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DCATS #2870

Closed linxy29 closed 1 year ago

linxy29 commented 1 year 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 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.

bioc-issue-bot commented 1 year ago

Hi @linxy29

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: DCATS
Type: Package
Title: Differential Composition Analysis Transformed by a Similarity matrix
Version: 0.99.0
Authors@R: 
    person("Xinyi", "Lin", , "linxy29@connect.hku.hk", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-7780-2461"))
Description: Methods to detect the differential composition abundances between 
    conditions in singel-cell RNA-seq experiments, with or without replicates, 
    use total cell number or specific reference group as normalization term.
License: GPL (>= 3)
Depends: R (>= 4.1.0), stats
Imports: 
    MCMCpack, 
    matrixStats, 
    robustbase, 
    aod,
    e1071
Suggests: 
    testthat (>= 3.0.0),
    knitr,
    Seurat,
    SeuratObject,
    SeuratData,
    tidyverse,
    rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.2.1
biocViews: SingleCell
Encoding: UTF-8
LazyData: true
Config/testthat/edition: 3
bioc-issue-bot commented 1 year ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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 1 year ago

This issue was deemed inappropriate for our issue tracker by a member of the Bioconductor team.

This issue tracker is intended only for packages which are being submitted for consideration by Bioconductor.

Any other use of the tracker is not approved. If you feel this designation is in error, please send us email and include the URL of this issue.

This issue will now be closed.

bioc-issue-bot commented 1 year 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: "ABNORMAL". 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/DCATS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

vjcitn commented 1 year ago

Your package works primarily with Seurat infrastructure. Would your package be able to process data in the SingleCellExperiment data structure?

linxy29 commented 1 year ago

Yes, this package can also be used to process data in the SingleCellExperiment data structure. The input metrics can be derived from SingleCellExperiment data structure or Seurat object.

vjcitn commented 1 year ago

package 'SeuratData' is not available for Bioconductor version '3.17' -- packages depended on or imported must be in CRAN or Bioconductor. Please follow the guidelines.

linxy29 commented 1 year ago

Thank you for your reminder. 'SeuratData' is not used in the revised version of DCATS.

bioc-issue-bot commented 1 year ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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

linxy29 commented 1 year ago

Dear reviewers,

'DCATS' have been updated to fix errors. Thank you.

jianhong commented 1 year ago

Please fix those two errors first.

linxy29 commented 1 year ago

Hi Jianhong,

I've subscribed to the mailing list, and added examples on the man pages. Please checked the screenshot as follows.

image
lshep commented 1 year ago

Please push your changes to git.bioconductor.org with a valid version bump to trigger a new build. Helpful instructions were linked in previous comment: https://github.com/Bioconductor/Contributions/issues/2870#issuecomment-1440493503

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9c0fef010b276b6105bbed6b6e28aa242fcffcec

bioc-issue-bot commented 1 year 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/DCATS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

linxy29 commented 1 year ago

Dear reviewer,

'DCATS' have been updated to fix errors. Thank you.

jianhong commented 1 year ago

Package 'DCATS' Review

Thank you for submition your package to Bioconductor. The package passed check and build. Let us start from several things that need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please condsider; Important: must be addressed.

The DESCRIPTION file

The NAMESPACE file

General package development

══ Failed tests ════════════════════════════════ ── Failure ('test_prior.R:39:3'): whether phi estimation works ──────────── as.numeric(round(phi, 6)) (actual) not equal to 0.00793 (expected).

actual: 0.0088 expected: 0.0079

R code

linxy29 commented 1 year ago

Dear reviewers,

I followed the guidance in the link, http://contributions.bioconductor.org/git-version-control.html#new-package-workflow, and updated DCATS. The package version is changed. When I rerun the push commend again, I got: Warning: No xauth data; using fake authentication data for X11 forwarding. X11 forwarding request failed on channel 0 Everything up-to-date

But I didn't receive an email with the build report. I guess something went wrong. How could I fix this?

Thank you for your help.

lshep commented 1 year ago

Please make sure you are pushing to git.bioconductor.org and not github. The git.bioconductor.org version is still 0.99.1 and has not been updated since Mar 8. If you continue to have issues please include the commands you ran with the full output including git remotes -v

linxy29 commented 1 year ago

Dear Ishep,

I still have the issue mentioned above. Following is the output of commends:

image

Thank you for your help.

lshep commented 1 year ago

what is your OS?

linxy29 commented 1 year ago

Following is the output I got after typing "cat /etc/os-release" : NAME="CentOS Linux" VERSION="8" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="8" PLATFORM_ID="platform:el8" PRETTY_NAME="CentOS Linux 8" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:8" HOME_URL="https://centos.org/" BUG_REPORT_URL="https://bugs.centos.org/" CENTOS_MANTISBT_PROJECT="CentOS-8" CENTOS_MANTISBT_PROJECT_VERSION="8"

lshep commented 1 year ago

So I think the Xauth is unique to your system since we have never seen it before. I just googled and there are a few different threads you can look at for debugging -- perhaps this from stackoverflow.

As far as pushing to git.bioconductor.org upstream. I noticed your default branch on github is master? If your default local repo branch is master than you may have to do something like git push upstream master:devel

linxy29 commented 1 year ago

Dear Ishep,

I tried the solution in the link from StackOverflow. They didn't work. So I tried to push the changes from another server. This time I got the following error message when running "git push upstream devel". Is there any way to solve this error?

error: src refspec devel does not match any error: failed to push some refs to 'git.bioconductor.org:packages/DCATS.git'

When I run "git remote -v", I got:

origin git@github.com:holab-hku/DCATS.git (fetch) origin git@github.com:holab-hku/DCATS.git (push) upstream git@git.bioconductor.org:packages/DCATS.git (fetch) upstream git@git.bioconductor.org:packages/DCATS.git (push)

lshep commented 1 year ago

Is your local branch named something different than "devel" -- like "master" or "main" ? git branch should show you the name. If so whatever that name is (for example we will say "master") in order to push to devel on git.bioconductor.org you would need to do something like git push upstream master:devel

jianhong commented 1 year ago

Did you try:

git checkout devel
git merge origin master # if you need to merge from master
git push upstream devel
bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1fd9360e74013f787ba2af227bb687202687f6ea

bioc-issue-bot commented 1 year 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, 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. 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/DCATS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

linxy29 commented 1 year ago

Thanks @lshep @jianhong, problems solved.

Follwoing is point by point response to the previous review. All important and most of the note were fixed.

The DESCRIPTION file

The NAMESPACE file

General package development

R code

Documentation

jianhong commented 1 year ago

Please update the depends to:

Depends: R (>= 4.3.0), stats
jianhong commented 1 year ago

Package 'DCATS' Review

It is almost there. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please condsider; Important: must be addressed.

General package development

R code

Documentation

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2dfd2e0ca1477cd30c59250386152c9e5bffd574

bioc-issue-bot commented 1 year 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/DCATS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

linxy29 commented 1 year ago

Dear reviewers,

DCATS is revised based on the review comments.

General package development

R code

Documentation

jianhong commented 1 year ago

Package 'DCATS' Review

Please fix the following notes and then I think it is ready to be accepted. There is warning in the biocheck but I can not repeat that. I check the documentation and mark it as false warning.

Code: Note: please condsider; Important: must be addressed.

R code

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 82d2c76590f43fb4da0703cf386cd4af0a419805

linxy29 commented 1 year ago

Dear reviewers,

DCATS is revised based on the review comments.

R code

bioc-issue-bot commented 1 year 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/DCATS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jianhong commented 1 year ago

@vjcitn Thank you for fix all the comments. I checked the build report, and found that I missed several things:

@lshep Could you please double check about the warning message

* WARNING: Empty or missing \value sections found in man pages.

I must missing something and I can not locate the warning message.

linxy29 commented 1 year ago

@jianhong Hi jianhong, clusterRes is one column of an input dataframe. I'm not sure how to address this NOTE.

jianhong commented 1 year ago

check function as.formula, eg

as.formula("clusterRes ~ .")
linxy29 commented 1 year ago

@jianhong Hi jianhong, I assume the NOTE 'Undefined global functions or variables: clusterRes' means in the svm_simMat function, there is no defined clusterRes when it is used in the code 'svmfit <- e1071::svm(clusterRes ~ ., data = dataframe[-idxV[[i]],], kernel = "radial")'. But the clusterRes is actually from a input dataframe. It is not defined separately, so I guess this NOTE is not a problem needed to be addressed?

jianhong commented 1 year ago

Try my suggestion does not hurt.

linxy29 commented 1 year ago

Sure, jianhong. Could you specify what you want me to check in function as.formula, eg as.formula("clusterRes ~ .")?

jianhong commented 1 year ago

line 33 in svm_simMat.R, change

svmfit <- e1071::svm(clusterRes ~ ., data = dataframe[-idxV[[i]],], kernel = "radial")

to

svmfit <- e1071::svm(as.formula("clusterRes ~ ."), data = dataframe[-idxV[[i]],], kernel = "radial")
linxy29 commented 1 year ago

Dear reviewers,

I failed to trigger a new build again. I used the same code as what I used before. The version of DCATS was changed from 0.99.3 to 0.99.4. My local branch named 'devel'. Following is the output of git remote -v, git checkout devel, and git push upstream devel.

(base) [linxy29@hpc02 DCATS]$ git remote -v origin git@github.com:holab-hku/DCATS.git (fetch) origin git@github.com:holab-hku/DCATS.git (push) upstream git@git.bioconductor.org:packages/DCATS.git (fetch) upstream git@git.bioconductor.org:packages/DCATS.git (push)

(base) [linxy29@hpc02 DCATS]$ git checkout devel Already on 'devel' Your branch is up to date with 'origin/devel'.

(base) [linxy29@hpc02 DCATS]$ git push upstream devel X11 forwarding request failed on channel 0 Everything up-to-date

What should I do in this case? Thank you for your help.

lshep commented 1 year ago

Could you try again with just doing a version bump and show everything from commit to push? Sometime the system gets confused when you do the version bump in a merge and with subsequent commits after. When I do a checkout of your code, the version bump to 0.99.4 was on April 24 but then you had additional commits and pushes without a version bump today.

ie.

git checkout devel
## version bump DESCRIPTION to 1.99.5
git add DESCRIPTION
git commit 
git push upstream devel
bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 73f462c2895e223072096819c94eb8f7f1a6c3f0

bioc-issue-bot commented 1 year 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/DCATS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.