fomotis commented 3 years ago

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

Repository: https://github.com/fomotis/cyanoFilter

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

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bioc-issue-bot commented 3 years ago

Hi @fomotis

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: cyanoFilter
Type: Package
Title: Phytoplankton Population Identification using Cell Pigment and 
    Complexity Information
Version: 0.99.4
Authors@R: c(person("Oluwafemi", "Olusoji", 
    email = "oluwafemi.olusoji@uhasselt.be", 
    role = c("cre", "aut")),
    person("Aerts", "Marc", email = "marc.aerts@uhasselt.be", role = "ctb"),
    person("Delaender", "Frederik", email = "frederik.delaender@unamur.be", 
    role = "ctb"),
    person("Neyens", "Thomas", email = "thomas.neyens@uhasselt.be", 
    role = "ctb"),
    person("Spaak", "jurg", email = "jurg.spaak@unamur.be", role = "aut"))
Description: An approach to filter out and/or identify phytoplankton cells from 
    all particles measured via flow cytometry pigment and cell complexity 
    information. It does this using a sequence of one-dimensional gating on 
    predefined channels measuring certain pigmentation and complexity. The package is especially
    tuned for cyanobacteria, but will work fone for plankton communities that consist of specialists.
URL: https://github.com/fomotis/cyanoFilter
BugReports: https://github.com/fomotis/cyanoFilter/issues
Depends: R(>= 4.1.0), Biobase(>= 2.48.0)
Imports: 
    flowCore(>= 2.0.1),
    flowDensity(>= 1.22.0),
    ggplot2(>= 3.3.2),
    GGally(>= 2.0.0),
    graphics(>= 4.0.1),
    grDevices(>= 4.0.1),
    methods(>= 4.0.1),
    stats(>= 4.0.1),
    utils(>= 4.0.1)
License: MIT + file LICENSE
biocViews: FlowCytometry, Clustering, OneChannel
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: 
    dplyr,
    magrittr,
    knitr,
    stringr,
    rmarkdown,
    tidyr
VignetteBuilder: knitr
Config/testthat/edition: 3

bioc-issue-bot commented 3 years ago

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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.

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bioc-issue-bot commented 3 years ago

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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

fomotis commented 3 years ago

The errors have been corrected, and the changes have been uploaded to Bioconductor upstream.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a95de6d4dc4bc10e6e7c81fdca21263a13f43292

bioc-issue-bot commented 3 years ago

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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 3 years ago

Hi Olusoji, @fomotis

Thank you for your submission. Please see the review below.

Best regards, Marcel

cyanoFilter #1917

Are you depending on other packages that are using Biobase? Otherwise it is recommended to use SummarizedExperiment. Some of my feedback here is based on that assumption that Biobase is no longer used. This may be different if your workflow uses Biobase extensively. Consider separating the plotting and infrastructure functionality into different packages. This will avoid the growth of dependencies on packages that only use the infrastructure classes in your package.

DESCRIPTION

Can you provide more information about the Config/testthat/edition field?
Is the Biobase dependency necessary? See note above.
Some package version dependencies are overkill. You can remove them for the internal packages such as graphics, methods, stats, utils, and grDevices because those are tied to the R version.
Unless you are using a specific feature in that version of the package, you don't need to specify the version number dependency.

NAMESPACE

For package consistency, use either camelCase or snake_case function naming conventions.
Looks good.

vignettes

(optional) It is easier to review and maintain a vignette whose text is not flowing off the side of the page. Keep the total column width to 80 characters.
Avoid loading the tidyverse because it is not listed in the Suggests field and the package loads a boatload of unnecessary dependencies for the vignette. Consider only loading dplyr.

R

Set your default values to the intended value, e.g., when proportion = NULL, the function changes it to proportion = 1. Why not have 1 as the default value?
Avoid accessing elements of your class with the @ symbol. Create a formal interface to your class.
Make sure that your logic makes sense, e.g., in R/debris_nc.R there is an if else statement that appears to do the same thing in both conditions.
Isolate code differences within if else logic and only change the parameter that changes, e.g., pks <- if (lp2 >= 2) min(pks) else pks in R/debris_nc.R. This would reduce the number of lines of code and places where you could have bugs / errors.
There seems to be a typo in line 46 of R/good_measurement.R. It appears that the code should be !is.null(mxd_cellpML)
I would recommend an alternative name to the exprs function and slot name in your class because it is considered legacy code for extracting and storing an ExpressionSet.
The tag Error does not need to be in your stop calls: see stop("Error:")
It will be confusing to the user to have two new_flowframe functions. Can these be reduced to one?
Avoid using AnnotatedDataFrame and use S4Vectors::DataFrame.
Consider using a different name for your summary method because the arguments do not match the S3 generic. Also, you're combining systems here with S4 and S3 which may confuse users.

Reduce cyclomatic complexity by simplifying these lines for checking inputs in phyto_filter:

} else if(!is.null(pig_channels) & is.null(com_channels)) {

channels <- pig_channels
#gate based on the pigments

} else if(is.null(pig_channels) & !is.null(com_channels)) {

channels <- com_channels
#gate based on the complexity channels

} else {

channels <- c(pig_channels, com_channels)
#gate based on the pigments

}

to this:

channels <- c(pig_channels, com_channels)

tests

It is highly recommended that you add tests to your code to keep it robust.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 127f77544fec1845936eef79670c28534fc2ebc7

fomotis commented 3 years ago

Hello. I try to respond to most of the suggestions made in this new version.

However, I am afraid the dependency on Biobase is from my dependencies (flowCore and flowDensity).

bioc-issue-bot commented 3 years ago

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, 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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9ef430b96c75254356f48e5aa22160daffd6cd6e

bioc-issue-bot commented 3 years ago

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, 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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 3 years ago

Hi Olusoji Oluwafemi Daniel @fomotis

That's okay, you can depend on Biobase. I am unable to test the package locally because of an issue with flowDensity:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object 'flowWorkspace.so':
  flowWorkspace.so: undefined symbol: _ZN7cytolib11polygonGate6extendERNS_12MemCytoFrameEf

Please respond the the review line by line and make sure that the objects that you are using in the code are documented or that you are using utils::globalVariables.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  PhytoFilter clusterExtract clusterExtractp debrisNc
  getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
  reducedFlowframe rowNumbers summaries
Undocumented S4 methods:
  generic 'summaries' and siglist 'DebrisFilter'
  generic 'summaries' and siglist 'MarginEvents'
  generic 'summaries' and siglist 'PhytoFilter'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 85d933d77b648152631d68b35f1532607b549cfa

bioc-issue-bot commented 3 years ago

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, skipped". 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2e455921f4e7af16f0118d75c9f3de859b84a971

fomotis commented 3 years ago

@LiNk-NY concerning the error with flow Density. I really don't know why. I face the same with Travis build. However, it works perfectly on windows. Tried it with my partner's Mac as well, and it builds just fine.

bioc-issue-bot commented 3 years ago

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, skipped". 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 3 years ago

Hi Olusoji, @fomotis

Please respond to the review when you're ready. I was able to install flowDensity recently and tried to check the package but got this error because there are some version enforcements that are not necessary in the DESCRIPTION file:

* checking package dependencies ... ERROR
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

Best, Marcel

fomotis commented 3 years ago

Hello Marcel,

Sorry for my delayed response.

I already removed all dependencies in the latest description file. You can have a look. The only restriction has to do with the R version. This is due to a Bioconductor requirement that requires the current R devel version. Is it okay to remove this as well? If it is, then I can easily fix that.

Best, Daniel

LiNk-NY commented 3 years ago

The restriction to the R version is okay to have in the DESCRIPTION. Either way, Bioconductor devel only works with R-devel.

Best, Marcel

fomotis commented 3 years ago

@LiNk-NY

Description

Can you provide more information about the Config/testthat/edition field? Test Field Removed since I didn't really do anything with the testthat package
Is the Biobase dependency necessary? See note above. Yes because of the flowCore dependency
Some package version dependencies are overkill. You can remove them for the internal packages such as graphics, methods, stats, utils, and grDevices because those are tied to the R version. All Package version dependencies have been removed
Unless you are using a specific feature in that version of the package, you don't need to specify the version number dependency. All Package version dependencies have been removed

Vignette

(optional) It is easier to review and maintain a vignette whose text is not flowing off the side of the page. Keep the total column width to 80 characters. Tried to do that in the new version. I am not sure I achieved it though
Avoid loading the tidyverse because it is not listed in the Suggests field and the package loads a boatload of unnecessary dependencies for the vignette. Consider only loading dplyr. Done

R

Set your default values to the intended value, e.g., when proportion = NULL, the function changes it to proportion = 1. Why not have 1 as the default value? Default value now 1
Avoid accessing elements of your class with the @ symbol. Create a formal interface to your class. The @ symbol was not really for my class objects. I have used interfaces everywhere in the package
Make sure that your logic makes sense, e.g., in R/debris_nc.R there is an if else statement that appears to do the same thing in both conditions. I could not find the block of code you were referring to, but I made some changes to this function
Isolate code differences within if else logic and only change the parameter that changes, e.g., pks <- if (lp2 >= 2) min(pks) else pks in R/debris_nc.R. This would reduce the number of lines of code and places where you could have bugs / errors. Done. Thank you for this observation.
There seems to be a typo in line 46 of R/good_measurement.R. It appears that the code should be !is.null(mxd_cellpML). Indeed. thank you again for this observation
I would recommend an alternative name to the exprs function and slot name in your class because it is considered legacy code for extracting and storing an ExpressionSet. There is no exprs function in the package. I merely used exprs function from
The tag Error does not need to be in your stop calls: see stop("Error:") Correctedd all occurrences of this. Thank for this observation
It will be confusing to the user to have two new_flowframe functions. Can these be reduced to one? This is a tough one. The two functions are somewhat different. I just happen to be bad at naming
Avoid using AnnotatedDataFrame and use S4Vectors::DataFrame. This is more about flowCore dependency
Consider using a different name for your summary method because the arguments do not match the S3 generic. Also, you're combining systems here with S4 and S3 which may confuse users. Changed this to summaries() which is entirely S4
Reduce cyclomatic complexity by simplifying these lines for checking inputs in phyto_filter: Done. Thank you for the suggestion

Regards, Daniel

lshep commented 3 years ago

If you have made changes and are ready for a re-review, please remember to bump the version number and push to git.bioconductor.org to trigger a new build report.

fomotis commented 3 years ago

Hello @lshep,

I already did that. I am yet to get another feedback on the current push.

Regards, Daniel

LiNk-NY commented 3 years ago

Hi Daniel, @fomotis Sorry for the delay. I am not seeing the build report for the changes that you've made. Can you try again by bumping the version and pushing to the Bioc git repository? Thank you. I will have a quick look at the changes.

Update: Last commit to Bioc git repo was Mar 11:

commit 2e455921f4e7af16f0118d75c9f3de859b84a971 (HEAD -> master, origin/master, origin/HEAD)
Author: fomotisUhasselt <oluwafemi.olusoji@uhasselt.be>
Date:   Thu Mar 11 16:06:06 2021 +0100

    Solved some Mac and Linux related build issues

Please make sure you are pushing to the right location.

Best, Marcel

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 01cd1ffe41a978e672df32371ccf9318a4b3c8f8

bioc-issue-bot commented 3 years ago

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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 3 years ago

Hi Daniel, @fomotis

Make sure that your logic makes sense, e.g., in R/debris_nc.R there is an if else statement that appears to do the same thing in both conditions. I could not find the block of code you were referring to, but I made some changes to this function

This looks the same in both conditions. It looks like it does not need to be in an if else block.

    if(sum(ch_chlorophyll_peaks$P.h[ch_chlorophyll_peaks$Peaks >= 0] > ph)
       < lp) {

        ch_chlorophyll_peaks2 <- flowDensity::getPeaks(flowframe, 
                                                       ch_chlorophyll,
                                                       tinypeak.removal = ph)

    } else {

        ch_chlorophyll_peaks2 <- flowDensity::getPeaks(flowframe, 
                                                       ch_chlorophyll,
                                                       tinypeak.removal = ph)

    }

I would recommend an alternative name to the exprs function and slot name in your class because it is considered legacy code for extracting and storing an ExpressionSet. There is no exprs function in the package. I merely used exprs function from

Thanks for the update. It looks like it is coming from flowCore which probably imports it from Biobase.

It will be confusing to the user to have two new_flowframe functions. Can these be reduced to one? This is a tough one. The two functions are somewhat different. I just happen to be bad at naming

After a quick look, you should be able to combine them into one function because they seem to be doing similar things.

Best, Marcel

fomotis commented 3 years ago

Okay @LiNk-NY,

I will have a look at these and update things accordingly.

Regards, Daniel

LiNk-NY commented 3 years ago

Hi Daniel, @fomotis Any updates?

fomotis commented 3 years ago

none yet. been having some baby troubles lately. Will work on the updates tonight

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4e90d29ee7256ca3ab7c462f8d2d518ebb08fb36

fomotis commented 3 years ago

Hello @LiNk-NY ,

I finally executed both changes.

Regards, Daniel

bioc-issue-bot commented 3 years ago

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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ff581fdfb1220c91a895f2048cd8740e87bfaeb1

bioc-issue-bot commented 3 years ago

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, skipped". 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 49a2a9a856619f326307844939c4c2ae99b766b3

bioc-issue-bot commented 3 years ago

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. 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/cyanoFilter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 3 years ago

Hi Daniel, @fomotis I hope all is well with you. Thanks for making those changes. Please remove the commented code when you get a chance.

Thank you for your submission to Bioconductor. Your package has been accepted.

Best regards, Marcel

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

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