flowGraph

[aya49]

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

• Repository: https://github.com/aya49/flowGraph

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.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance 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.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

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

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

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

[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. 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]

whew

[LiNk-NY]

Hi Alice, @aya49

Thanks for making those changes!

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.

I'm not sure if users will want to save plots from exploratory analyses... But thanks for keeping the path=NULL.

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.

I don't think using base:: is necessary. Perhaps by only adding Matrix to the Imports field in the description and using Matrix::sparseMatrix etc. in the package code, you can avoid these warnings...

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

I'm not sure it makes a difference but I'd move them to the standard location as promoted by usethis::use_testthat.

[aya49]

Hi Marcel @LiNk-NY

Thank you for the suggestions 💯

I don't think using base:: is necessary. Perhaps by only adding Matrix to the Imports field in the description and using Matrix::sparseMatrix etc. in the package code, you can avoid these warnings...

Done

I'm not sure it makes a difference but I'd move them to the standard location as promoted by usethis::use_testthat.

and done!

Alice

[LiNk-NY]

Hi Alice, @aya49

It's looking good! I ran build and check on the package and encountered this issue:

* checking examples ... ERROR
Running examples in 'flowGraph-Ex.R' failed
The error most likely occurred in:

> ### Name: fg_plot_qq
> ### Title: Creates a QQ plot of a summary statistic.
> ### Aliases: fg_plot_qq
> 
> ### ** Examples
> 
> 
>  no_cores <- 1
>  data(fg_data_pos15)
>  fg <- flowGraph(fg_data_pos15$count, class=fg_data_pos15$meta$class,
+                  no_cores=no_cores)
preparing input; 
10:42:33-10:42:33 > 19:00:00
preparing feature(s): mapping out cell population relations
NOTE: markers/measurements should not contain underscores_!
- 8 pops @ layer 1
10:42:33-10:42:33 > 19:00:00
- 24 pops @ layer 2
10:42:33-10:42:34 > 19:00:00
- 32 pops @ layer 3
10:42:34-10:42:34 > 19:00:00
cell population meta data created: 10:42:33-10:42:34 > 19:00:00
preparing feature(s): node proportion 
10:42:34-10:42:34 > 19:00:00
preparing feature(s): proportion on edges 
10:42:34-10:42:34 > 19:00:00
preparing feature(s): SpecEnr 
skipped
10:42:34-10:42:34 > 19:00:00
- claculating summary statistics (for class class: exp & control) t_diminish for node feature SpecEnr
10:42:34-10:42:34 > 19:00:00
total time used: 10:42:33-10:42:34 > 19:00:01
> 
>  fg_plot_qq(fg, type="node", summary_meta=NULL, adjust_custom="byLayer", index=1,
+          interactive=TRUE, logged=FALSE)
Error in DSVG_(file = file, width = width, height = height, bg = bg, pointsize = pointsize,  : 
  Graphics API version mismatch
Calls: fg_plot_qq -> <Anonymous> -> do.call -> <Anonymous> -> DSVG_
Execution halted

Do you have an idea of what is causing this? Thank you.

Also, there is a NOTE that should be resolved.

* checking R code for possible problems ... NOTE
fg_feat_node_exprop_new : <anonymous> : <anonymous>: no visible binding
  for global variable ‘ep_’
fg_load: no visible binding for global variable ‘markers’
fg_load: no visible binding for global variable ‘fg_graph’
fg_load: no visible binding for global variable ‘elist’
fg_load: no visible binding for global variable ‘pl’
fg_load: no visible binding for global variable ‘etc’
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’
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’
show,flowGraph: no visible binding for global variable ‘fg’
Undefined global functions or variables:
  ID avg_count cohensd_size colour d_size elist ep_ etc fg fg_graph
  from from.x from.y label label_long log_p_value markers phenogroup
  phenotype pl to to.x to.y val x y

Thanks!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 768f16bd29ae0aab2b650db25fcf8eb23e1e7af6

[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. 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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 41f6e2af20e4958b8381a4044c37d5c555b40d7f

[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. 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]

Received a valid push on git.bioconductor.org; starting a build for commit id: b266bc767dead381484ec686cc4975e3a74ad773

[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. 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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 6c2f3a2b82e346f2c31301dc312c75e5d6ddc55f

[aya49]

Hi Marcel @LiNk-NY

For the error, I can't seem to replicate it on my local computer, let me do a version bump and see if it persists. If not, I did a quick search and people have similar Graphics API version mismatch errors in between R version upgrades because of outdated packages. Are there more messages related to this error?

For the notes, most of the variables with no physical bindings are for ggplot2's aes function, I've replaced this with aes_. For the variables loaded, I've used the attach and get functions instead so this should be alright now.

Hopefully, that cleans everything up. Let me know if the first error persists... D:

Thank you, Alice

[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. 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.

[LiNk-NY]

Hi Alice, @aya49 Usually, to avoid the variables loaded message, I would do something like:

dataenv <- new.env(parent = emptyenv())
load("/file/path/to/data.rda", envir = dataenv)
variable1 <- dataenv[["variable1"]]

Thanks for making those changes! It looks good!

Best, Marcel

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/aya49.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("flowGraph"). The package 'landing page' will be created at

https://bioconductor.org/packages/flowGraph

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

[aya49]

thank you for the tip @LiNk-NY duly noted :-D, i will look through the code again to apply this.

and oh boy, what a great way to end the semester!