Package Pirat

[samWieczorek]

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

• Repository: https://github.com/prostarproteomics/Pirat

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 Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.

• [ 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.

• [x ] I am familiar with the Bioconductor code of conduct and agree to abide by it.

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 questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

[lshep]

If its accepted it will be added to the devel branch and will be "released" in oct/nov bioc 3.20 release. You will still be able to reference the short url, have a bioconductor landing page, and since devel still runs on 4.4 be available to users.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2ff22acb8cda354573728b159b4dddf0e358ec2d

[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): Pirat_0.99.16.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/Pirat 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: 70c0dc74087d8bd9b55c401c6ae1c6ee9b28e343

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2c0542bbeb3ac719eb311a680184ce55a6afab25

[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: "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): Pirat_0.99.17.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/Pirat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[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): Pirat_0.99.18.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/Pirat 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: 996ea31a9a26ff0ab9d7d628f14e6bab3ece7f29

[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): Pirat_0.99.19.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/Pirat 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: 1ef8b17e18ee40d97ffc9353e4fff6870bc8a840

[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): Pirat_0.99.20.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/Pirat 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: 9482a3f7d5fb9f0d1e619a456d05dfa85414cdf8

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ae46f21d8725fa6069481c0c242888b4fc48b2d8

[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): Pirat_0.99.21.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/Pirat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[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): Pirat_0.99.22.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/Pirat 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: 45f4d14b77616c1ba787283d0d28bcf724571cb1

[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.

Congratulations! The package built without errors or warnings on all platforms.

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): Pirat_0.99.23.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/Pirat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi @samWieczorek Thanks for following up. Please respond to the review points as there are a few items that should be resolved before acceptance. It seems like the package will not be able to make it in time for the release. Best, Marcel

[samWieczorek]

Hi Marcel, I think i did not understand where I have to answer the review points. I posted a message her : https://github.com/Bioconductor/Contributions/issues/3308 to explain that I have fixed many of those points. The last ones have been fixed Monday morning.

My last push on the github bioconductor repository has the status Ok

I will reply in the first email

Best

Sam

De : Marcel Ramos @.> Envoyé : mardi 30 avril 2024 17:19 À : Bioconductor/Contributions @.> Cc : WIECZOREK Samuel @.>; Mention @.> Objet : Re: [Bioconductor/Contributions] Package Pirat (Issue #3308)

Hi @samWieczorekhttps://github.com/samWieczorek Thanks for following up. Please respond to the review points as there are a few items that should be resolved before acceptance. It seems like the package will not be able to make it in time for the release. Best, Marcel

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3308#issuecomment-2085632574, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAWHDHRW43KH7X4ZW6JHQKDY76Y57AVCNFSM6AAAAABDEHBRESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBVGYZTENJXGQ. You are receiving this because you were mentioned.Message ID: @.**@.>>

[LiNk-NY]

Hi Marcel, I think i did not understand where I have to answer the review points. I posted a message her : #3308 to explain that I have fixed many of those points. The last ones have been fixed Monday morning. My last push on the github bioconductor repository has the status Ok I will reply in the first email

Hi Samuel, @samWieczorek Please respond the individual items in the review so that I may see which ones are still outstanding and take a look at the changes made so far.

Thank you.

-Marcel

[samWieczorek]

De : Marcel Ramos @.> Envoyé : jeudi 25 avril 2024 20:47 À : Bioconductor/Contributions @.> Cc : WIECZOREK Samuel @.>; Mention @.> Objet : Re: [Bioconductor/Contributions] Package Pirat (Issue #3308)

Hi @samWieczorekhttps://github.com/samWieczorek

Thank you for your submission. Please see the review below and respond to each item for the review to continue.

Best regards, Marcel

---

Pirat #3308https://github.com/Bioconductor/Contributions/issues/3308 DESCRIPTION

• Looks good.

NAMESPACE

• Looks good.
• There seems to be a shiny app provided as part of the package. Consider moving that functionality to a dedicated shiny package. Has been removed

vignettes

· Avoid using 1:N notation and use seq_len or seq instead in the "transcriptomic integration" section. Fixed

· Minor: which is not needed for subsetting when a logical vector would work the same, e.g., in "samples-wise correlations" section. If there are NAs, use na.rm = TRUE with colSums, etc. Fixed

· Minor: Consider wrapping text to a max character limit of 80 columns. It is easier to review and read. Fixed

R

• Add a description to all fields in the data documentation @.*** field in R/doc-data.R) Fixed

• Remove or fix commented code in the estimate_gamma(), impute_block_llk_reset(), impute_block_llk_reset_PG() functions, etc. Fixed. The few remaining comments are only to better understand pieces of code

• It seems like mcar is not an override for gamma_1 to be 0 as it is in a multiple or | statement. Provide a more accurate description in the documentation for estimate_gamma. The manner we use mcar is an override because we use ‘|’ operator. Example : if mcar==TRUE then mcar | … | … <- TRUE

• Separate plots and calculation functions e.g., in estimate_psi_df.Removed

• Rename install_Pirat to more accurately reflect the intention of the function. Fixed

• Move the shiny app to another package. Not all users may want to use the shiny functionality. Fixed

• Use more descriptive argument names e.g., ARG_VALUE_1 does not help the user. Fixed

• Avoid using cat in functions that are not print or show methods, e.g., in pipeline_llkimpute. Fixed

• Provide the full list options in the argument as a character vector and use match.arg in the body of the function, e.g., for extension argument in pipeline_llkimpute, set it to extension = c("a", "b", "c"). This way the user can see the full list of options in the usage section of the documentation. Fixed

• Avoid using 1:N notation and use seq_len or seq for for loops; see get_indexes_embedded_prots Fixed

• Consider moving plotting functions to another package. The package currently has basilisk / python deps, shiny, and ggplot. This would render the package fragile if any of those components begin to fail. Shiny has been removed. Ggplot is mandatory because we need the plot generated with ggplot plot to control the algorithm quality

• Avoid nested for loops where possible; see split_large_pg. This is not possible in this case. Each PG which is too big is splitted in a different manner because they have different sizes and we must iterate on the new PGs to correctly complete them. Without a second loop, the code may be much more complex

• AFAIK, basilisk and reticulate operate differently yet you use them both. Can you explain why both are needed? I have removed calls to reticulate where it is possible (in the install_Pirat_env() function) and replaced by functions from basiliskpackage However, I need the function import() from the reticulate package to import a little Python package stored in the inst/myModules directory. This is explained in the documentation and examples of the package basilisk. The function reticulate ::import() has no equivalent in the basilisk package

• Resolve the following R CMD check NOTE:

• checking R code for possible problems ... NOTE

estimate_gamma: no visible global function definition for ‘lm’

estimate_psi_df: no visible binding for global variable ‘var’

estimate_psi_df: no visible binding for global variable ‘x’

mod_Pirat_server : : no visible global function definition

for ‘observe’ Fixed

plot_pep_correlations: no visible global function definition for ‘cor’

plot_pep_correlations: no visible binding for global variable ‘group’

remove_NA_pep_reset: no visible global function definition for

‘remove_pep_from_idx’ Fixed

Undefined global functions or variables:

cor group lm observe remove_pep_from_idx var x

Consider adding

importFrom("stats", "cor", "lm", "var")

to your NAMESPACE file. Only group remains as an Undefined global functions or variables but it is used in the ggplot2::aes() function.

• Add .github folder to .Rbuildignore Fixed

tests

• Increase coverage where needed:

covr::package_coverage(type = "all")

Pirat Coverage: 68.83%

R/mod_Pirat.R: 0.00%

R/reset_data.R: 0.00%

R/split_funcs.R: 48.28%

R/plots.R: 63.46%

R/pirat_utils.R: 82.29%

R/pipeline_impute.R: 92.78%

R/estimate_funcs.R: 93.88%

R/install.R: 100.00%

R/SE.R: 100.00%

R/utils.R: 100.00%

New covr :

covr::package_coverage(type = "all") Pirat Coverage: 89.93% R/pirat_utils.R: 83.16% R/plots.R: 86.54% R/estimate_funcs.R: 91.43% R/pipeline_impute.R: 92.75% R/install.R: 100.00% R/SE.R: 100.00% R/split_funcs.R: 100.00%

I hope i twill be sufficient

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3308#issuecomment-2077951738, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAWHDHV5CQRDTIF2JUEKWRDY7FFTLAVCNFSM6AAAAABDEHBRESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZXHE2TCNZTHA. You are receiving this because you were mentioned.Message ID: @.**@.>>

[LiNk-NY]

• Avoid using cat in functions that are not print or show methods, e.g., in pipeline_llkimpute. Fixed

• Provide the full list options in the argument as a character vector and use match.arg in the body of the function, e.g., for extension argument in pipeline_llkimpute, set it to extension = c("a", "b", "c"). This way the user can see the full list of options in the usage section of the documentation. Fixed

I don't see where these were fixed. Any ideas?

Note that there is a StagedInstall field in the DESCRIPTION. It may be removed in the future according to WRE. Is there a reason why it should be set to "no"?

Thanks, Marcel

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f6a8619ccecb1b58d46056ebaa1317a41a69d54

[samWieczorek]

De : Marcel Ramos @.> Envoyé : mardi 30 avril 2024 22:37 À : Bioconductor/Contributions @.> Cc : WIECZOREK Samuel @.>; Mention @.> Objet : Re: [Bioconductor/Contributions] Package Pirat (Issue #3308)

• Avoid using cat in functions that are not print or show methods, e.g., in pipeline_llkimpute. Fixed

A mistake. A last change of this file and I forgot to remove again the calls to cat() and print(). It is ok now

• Provide the full list options in the argument as a character vector and use match.arg in the body of the function, e.g., for extension argument in pipeline_llkimpute, set it to extension = c("a", "b", "c"). This way the user can see the full list of options in the usage section of the documentation. Fixed

Same reason as above (same file) is ok now

I don't see where these were fixed. Any ideas?

Note that there is a StagedInstall field in the DESCRIPTION. It may be removed in the future according to WREhttps://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file-1. Is there a reason why it should be set to "no"?

This is needed for the package basilik, and it is described in its documentation

StagedInstall: no should be set, to ensure that Python packages are installed with the correct hard-coded paths within the R package installation directory.

https://www.bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html#for-package-developers

Many thanks

Sam

Thanks, Marcel

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3308#issuecomment-2087167999, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAWHDHRXZZOVMHMNJ5Q7ULDY776HTAVCNFSM6AAAAABDEHBRESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBXGE3DOOJZHE. You are receiving this because you were mentioned.Message ID: @.**@.>>

[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): Pirat_0.99.24.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/Pirat 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: f59fb0f9a5b5cc197564cf9bd76711af41a8644a

[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.

Congratulations! The package built without errors or warnings on all platforms.

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): Pirat_0.99.25.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/Pirat to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi @samWieczorek Thank you for updating the package. The package has been accepted. Best regards, Marcel

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[samWieczorek]

Many thanks !

Sam

De : Marcel Ramos @.> Envoyé : mercredi 1 mai 2024 16:20 À : Bioconductor/Contributions @.> Cc : WIECZOREK Samuel @.>; Mention @.> Objet : Re: [Bioconductor/Contributions] Package Pirat (Issue #3308)

Hi @samWieczorekhttps://github.com/samWieczorek Thank you for updating the package. The package has been accepted. Best regards, Marcel

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3308#issuecomment-2088533491, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAWHDHXH5MWBHRLG2K7YGLTZAD22FAVCNFSM6AAAAABDEHBRESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBYGUZTGNBZGE. You are receiving this because you were mentioned.Message ID: @.**@.>>

[samWieczorek]

Hi

Thanks for the accepted my package Pirat. Maybe I missed someting but I cannot see it in the packages of the release 3.19. Is there something more I have to do ?

Best regards

Sam

De : bioc-issue-bot @.> Envoyé : mercredi 1 mai 2024 16:20 À : Bioconductor/Contributions @.> Cc : WIECZOREK Samuel @.>; Mention @.> Objet : Re: [Bioconductor/Contributions] Package Pirat (Issue #3308)

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectationshttp://contributions.bioconductor.org/reviewer-resources-overview.html.

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3308#issuecomment-2088533671, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAWHDHXFEU57A7HJS2PWENLZAD22TAVCNFSM6AAAAABDEHBRESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBYGUZTGNRXGE. You are receiving this because you were mentioned.Message ID: @.**@.>>

[lshep]

I have not ingested new packages yet into the daily builds; we were updating are DOI generation and had to wait for it to be completed. The package since accepted after the release will be included in 3.20 but you can use the short link to advertise bioconductor.org/packages/Pirat as once it is in the system and landing pages generated this short link will always default to the release version of the package and while still in 3.20 the devel pages. Since Bioconductor 3.19 and 3.20 users should still be able to utilize the package will minimal effort until 3.20 is officially released.

[lshep]

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/samWieczorek.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("Pirat"). The package 'landing page' will be created at

https://bioconductor.org/packages/Pirat

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.