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flowGraph #1703

Closed aya49 closed 3 years ago

aya49 commented 4 years ago

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]'

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 4 years ago

Hi @aya49

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: flowGraph
Type: Package
Title: Identifying differential cell populations in flow cytometry data accounting for marker frequency.
Version: 0.99.0
Description: Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given flowType objects.
Date: 2019-11-30
Authors@R: Alice Yue <aya43@sfu.ca>
Maintainer: Alice Yue <aya43@sfu.ca>
License: Artistic-3.0
VignetteBuilder: knitr
Depends: R (>= 3.5)
Imports: 
    data.table,
    effsize,
    flowType, 
    foreach, 
    future, 
    graphics, 
    grDevices, 
    gridExtra,
    ggrepel, 
    ggplot2,
    ggiraph,
    htmlwidgets,
    igraph, 
    Matrix, 
    methods,
    plotly,
    RColorBrewer,
    parallel, 
    purrr,
    furrr,
    pracma,
    Rdpack,
    stats,
    stringr,
    stringi,
    visNetwork
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    testthat (>= 2.1.0)
biocViews: 
    FlowCytometry, 
    StatisticalMethod, 
    ImmunoOncology, 
    Software, 
    CellBasedAssays, 
    Visualization
BugReports: https://github.com/aya49/flowGraph/issues
URL: https://github.com/aya49/flowGraph
RoxygenNote: 7.1.1
RdMacros: Rdpack
LazyData: no
mtmorgan commented 4 years ago

Please correct the use of Authors@R --

Authors@R: person("Alice", "Yue", email = "aya43@sfu.ca", role = c("aut", "cre"))

There is no need for a Maintainer: field.

aya49 commented 4 years ago

Corrected and committed, thank you :)!

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 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, 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. 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/flowGraph to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

aya49 commented 4 years ago

[ ]: not sure what I should do about it [x]: I did something about it ?: Will need to re-build to be sure if it's fixed

I made an attempt at the errors and warnings :D

errors:

warnings:

LiNk-NY commented 4 years ago

Hi Alice, @aya49 You cannot depend on a deprecated package. Please either have the maintainer un-deprecate it immediately or submit flowTypeFilter first before you submit this package. The other option is to remove the flowType code entirely from the package. The fourth and least popular option is to copy the necessary code from flowType into your package with proper attribution. Thanks.

aya49 commented 4 years ago

Hi Marcel,

Thank you for the comment, I removed the dependency on flowType and committed an updated version of flowGraph.

Alice

LiNk-NY commented 3 years ago

Hi Alice, @aya49

I was reviewing your package but I see that you still mention flowType quite a lot in the package (grep -rn "flowType" * | wc -l > 39). You haven't completely removed it. Please do so before the review can continue.

Best regards, Marcel

flowGraph #1703

DESCRIPTION

aya49 commented 3 years ago

Thank you for the review Marcel,

Ok, I will completely remove flowType D:, the places where flowType is still mentioned are the unit tests but they are commented out, so I don't have to rewrite them after flowTypeFilter comes out, Roxygen documentations in flowGraph_constructor which I have commented out so it is not in the manual, also I mention it in the Vignette as a future option for input generation for completeness sake. Does that sound alright?

For the number of imported packages, the list is long, but as long as the user imports effsize, furrr, ggiraph, igraph, visNetwork, and stringr, all the other packages are automatically imported. I re-organized the DESCRIPTION file to reflect this. I got warnings from bioccheck to also import Rdpack, data.table, and gridExtra which I don't explicitly use but I don't mind adding if it's required.

LiNk-NY commented 3 years ago

Hi Alice, @aya49

You can add all of those changes to a branch and merge that branch if and when flowTypeFilter is accepted to Bioconductor. Currently, flowType is not an existing package from the build system perspective and should not be mentioned to avoid confusing users.

all the other packages are automatically imported.

Are you using functions from those packages? If not, I would remove them from the Imports field even if they're imported lower in the dependency chain.

Please commit your changes and bump the version so that we can see what warnings the package is getting from BiocCheck. Thanks!

-Marcel

aya49 commented 3 years ago

Hi Marcel,

I've removed flowType mentions and commited to the repository.

I do use functions from them, so I kept them. I don't use functions from the data.table, Rdpack, and gridExtra packages though, but it's imported as per the warnings.

For the version bump, I read the https://bioconductor.org/developers/how-to/version-numbering/ webpage and I bumped the version from 0.99.0 to 0.99.1, I wanted to confirm if that was what you meant?

Thank you, Alice

P.S. Note the two messages I'm not sure about are:

LiNk-NY commented 3 years ago

Hi Alice, @aya49 I do not see the build report in the comments here. Did you push upstream to git@git.bioconductor.org? Thanks. -Marcel

aya49 commented 3 years ago

Hi Marcel,

We're doing a conductor test so all our remote machines are turned off and I don't have access to push locally, so I will push hopefully by Thursday if not tomorrow night, fingers crossed.

Thank you for the help, and uber patience :) Alice

edit: sorry for the multiple pushes O_O, that was an unfortunate series of events 👍

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 44f90ae3d84148be56aae66dd91881d86c155152

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/flowGraph 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: ca2b3f08f1c7d7f97bb9e97ce2eaeae0d4311c33

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/flowGraph 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: 79365dcfce6902da69f17ae90936b7c79f38ff60

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/flowGraph 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: b9f35ba22a71df35f78a9038070be9022822046a

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

aya49 commented 3 years ago

hi marcel @LiNk-NY

i wanted to follow up this issue and confirm the specifics on what i should do to move further with the submission :)

thank you, alice

LiNk-NY commented 3 years ago

Hi Alice, @aya49

As you may have noticed, we have been busy reviewing other packages that were submitted in time for the release. Sorry for the delay. I will review your package today. Best, Marcel

aya49 commented 3 years ago

thank you marcel! hope everything goes well with this release cycle :)

LiNk-NY commented 3 years ago

Hi Alice, @aya49

Please address these remarks from R CMD check: 

* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
  Artistic-3.0
Standardizable: FALSE

* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘flowGraph’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.

* checking R code for possible problems ... NOTE
fg_feat_node_exprop_new : <anonymous> : <anonymous>: no visible binding
  for global variable ‘ep_’
fg_plot_box: no visible binding for global variable ‘val’
fg_plot_box: no visible binding for global variable ‘ID’
fg_plot_box_set: no visible binding for global variable ‘val’
fg_plot_box_set: no visible binding for global variable ‘ID’
fg_plot_pVSdiff: no visible binding for global variable ‘log_p_value’
fg_plot_pVSdiff: no visible binding for global variable ‘cohensd_size’
fg_plot_pVSdiff: no visible binding for global variable ‘avg_count’
fg_plot_pVSdiff: no visible binding for global variable ‘phenotype’
fg_plot_pVSdiff: no visible binding for global variable ‘phenogroup’
fg_plot_qq: no visible binding for global variable ‘y’
fg_plot_qq: no visible binding for global variable ‘x’
fg_plot_qq: no visible binding for global variable ‘cohensd_size’
fg_plot_qq: no visible binding for global variable ‘phenotype’
fg_plot_qq: no visible binding for global variable ‘d_size’
fg_plot_qq: no visible binding for global variable ‘phenogroup’
flowGraph: ... may be used in an incorrect context: ‘fg_save_plots(fg,
  plot_path = paste0(path, "/plots"), ...)’
plot_gr: no visible binding for global variable ‘x’
plot_gr: no visible binding for global variable ‘y’
plot_gr: no visible binding for global variable ‘from.x’
plot_gr: no visible binding for global variable ‘to.x’
plot_gr: no visible binding for global variable ‘from.y’
plot_gr: no visible binding for global variable ‘to.y’
plot_gr: no visible binding for global variable ‘colour’
plot_gr: no visible binding for global variable ‘label’
plot_gr: no visible binding for global variable ‘from’
plot_gr: no visible binding for global variable ‘to’
plot_gr: no visible binding for global variable ‘label_long’
plot_gr: no visible binding for global variable ‘phenotype’
plot_gr: no visible binding for global variable ‘phenogroup’
Undefined global functions or variables:
  ID avg_count cohensd_size colour d_size ep_ from from.x from.y label
  label_long log_p_value phenogroup phenotype to to.x to.y val x y

* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'fg_save_plots':
fg_save_plots
  Code: function(fg, plot_path, plot_types = "node", interactive =
                 FALSE, adjust_custom = "byLayer", label_max = 10,
                 box_no = 20, paired = FALSE, logged = FALSE,
                 filter_adjust0 = 1, filter_es = 0, filter_btwn_tpthres
                 = 1, filter_btwn_es = 0, overwrite = TRUE, node_labels
                 = "NONE", ...)
  Docs: function(fg, plot_path, plot_types = "node", interactive =
                 FALSE, adjust_custom = "byLayer", label_max = 10,
                 box_no = 20, paired = FALSE, logged = FALSE,
                 filter_adjust0 = 1, filter_es = 0, filter_btwn_tpthres
                 = 1, filter_btwn_es = 0, overwrite = TRUE, ...)
  Argument names in code not in docs:
    node_labels
  Mismatches in argument names:
    Position: 15 Code: node_labels Docs: ...

From BiocCheck

 * WARNING: Update R version dependency from 4.0 to 4.1.

  * NOTE: 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

 * NOTE: Avoid sapply(); use vapply()
      Found in files:
        01_flowgraph_accessors.R (line 460, column 34)
        01_flowgraph_accessors.R (line 466, column 38)
        02_flowgraph_features.R (line 628, column 24)
        02_flowgraph_features.R (line 632, column 31)
        02_flowgraph_features.R (line 634, column 31)
        03_flowgraph_summary.R (line 301, column 14)
        03_flowgraph_summary.R (line 303, column 14)
        03_flowgraph_summary.R (line 308, column 14)
        03_flowgraph_summary.R (line 310, column 14)
        03_flowgraph_summary.R (line 320, column 14)
        03_flowgraph_summary.R (line 324, column 14)
        03_flowgraph_summary.R (line 333, column 15)
        03_flowgraph_summary.R (line 337, column 15)

    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        04_flowgraph_plots.R (line 637, column 40)

   * WARNING: Use TRUE/FALSE instead of T/F
      Found in R/ directory functions:
        fg_save_plots()

   * NOTE: Avoid '<<-' if possible (found in 1 files)

   * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      flowGraph.Rd
LiNk-NY commented 3 years ago

Hi Alice, @aya49

An important point that I must stress is that contributed packages should provide interoperability with other Bioconductor packages. Currently, flowGraph does not do that. Can you please speak to this? Thank you. See item number 8 here: https://www.bioconductor.org/developers/package-guidelines/#description

Best regards, Marcel

flowGraph #1703

LICENSE

DESCRIPTION

NAMESPACE

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7b391c82ca88ebc81e1e2b89a3addd75224f477b

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/flowGraph 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: fb87acad1113bd32b83f2d677be69dedb2b70260

aya49 commented 3 years ago

hi marcel @LiNk-NY ,

interoperability: the package conducts downstream analysis for flow cytometry data. input flow cytometry data is stored in an S4 class from the flowCore package which also does all the pre-processing. then taking this S4 object as input, flowType is used as one of the many many cell population phenotype identification tools. flowGraph previously depended on flowType's Phenotypes object as input, but now it takes a generic matrix as input since flowType is going to get replaced with flowTypeFilter which is not available at the moment. so flowGraph is now kind of stand-alone during this time of transition.

Warning: Non-standard license specification: Artistic-3.0 is not allowed? :(

Warning: no function found corresponding to methods exports from ‘flowGraph’ for: ‘show’: i've been trying to troubleshoot this for some time, i don't see this as a warning anymore but is it still an issue?

no visible binding: these are ggplot2 data frame columns...

WARNING: Update R version dependency from 4.0 to 4.1.: but i guess i should keep it to 4.0 for this issue because when i update it to 4.1 i get an error instead?

thank you! alice

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". 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/flowGraph 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: ec0e12d844fc6618a634dc59870502b0ab99e57a

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

aya49 commented 3 years ago

i changed the license from Artistic 3.0 to 2.0

LiNk-NY commented 3 years ago

Hi Alice, @aya49

Thank you for following up. Perhaps flowGraph should be submitted after the flowTypeFilter. See the rest of the review below.

Best, Marcel

R

tests

vignette

aya49 commented 3 years ago

Done:

Hi Alice, @aya49

Thank you for following up. Perhaps flowGraph should be submitted after the flowTypeFilter. Thank you for the suggestion. I'm not sure when flowTypeFilter will come out, it's a thesis for a master's student so it might take a couple of months, a year or two. This package corresponds to a paper we've submitted so having it up would be good. It's also a stand-alone package now and users don't necessarily have to create their input using flowTypeFilter. So I hope it would be able to go out as is. We can, for sure, modify it after flowTypeFilter comes out to the way it was before though.

See the rest of the review below.

Best, Marcel

R

* Remove any commented code in `.R` files.

Done

* Avoid any `.onLoad` hooks for data in `00_data.R`.

This was commented out, and now taken out.

* Default arguments to writing files should be `FALSE` or files should
  be saved to the `tmp` directory via `tempdir`

path=NULL sets saving files in the constructor function to false by default. the save_plots parameter is only evaluated if path!=NULL.

* In general, graphics should not be saved to the user's system. Users should
  be allowed to choose their own format.

path=NULL for all plotting functions, and it's not mentioned in the vignette. This is for if the user chooses to save everything to file directly from the constructor. Even then it's only for exploratory analysis, the users would most likely want to create their own plots.

* What is the reasoning for saving data as `.rds`? Wouldn't it suffice to
  save the entire object if you will be using R to load the `.rds` files anyway?
  (`fg_save` and `fg_load`)

Initially, I made the package so that I'd save the object as one Rdata file and just explore it in R. But I changed this so that common files user wants to see would be saved as csv and plots in a folder because not many people in our lab use R. This way, we just use the constructor function once and it saves everything to file and people can analyze the csv files in another program.

But you're right, I saved all the separate rds's as a single other.Rdata file :)

* `base` should be the default package loaded and therefore you do not need
  to use references such as `base::sort`. Are there other packages interferring
  with using `sort`, `which`, `length`, etc.?

I got warnings about is.null, name, length, nrow, and apply saying that imported packages also have these functions so I added base:: to them. A lot of them from the Matrix package that I use to make sparse matrices. I can try taking it out... a bit nervous though.

* Avoid direct slot access via `@` in package code. Please include a formal
  interface for your class. I see you have `fg_get*` but perhaps the functions
  you provide are not enough. See
  https://www.bioconductor.org/developers/package-guidelines/#rcode

I've taken out most of the @'s in the package... apart from the functions that need to modify the actual fg object.

* The `overwrite` argument should be `FALSE` by default in `fg_add_summary`.

Done.

tests

* It is strongly recommended that you add unit tests for code robustness.

I have a test script in the test folder, do I need to change it?

vignette

* It looks good.

;__;)b

* I would recommend keeping the sample code in the vignette straight forward
  and simple for your users.

* This means avoiding the nested `gr$v$label` calls and using `grep` to set a
  nested variable. It seems like only package authors would know about these
  since they are quite nested which is not good for usability.

I moved plot customization into the appendix. I think this might be useful for advanced users who don't want to write their plotting functions from scratch which is another option they have.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6d8bb9836392ca28f7efa21ef543c3bea5409286

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/flowGraph 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: f834a6f48ca577bb60eb28cef82dc381dfa0d9de

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". 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/flowGraph 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: 002842475ecc4701769e1a069940da28d5b2300c

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". 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/flowGraph 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: e90e1ce2668143859cc83f462581c482cc663a90

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". 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/flowGraph 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: 15e9d8fd3ea69714e284cbcec5a088b09cfd8556

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". 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/flowGraph 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: f0fea3b30b54acb907ed837bede0e0522eb4fdc3

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". 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/flowGraph 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: 739b829e55d41ac2ce8b35e717730bd8b7ae8e80