goSorensen

[pablof1988]

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[bioc-issue-bot]

Hi @pablof1988

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: goSorensen
Type: Package
Title: Statistical inference based on the Sorensen-Dice dissimilarity
        and the Gene Ontology (GO)
Version: 0.99.0
Author: Pablo Flores, Jordi Ocana, Alexandre Sanchez-Pla, Miquel Salicru
Authors@R: person("Pablo", "Flores", email = "p_flores@espoch.edu.ec", role = c("aut", "cre"))
Maintainer: Pablo Flores <p_flores@espoch.edu.ec>
Description: This package implements inferential methods to compare gene lists (in this first 
    release, to prove equivalence) in terms of their biological meaning as expressed in the
    GO. The compared gene lists are characterized by cross-tabulation frequency tables of
    enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index.
    The fundamental guiding principle is that two gene lists are taken as similar if they share a
    great proportion of common enriched GO items.
Suggests: knitr, rmarkdown
Depends: R (>= 4.1.0), devtools, GO.db, org.Hs.eg.db, goProfiles,
        clusterProfiler, stats
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
NeedsCompilation: no
Packaged: 2022-04-16 10:28:45 UTC; jordi
biocViews: Annotation, GO, GeneSetEnrichment, Software, Microarray, Pathways, GeneExpression, MultipleComparison, GraphAndNetwork

[vjcitn]

remove .Rproj. verify that BiocCheck is passed on a clean machine. remove build/vignette.rds

[pablof1988]

Thank you. Changes are done and these are in the git-hub repository (https://github.com/pablof1988/goSorensen). Say me please, where I have to send these changes ?

Best regards.

[bioc-issue-bot]

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

[pablof1988]

Dear reviewer.

I just have pushed the changes to git Bioconductor.

Best regards

[ococrook]

Hi, thanks for submitting @pablof1988

It looks like there are some ERRORs etc to clean-up before we can get the review started. Could you take a looked at the build report and make the changes required for the package to build cleanly? It looks like your examples are also too long, these should be quick code snippets that simply demonstrate the function and do not do much analysis. Once you've address that, I can review the package in more detail.

Best wishes,
Olly

[pablof1988]

Dear Oliver

Thank you for your comments. Ok, I'll try to improve the examples but I have a problem about the errors you mention: The build report says "ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both", I have done it, I have deleted Author/ Maintainer fields and I have used only Authors@R (exactly the same as shown in the image at the bottom), however, when running the build report, the Author and Maintainer fields are generated automatically and I don't know what to do to solve it.

Best wishes.

Pablo.

[ococrook]

Hi Pablo,

Have you push to the bioconductor git to trigger a new build - remember you'll need to increment the version to 0.99.1? Let me know if you need help doing that.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: c457e64c8d9c5bec4d8af7d26152778e3964c2f7

[pablof1988]

Dear Oliver.

I just have pushed to Bioconductor git ´the change of version. I hope I did it well, I send a capture.

Best regards,

Pablo.

[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: "TIMEOUT".
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/goSorensen 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: 87397879a470feba508cd982a1dc17cd7095715f

[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: "TIMEOUT".
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/goSorensen 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: c46e712edb9a679d8482bbdcf9a17553824ecbc9

[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: "TIMEOUT".
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/goSorensen 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: c22cc2539dc5bfb444acc87305a10b89c5873bc6

[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: "TIMEOUT".
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/goSorensen 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: 0541653fc393b7f7c6ae8f085098644b436d3341

[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/goSorensen 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: 0506dee21f6274d77457cd3ede1d28870d64b3cd

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

[pablof1988]

Dear @ococrook

We would like to comment you that CHECK, generates a ‘warning’ providing notice of the presence of ‘library’ statements in the package code (literally says: "WARNING: Avoid the use of 'library' or 'require' in R code"). These statements are at function ‘buildEnrichTable’ which in the first versions of the package was too slow, because it performs countless enrichment tests. The solution we found was make it parallel, but due to some particularities of parallel computing in Windows, each node running in parallel needs additional information on node-local variables and packages. If these ‘library’ statements were suppressed, parallelization would run still fine in Lynux and MacOS, but to produce an error in Windows.

Best regards.

[ococrook]

Hi Pablo

You can ignore that warning for the moment. The package looks good, I've got a few small requests left.

Small remaining changes

• The NEWS.md isn't upto date with the Description file
• There are still some unrobust constructs such as 1:n in your code, take a look at the (s,v,l)apply and edit based on the previous advice
• Some functions still provide errors that are a little hard to debug, because the inputs are not checked or the documentation is not quite clear. For example, dSorensen says x can be a character, but when I try dSorensen("Sec1", onto = "BP"), I get a cryptic error. I appreciate that I've purposely broken this function but your user will likely be more obtuse than me so help them provide the correct arguments.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 422fcd23671921bf1fd9a3ffa430bbcdd5832398

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

[pablof1988]

Hello @ococrook

We have worked on your observations, these are the changes (things fulfilled simply has a check):

• [✓] The NEWS.md isn't upto date with the Description file.
• [✓] There are still some unrobust constructs such as 1:n in your code, take a look at the (s,v,l)apply and edit based on the previous advice
• [✓] Some functions still provide errors that are a little hard to debug, because the inputs are not checked or the documentation is not quite clear. For example, dSorensen says x can be a character, but when I try dSorensen("Sec1", onto = "BP"), I get a cryptic error. I appreciate that I've purposely broken this function but your user will likely be more obtuse than me so help them provide the correct arguments.
  We have done changes in the help of functions duppSorensen, equivtestSorensen, dSorensen, seSorensen and buildEnrichTable. Now, it is controlled in a more informative way that the lists of genes that we provide to analyze match with their representation in the "universe of genes" in which we work.
  In addition, we have added a test script that executes the statement dSorensen("Sec1", onto = "BP"), where you can see more satisfactory results, different from those obtained previously.

Best regards

[ococrook]

Hi Pablo, looks good to me. Is there any chance you could remove the following notes if at all possible?

* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 8de78af1eafa777b5f5d143be97964cd17b73a51

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

[pablof1988]

Hello @ococrook

ok, changes are done and these notes have disappeared

Best regards

[ococrook]

Great, could you revist the warning from time to time to see if it can be removed.

[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.

[lshep]

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/pablof1988.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("goSorensen"). The package 'landing page' will be created at

https://bioconductor.org/packages/goSorensen

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.

[pablof1988]

Dear @ococrook @lshep

Please need your help. Seven days ago goSorensen package was accepted to publish in Bioconductor (We are very pleasure to publish an R package in Bioconductor. Thanks to accept it), but We are a bit worried since up to now the installation cannot be done using the classic "BiocManager::install("goSorensen")" which is used to install the packages found in Bioconductor, We understand that it is because package is not yet available/published, also, on the Bioconductor web page, the package still appears as a development version. Please coud you say me if We are forgetting some step? or is there some aditional thing that We have to do before publication? We have the ssh key and We have submited it to Bioconductor, maybe Have We to create a new ssh key? or Have We to change the version of package (currently is 0.99.13)?

Please help me!

[ococrook]

Hi @pablof1988

The package will be available via bioconductor at the next release. There are two releases per year. There will always be a devel version which you can also install. The devel version is the one that becomes available in the next release.

You'll be able to install your package using that command in a few months. Until that you can add the devel argument if you want the bioconductor version that will be released.

Does that answer your question?

Best,
Olly

[pablof1988]

Thank you very much for your answer@ococrook, now all is clear for me.

[pablof1988]

Good afternoon.

We have just updated the goSorensen package, adding new functions and results. We uploaded these changes to the GitHub repository. We would like to know what procedure we need to perform so that these changes can be displayed as a package update in a future release of Bioconductor. Will it update automatically (it just needs to be on GitHub)? Or should we submit the update to a review process? If so, how can I carry out that process?

[ococrook]

Hi!

You need to push the changes to Bioconductor: https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories

Let me know if you need help! We don't review changes to packages - of course if your package ends up with Errors after updating, these will need to be fixed.

[pablof1988]

Ok, Thank you for the help; I will try it

[pablof1988]

Hello @ococrook

Please help me!!

I have tried to push the changes to Bioconductor, but I have not been successful because when doing, for example, "git fetch --all" or, more specifically, "git fetch upstream," the message "git@git.bioconductor.org: Permission denied (publickey)" appears.
I guess this problem is produced because I now have a different computer than the one I used when I uploaded the changes for the first version of the package. I remember that before, it simply asked me for the password and let me continue. The problem is that now it does not ask me for this password, which I remember but can't use.

[pablof1988]

Hello again, @ococrook.

To give a possible solution to the above problem mentioned, I created a new ssh key, and I associated this key to the git project using the following git code: "git remote set-url upstream git@github.com:pablof1988/goSorensen.git" This process allowed me to use the ssh key and delete the error message mentioned above. Now all the processes run, but I wonder if the changes were really sent to Bioconductor, for I remind that when one sends something to Bioconductor, a notification immediately arrives, but this time nothing has arrived.
Can you please help me? Likely I am making some mistakes.

[ococrook]

If you push to the bioc branch again, it would tell you everything is upto date. Remember you are pushing to devel, so you can also clone the devel branch at bioc and check that it's the same

[pablof1988]

When I do "git push upstream master," it shows a message "Everything up-to-date." So, I suppose all is ok, and the changes are in Bioconductor.