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ClustAll #3253

Closed asiort closed 6 months ago

asiort commented 9 months ago

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bioc-issue-bot commented 9 months ago

Hi @asiort

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: ClustAll
Type: Package
Title:  ClustAll: Data driven strategy to find groups
        of patients within complex diseases
Version: 0.99.0
Authors@R: c(person("Asier", "Ortega-Legarreta", role = c("aut","cre"),  
 email = "aortegal@navarra.es", 
 comment = c(ORCID = "0009-0000-3563-5362")),
 person("Sara", "Palomino-Echeverria", role = c("aut"),  
 email = "spalomie@navarra.es"))
Imports: FactoMineR, bigstatsr, clValid, clusteval, doSNOW,
        parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3,
        methods, ComplexHeatmap, RColorBrewer, circlize, ggplot2, grid,
        stats, utils
Suggests: knitr
Description: Data driven strategy to find hidden groups of patients with complex
        diseases using clinical data. ClustAll facilitates the unsupervised 
        identification of multiple robust stratifications. ClustAll, is able to 
        overcome the most common limitations found when dealing with clinical 
        data (missing values, correlated data, mixed data types). 
Depends: R (>= 4.2.0)
License: GPL-2
Encoding: UTF-8
biocViews: Software, StatisticalMethod, Clustering, DimensionReduction,
 PrincipalComponent
RoxygenNote: 7.2.3
VignetteBuilder: knitr
git_url: https://github.com/TranslationalBioinformaticsUnit/ClustAll
NeedsCompilation: no
Packaged: 2023-08-10 12:55:36 UTC; asier.ortega
lshep commented 9 months ago

All package dependencies must be active on CRAN or Bioconductor. clusteval was removed from CRAN in June of 2021. See https://cran.r-project.org/web/packages/clusteval/index.html . You must not use this package as a dependency or reach out to the clusteval maintainers to reinstate on CRAN.

asiort commented 8 months ago

I have fixed the dependencies problem and updated my GitHub repository. But when I push to git@git.bioconductor.org:packages/ClustAll I have problems with the credentials.

I am following the tutorial 21.5.1 New package workflow but when doing "git fetch --all" I get the following error: """ $ git fetch --all Fetching origin Fetching upstream git@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists. error: could not fetch upstream """ How could I fix it?

Thanks in advance.

lshep commented 8 months ago

I will put this through to getting on our git and getting our build reports but when I ran this locally there were many ERROR and Warnings that need to be cleaned up before a reviewer will be assigned for in depth review.

bioc-issue-bot commented 8 months ago

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 8 months ago

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: "TIMEOUT, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.2 LTS): ClustAll_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a985ad8b41db50da15a8b0d2286e2240e6991d55

bioc-issue-bot commented 8 months ago

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: "TIMEOUT, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ClustAll_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 504754a588eee6f5dc3022661b01080ed1c6bd80

bioc-issue-bot commented 8 months ago

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: "TIMEOUT, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: ERROR before build products produced.

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

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a18c83c9021de08e4c6fdcebccc79a9395489759

bioc-issue-bot commented 7 months ago

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, 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): ClustAll_0.99.3.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fdc2d1d31f6670d3ba8d9f7ab00ec2f7fb7ba303

bioc-issue-bot commented 7 months ago

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: "TIMEOUT, 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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ClustAll_0.99.4.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7517e9e4d9bf7521bfc8eb41840c94937f81b0db

bioc-issue-bot commented 7 months ago

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): ClustAll_0.99.5.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.5.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 260f3297f151c5e4882d5045c996bac8b74acf20

bioc-issue-bot commented 7 months ago

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): ClustAll_0.99.6.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.6.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8eba6c6945cb3af9bb09d373c16f3798d124d3b6

bioc-issue-bot commented 7 months ago

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): ClustAll_0.99.7.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.7.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4831c5d3f5d905eb3349a863cf704c527fbc0f1a

bioc-issue-bot commented 7 months ago

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): ClustAll_0.99.8.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.8.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ce93dbbc4e87d97d01c4fcd2fabda9b4567567b0

bioc-issue-bot commented 7 months ago

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): ClustAll_0.99.9.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.9.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1cf4670c11d31135d4e634d978ae431a7ad3c82a

bioc-issue-bot commented 7 months ago

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): ClustAll_0.99.10.tar.gz macOS 12.7.1 Monterey: ClustAll_0.99.10.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

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

DarioS commented 7 months ago

I have evaluated the package and identified some improvements which are needed.

Slot "dataImputed": NULL

Slot "dataValidation": [1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 1 2 1 1 1 1 1 2 2 1 2 2 1 1 1 1 2 1 2 2 1 1 1 1 2 1 2 2 1 2 1 2 2 1 1 [82] 1 2 2 1 2 2 2 1 1 1 2 1 1 2 2 1 1 1 2 2 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 2 2 2 1 2 2 1 1 1 2 2 1 2 1 2 2 1 2 2 1 1 2 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 [163] 2 1 2 1 1 2 2 1 1 2 2 1 1 1 1 2 1 1 2 2 2 1 2 1 2 1 1 1 2 1 1 2 2 1 2 2 2 2 1 2 2 2 1 2 1 2 1 1 2 1 2 2 2 2 1 1 2 2 1 1 1 2 1 1 1 1 1 2 2 1 1 2 1 1 2 2 1 2 1 1 1 [244] 1 2 1 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 2 1 2 1 1 2 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 2 1 2 [325] 1 1 1 1 2 2 2 1 1 1 1 2 1 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 2 2 1 2 2 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 2 1 1 2 2 1 1 1 1 1 1 2 1 1 1 1 [406] 1 1 1 2 1 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 2 2 1 2 1 1 1 1 1 2 1 1 2 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 [487] 1 2 1 2 1 1 2 1 1 1 1 1 2 2 1 2 1 2 1 1 1 1 1 2 1 1 2 1 2 1 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 [568] 2 1

Slot "nImputation": [1] 0

Slot "processed": [1] FALSE

Slot "summary_clusters": NULL

Slot "JACCARD_DISTANCE_F": NULL


- Vignette needs work. The breast cancer example consists of a bunch of headings and code blocks with no interpretation of output. Also, the first part is just a list of arguments and definitions from the functions. Don't duplicate such information.
- There is only one unit test and it simply creates an S4 object. Needs non-trivial testing for correctness of calculations.
asiort commented 7 months ago

@DarioS Thanks for evaluating the package. I will implement your suggestions as soon as possible :)

bioc-issue-bot commented 6 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0bb53604a63e2a45c59e66fa0ccd62ec3098d419

bioc-issue-bot commented 6 months ago

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): ClustAll_0.99.11.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

asiort commented 6 months ago

@DarioS I have implemented the changes you suggested:

> obj_noNA1
ClustAllObject
Data: Number of variables: 30. Number of patients: 569
Imputation: NO.
Number of imputations: 0
Processed: TRUE
Number of stratifications: 72

Thanks for your time!

DarioS commented 6 months ago

The issues have been partially addressed. I still think that the vignette and code both have room for improvement.

Also, one minor observation. The package is called ClustAll but, in the vignette, it varies between ClustALL and ClustAll. ALL makes me think of Acute Lymphoblastic Leukemia, so perhaps it is best to use ClustAll consistently.

bioc-issue-bot commented 6 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a08deabffe073cdf4bccae971ea50b623ec39e85

bioc-issue-bot commented 6 months ago

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): ClustAll_0.99.12.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 6 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e0657fb225942262b870d89f1b04a2923da1a3e2

bioc-issue-bot commented 6 months ago

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): ClustAll_0.99.13.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/ClustAll to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

asiort commented 6 months ago

Hi @DarioS I've implemented the new suggestions:

Regarding the tests:

Regarding the Vignette:

Regarding the for loops:

Find here the for loops that I modified into applys:

Here are the for loops that I consider necessary:

Please let me know if any other improvements would be necessary to implement or discuss. Thanks again for your time.

DarioS commented 6 months ago

Thank you.

bioc-issue-bot commented 6 months ago

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.

lshep commented 6 months ago

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/asiort.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("ClustAll"). The package 'landing page' will be created at

https://bioconductor.org/packages/ClustAll

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.