zitools submission

[cmeyring]

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

• Repository: https://github.com/kreutz-lab/zitools

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[bioc-issue-bot]

Hi @cmeyring

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: zitools
Title: Analysis of zero-inflated count data 
Version: 0.99.0
Authors@R: 
    person("Carlotta", "Meyring", , "carlotta.meyring@uniklinik-freiburg.de", role = c("aut", "cre"),
 comment = c(ORCID = "0009-0000-6201-7615"))
Description:
  zitools allows for zero inflated count data analysis by either using 
  down-weighting of excess zeros or by replacing an appropriate proportion of 
  excess zeros with NA. Through overloading frequently used statistical 
  functions (such as mean, median, standard deviation), plotting functions 
  (such as boxplots or heatmap) or differential abundance tests, it allows a 
  wide range of downstream analyses for zero-inflated data in a less biased 
  manner.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports: phyloseq,
pscl, 
ggplot2,
MatrixGenerics,
SummarizedExperiment,
stats, 
VGAM, 
matrixStats, 
tidyr,
tibble,
dplyr,
DESeq2,
reshape2, 
RColorBrewer,
magrittr, 
BiocGenerics,
graphics,
utils
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    testthat (>= 3.0.0), 
    tidyverse
Config/testthat/edition: 3
Collate: 
    'data.R'
    'globals.R'
    'ziMain.R'
    'helper.R'
    'inherited_functions.R'
    'plots.R'
    'utils.R'
Depends: R (>= 4.3.0), 
methods
VignetteBuilder: knitr
biocViews: Software, StatisticalMethod
LazyData: true

[vjcitn]

THanks for your submission. There's a lot going on here that should be remedied before review. First, I saw

Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-weights.R:27:5'): Compare results for sd, mean, rowMeans2 and colMeans2 on Zi object with weights equal to 1 to the case where Zi@inputcounts is used ──
  unname(rowMeans2(ZiW1)) (`actual`) not identical to rowMeans2(ZiW1@inputcounts) (`expected`).

  `names(actual)` is absent
  `names(expected)` is a character vector ('1', '2', '3', '4', '5', ...)
  ── Failure ('test-weights.R:28:5'): Compare results for sd, mean, rowMeans2 and colMeans2 on Zi object with weights equal to 1 to the case where Zi@inputcounts is used ──
  unname(colMeans2(ZiW1)) (`actual`) not identical to colMeans2(ZiW1@inputcounts) (`expected`).

  `names(actual)` is absent
  `names(expected)` is a character vector ('1', '2', '3', '4', '5', ...)

  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... NONE
  'my-vignette.Rmd' using 'UTF-8'... OK

and that should be corrected. Additionally, don't call your vignette "my-vignette.Rmd". Please use a package-oriented name. There is a download.file in the vignette, but the file is in the github repo and is small so it could just be placed in /data. In general we don't have downloads to working folder but ask that developers put retrieved artifacts in BiocFileCache, and the retrieval needs to be from a durable source, possibly ExperimentHub. There should be no .Rproj file in the submitted repo.

[vjcitn]

hi do u plan on revising?

[cmeyring]

Hi, yes I’ll revise beginning from next week. Von meinem iPhone gesendetAm 12.09.2023 um 20:41 schrieb Vince Carey ***@***.***>: hi do u plan on revising? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

[cmeyring]

Hello Vince,

thanks for the comment. I've updated the submitted repository, but I still have two questions: When I am running the tests of the package I don't get a error message. What command did you use to run the tests?
And for the download.file, it is a dataset from another working group. I am probably not allowed to store the file in data, right? Therefore, I added the download.file.

Thanks in advance

[vjcitn]

I am working with the checkout

(base) %vjc> cd zitools
(base) %vjc> git log
commit fef06599d56709e7676c02a761926c9a051fdd52 (HEAD -> main, origin/main, origin/HEAD)
Author: cmeyring <carlotta-meyring@web.de>
Date:   Mon Sep 18 11:46:53 2023 +0200

    remove .Rproj

I am using

R version 4.3.1 Patched (2023-08-27 r85021) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

I get

  Running ‘testthat.R’
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-weights.R:27:5'): Compare results for sd, mean, rowMeans2 and colMeans2 on Zi object with weights equal to 1 to the case where Zi@inputcounts is used ──
  unname(rowMeans2(ZiW1)) (`actual`) not identical to rowMeans2(ZiW1@inputcounts) (`expected`).
  
  `names(actual)` is absent
  `names(expected)` is a character vector ('1', '2', '3', '4', '5', ...)
  ── Failure ('test-weights.R:28:5'): Compare results for sd, mean, rowMeans2 and colMeans2 on Zi object with weights equal to 1 to the case where Zi@inputcounts is used ──
  unname(colMeans2(ZiW1)) (`actual`) not identical to colMeans2(ZiW1@inputcounts) (`expected`).
  
  `names(actual)` is absent
  `names(expected)` is a character vector ('1', '2', '3', '4', '5', ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
  'zitools_tutorial.Rmd' using 'UTF-8'... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE

with R CMD build followed by R CMD check on

-rw-r--r--  1 vincent vincent   179407 Sep 30 23:41 zitools_0.99.0.tar.gz

[cmeyring]

Hello Vince,

the new version is pushed and I should work now.

[lshep]

There are still ERROR when we run this. Please run R CMD check with the most recent version of R and updated versions of Bioconductor packages

  Running ‘testthat.R’
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-weights.R:27:5'): Compare results for sd, mean, rowMeans2 and colMeans2 on Zi object with weights equal to 1 to the case where Zi@inputcounts is used ──
  unname(rowMeans2(ZiW1)) (`actual`) not equal to rowMeans2(ZiW1@inputcounts) (`expected`).
  
  `names(actual)` is absent
  `names(expected)` is a character vector ('1', '2', '3', '4', '5', ...)
  ── Failure ('test-weights.R:28:5'): Compare results for sd, mean, rowMeans2 and colMeans2 on Zi object with weights equal to 1 to the case where Zi@inputcounts is used ──
  unname(colMeans2(ZiW1)) (`actual`) not equal to colMeans2(ZiW1@inputcounts) (`expected`).
  
  `names(actual)` is absent
  `names(expected)` is a character vector ('1', '2', '3', '4', '5', ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted

[lshep]

You also cannot store data on github or personal spaces like dropbox. Example data for vignettes, man pages, and tests should be included with the package and/or using the ExperimentHub.

[lshep]

@cmeyring any update?

[bioc-issue-bot]

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.

[cmeyring]

Hello,
is it possible to reopen this issue? I was in between Master Thesis, PhD stages, and therefore, didn't have the time to adress the issues. However they are adressed now and I would like to reopen the issue, if that is possible.

Thanks in advance

[lshep]

Before this submission moves on in the review process:

• remove the git committed zip of the package zitools_0.0.0.9000.zip

• Please remove Readme.txt in R/ directory. The R directory should contain
  code files only.

• Please run R CMD build, R CMD check and R CMD BiocCheck. There are still
  ERROR's when running R CMD check and numerous Warnings and Notes from
  BiocCheck.

[cmeyring]

Everything should be fine now, R CMD build and check run without any errors and Warnings. BiocCheck also runs without any errors, however one warning occurrs to a set.seed usage which is needed in that particular function. However, at the end of the function the seed is reset to its old random seed.

[bioc-issue-bot]

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.

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[bioc-issue-bot]

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: "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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): zitools_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
git@git.bioconductor.org:packages/zitools to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[cmeyring]

The Warning when running BiocCheck is due to the usage of set.seed. However, it is needed when randomly dividing a matrix into smaller blocks to ensure a reproducible process. After the usage of the function, the seed is set back to its old seed before.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

[Kayla-Morrell]

@cmeyring - Thank you for submitting to Bioconductor. Please see the initial review of
the package below. The required changes must be made while the suggested
changes do not have to be (though we strongly encourage them). Comment back
here with updates that have been made and when the package is ready for a
re-review.

General package development

• REQUIRED: The README file should also provide Bioconductor installation instructions.

DESCRIPTION

• SUGGESTION: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field and structure it as a full paragraph.
• REQUIRED: Update R version dependency from 4.3.0 to 4.4.0.
• SUGGESTION: Provide the 'URL' field in DESCRIPTION.

NAMESPACE

• SUGGESTION: Consider adding importFrom("stats", "predict").

NEWS

• SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.

CITATION

• SUGGESTION: Checking CITATION. CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'.

Vignette

• SUGGESTION: We encourage the use of BiocStyle for formatting.
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• SUGGESTION: We encourage the use of table of contents.

Man pages

• SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?zitools.
• REQUIRED: All exported objects need to have runnable examples in the man page.

R code

• SUGGESTION: Checking R code for possible problems.
  calcWeights: no visible global function definition for predict
  omit_str_zero: no visible global function definition for predict
• REQUIRED: Avoid use of direct slot access with @. Accessor methods should be created and utlizied instead.
• REQUIRED: Avoid 1:...; use seq_len() or seq_along().
• REQUIRED: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 time).
• SUGGESTION: For formatting reasons, consider shorter lines. There are 72 lines that are > 80 characters long.
• SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 702 lines that are not.

Best,
Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: cf2da098373546c4ee561431b769c49870af6221

[bioc-issue-bot]

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: "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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): zitools_0.99.1.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
git@git.bioconductor.org:packages/zitools to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 859a17096bdc3bcecef4ebe296b4a845ae6ffc32

[bioc-issue-bot]

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: "WARNINGS, 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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): zitools_0.99.2.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
git@git.bioconductor.org:packages/zitools to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[cmeyring]

Hey Kayla,
thank you for the comments.
I pushed the updated package. However, there is an error when building on MacOS. I think this might be because there is not yet R.4.4 on merida1 (macOS) and therefore the R CMD build fails, as R.4.4 is required for the package.

I further adressed all the comments. However, I couldn't adress all, as stated below.

• REQUIRED: The README file should also provide Bioconductor installation instructions.

• SUGGESTION: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field and structure it as a full paragraph

• REQUIRED: Update R version dependency from 4.3.0 to 4.4.0

• SUGGESTION: Provide the 'URL' field in DESCRIPTION

• SUGGESTION: Consider adding importFrom("stats", "predict").

• SUGGESTION: Checking R code for possible problems.

adding importFrom("stats", "predict") is not working because the predict function is used from the pscl package and as I understood it is nor correctly defined as a method for the generic function stats::predict

• SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.

• SUGGESTION: Checking CITATION. CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'.

There is not yet a submitted preprint/publication. When the preprint is submitted the citation file will be added.

• SUGGESTION: We encourage the use of BiocStyle for formatting.

• REQUIRED: The 'Installation' section should show users how to download and load the package from Bioconductor. This code chunk should include eval = FALSE.

• SUGGESTION: We encourage the use of table of contents.

• SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?zitools.

• REQUIRED: All exported objects need to have runnable examples in the man page.

• REQUIRED: Avoid use of direct slot access with @. Accessor methods should be created and utlizied instead.

• REQUIRED: Avoid 1:...; use seq_len() or seq_along().

• REQUIRED: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 time).

The suppressed warnings message is used in the ziMain function because the class of the count matrix of the phyloseq object is an otu_table, however we extract the count matrix and define it as a matrix which is perfectly fine at that step, however, it will produce a warning and therefore, we decided to supress the warning as we only need the count matrix of the class matrix.

• SUGGESTION: For formatting reasons, consider shorter lines. There are 72 lines that are > 80 characters long.

• SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 702 lines that are not.

Best, Carlotta

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f45d497ccbf72259c0d37c386d7035b17000471

[bioc-issue-bot]

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: "WARNINGS, 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.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): zitools_0.99.3.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
git@git.bioconductor.org:packages/zitools to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

merida1 was run in error -- please ignore the error in the build report and proceed with the clean build displayed on linux

[Kayla-Morrell]

@cmeyring - Thank you for making the necessary changes. I have looked everything over and it all looks good. I'm more than happy to accept the package.

Best,
Kayla

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

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[lshep]

The default branch of your GitHub repository has been added to Bioconductor's
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https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

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