm not sure I'll have to look into it. in the meantime I'll kick off a manual build so @hpages can review. The manual build should post shortly.

[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: "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.

[BioVinci]

The error was due to the missing subscription to the bioconductor mailinglist. I have subsubscript in the meantime.

[hpages]

Please bump the version of the package to trigger a new build/check. Thanks!

[bioc-issue-bot]

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

d4f9291 version bump

[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.

[hpages]

Hi @BioVinci ,

Thanks for your efforts to improve the package. Please make sure to address all the issues I reported in my initial feedback. I'll summarize what still requires your attention:

1. The granulator::deconvolute() call that you show in the vignette still generates many WARNING: reaching max number of iterations. It also prints many screens of output which is poorly formatted. Such level of verbosity is not particularly useful. Please revisit what the function displays. Make sure it is useful, compact, and properly formatted. Note that you should use message() instead of print() or cat() to display the output so the user can suppress it by wrapping the call to the function in suppressMessages().

2. R CMD check note importFrom("grDevices", "colorRampPalette") is still present.

3. R CMD BiocCheck still produces a lot of notes.

4. Table 1 still doesn't render properly in the HTML version of the vignette.

5. Please use the left arrow (<-) instead of = for assignments.

Other things:

6. Your README.md file is out of sync with the current version of the package (e.g. the output of sessionInfo() still shows SummarizedExperiment). Note that copying/pasting the output of commands in the file is a bad idea as the static output is very likely to become out of sync again the next time your modify your package.

7. Also please remove vignette.html from the vignettes/ folder (this is also out of sync with the current package). The HTML version of the vignette is automatically generated by R CMD build and included in the resulting source tarball so does not belong to the package source tree.

Thanks, H.

[bioc-issue-bot]

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

5121ec6 initiate version bump

[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: "ABNORMAL". 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:

c630e7f initiate version bump