CPSM

[hks5august]

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[bioc-issue-bot]

Hi @hks5august

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: CPSM
Type: Package
Title: CPSM: Cancer patient survival model 
Version: 0.99.0
Authors@R: c(person("Harpreet", "Kaur", email = "hks04180@gmail.com", 
         role = c("aut", "cre"),
         comment = c(ORCID = "0000-0003-0421-8341")),
         person("Pijush", "Das", email = "topijush@gmail.com",
         role = c("aut")),
         person("Uma", "Shankavaram" , email = "uma@mail.nih.gov",
         role = c("aut")))
Description: The CPSM package provides a comprehensive computational pipeline 
   for predicting the survival probability of cancer patients. It 
   offers a series of steps including data processing, splitting 
   data into training and test subsets, and normalization of data. 
   The package enables the selection of significant features based on 
   univariate survival analysis and generates a LASSO prognostic 
   index score. It supports the development of predictive models for 
   survival probability using various features and provides 
   visualization tools to draw survival curves based on predicted 
   survival probabilities. Additionally, SPM includes functionalities 
   for generating bar plots that depict the predicted mean and median 
   survival times of patients, making it a versatile tool for 
   survival analysis in cancer research.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
  SummarizedExperiment,
	grDevices,
	Rcpp ,
	MASS ,
	dplyr ,
	reshape2 ,
	survival ,
	survminer ,
	ggplot2 ,
	MTLR ,
	SurvMetrics ,
	pec ,
	glmnet ,
	ggfortify ,
	rms ,
	preprocessCore ,
	survivalROC ,
	ROCR ,
	Hmisc ,
	Matrix ,
	svglite,
	stats,
  utils
Suggests:
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
URL: https://github.com/hks5august/CPSM/
BugReports: https://github.com/hks5august/CPSM/issues
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: GeneExpression, Normalization

[lshep]

Please don't use the export pattern to export all functions. Please list exported function explicitly and avoid exporting internal/helper functions.
Please also rename the vignette file to something more distinct. (Likely the name of the package) to avoid naming conflicts with other loaded packages. Currently without specifying your package the mixOmics vignette would open instead

> library(CPSM)
> vignette("vignette")
starting httpd help server ... done
Warning message:
vignette 'vignette' found more than once,
using the one found in '/home/lorikern/R-Libraries/R4.4-Bioc3.20/mixOmics/doc' 

There is a error in the tests

* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SurvPredPipe)
  Error in library(SurvPredPipe) : 
    there is no package called 'SurvPredPipe'

SurvPredPipe does not appear to be on CRAN or Bioconductor and cannot be used in your package. All dependencies must be on CRAN or Bioconductor.
I see you import SummarizedExperiment but currently don't see it utilized. Given the data is samples and features with expression values, it seems appropriate that your functions should work with a SummarizedExperiment and that this should be shown in perhaps a secondary vignette rather than utilizing data.frames.

[lshep]

may we expect updates soon?

[hks5august]

Thank you for reaching out to me. Yes, I am working on it. Hopefully, soon everything will works fine.

…

On Tue, Sep 24, 2024 at 1:42 PM lshep ***@***.***> wrote: may we expect updates soon? — Reply to this email directly, view it on GitHub <#3518 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEXFF7ZELN5XTURZUJ7ZJLZYGQA7AVCNFSM6AAAAABMU4HKZ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZRHEZDANRUG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[bioc-issue-bot]

This issue is being closed because there has been no progress
for an extended period of time. You may reopen the issue when
you have the time to actively participate in the review /
submission process. Please also keep in mind that a package
accepted to Bioconductor requires a commitment on your part to
ongoing maintenance.

Thank you for your interest in Bioconductor.

[hks5august]

Hello, I have updated the package and wanted to re-open the issue.

[hks5august]

Hello, I have updated the package and tried to resolve the issues. Now, I want to re-open the issue. Best Regards Harpreet Kaur, Ph.D

…

On Fri, Nov 8, 2024 at 9:58 AM bioc-issue-bot ***@***.***> wrote: This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance. Thank you for your interest in Bioconductor. — Reply to this email directly, view it on GitHub <#3518 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEXFFZW6O3ZJ6VAT2HBLOLZ7TGQRAVCNFSM6AAAAABMU4HKZ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINRUHE3DSMBWG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[hks5august]

Thank You for re-opening. We have fixed the issues. It should work now.

[hks5august]

Thank You Best Regards Harpreet Kaur, Ph.D

…

On Thu, Nov 21, 2024 at 7:37 AM lshep ***@***.***> wrote: Reopened #3518 <#3518> . — Reply to this email directly, view it on GitHub <#3518 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEXFFZLO4Q5QJ7VUV2P2P32BXHW5AVCNFSM6AAAAABMU4HKZ6VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJVGM4DCMRUHA2DIMQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[lshep]

As mentioned before I see you import SummarizedExperiment but currently don't see it utilized. Given the data is samples and features with expression values, it seems appropriate that your functions should work with a SummarizedExperiment and that this should be shown in perhaps a secondary vignette rather than utilizing data.frames. Bioconductor requires interoperability with standardized Bioconductor class objects . We also recommend renaming the vignette to something more distictive to avoid load
conflicts. We strongly recommend changing vignette.Rmd to CPSM.Rmd.

[hks5august]

Thank You for your suggestions.
In the updated CPSM package, we have made following changes:

1. Renamed vignette file from vignette.Rmd to CPSM.Rmd.
2. We have updated "data" example files which requires "SummarizedExperiment" packge. We have made required changes.

I believe updated CPSM package should works now. Thank You for your Consideration.
Best Regards

Harpreet Kaur, Ph.D

[lshep]

You likely want to create accessor methods to retrieve commonly used values. For instance instead of parsing your list with $ have a train_data(), train_clinical(), train_normalized(), that gets the value.... etc....

[hks5august]

Yes, We have implemented accessor methods to retrieve commonly used values, designed to integrate seamlessly with functions that automatically partition the dataset based on user-provided arguments. For instance, users can specify the column number where the expression values begin, and a dedicated variable accepts this input. The accessor methods then retrieve the corresponding values efficiently. This approach simplifies the process of using the example dataset and allows users to easily prepare and analyze their own datasets with flexibility and ease.

Thank You

Regards
Harpreet Kaur

[bioc-issue-bot]

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
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Bioconductor utilized your github ssh-keys for git.bioconductor.org
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Bioconductor Git Credentials Account

[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, 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:
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/CPSM 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: "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.

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

[hks5august]

Dear Bioconductor Team,

Thank you for your notification regarding the build error for my package, CPSM.

Upon reviewing the build report, it appears that the error is related to missing dependencies (MTLR, SurvMetrics, and pec). These packages are integral components of CPSM, and I believe their unavailability on the build system caused the error.

To address this issue, I would like to confirm:

1. Are these dependencies (MTLR, SurvMetrics, pec) available on the build system?
   If not, should I include installation instructions for these dependencies in the package documentation or use the Remotes field in the DESCRIPTION file to specify their source ?

Regards,
Harpreet Kaur, Ph.D

[lshep]

If they are current packages on CRAN/Bioconductor they should be available. We can look into why they were not being installed. You did specify them in the DESCRIPTION?

[hks5august]

Yes, they are mentioned under Import in the DESCRIPTION file.

Thank You
Harpreet Kaur, PhD

[lshep]

We've made sure they are installed and I just kicked off a new build manually. You should get a new report soon

[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 24.04.1 LTS): CPSM_0.99.0.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/CPSM to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hks5august]

Dear Bioconductor Team,
Thank you for your valuable feedback on the submission of the CPSM package. We have carefully reviewed the identified issues and updated the package accordingly. Below is a summary of the concerns raised and the steps taken to address them:

1. System Files Found (ERROR)
   Issue:
   The file CPSM.Rproj is tracked by Git but should not be included in the submission.
   Resolution:
   I have added the file to the .gitignore file to ensure it is no longer tracked.

2. R CMD CHECK
   Outcome:
   All checks passed successfully with 0 errors, 0 warnings, and 0 notes.

3. BiocCheck
   Outcome:
   There are no errors or warnings, but 5 notes remain. Below is the detailed explanation:
   a. Maintainer Subscription Note
   Issue:
   "Cannot determine whether the maintainer is subscribed to the Bioc-Devel mailing list."
   Resolution:
   The maintainer (Harpreet Kaur) is subscribed to the Bioc-Devel mailing list. I have updated the DESCRIPTION file to reflect this, adding:

Maintainer: Harpreet Kaur hks04180@gmail.com

b. Redundant 'stop' and 'warn' in Signal Conditions*
Issue:
Avoid redundancy in stop and warning calls.
Resolution:
I reviewed the code to ensure proper use of these functions. However, this note appears generic and no further action is needed.
c. Use of suppressWarnings/*Messages
Issue:
"Avoid 'suppressWarnings'/'suppressMessages' if possible (found 2 times)."
Resolution:
The use of suppressWarnings and suppressMessages is necessary in these cases to prevent irrelevant output from interfering with the package's functionality. There are no suitable alternatives in these scenarios.
d. Function Length Exceeds 50 Lines
Issue:
"The recommended function length is 50 lines or less. There are 7 functions greater than 50 lines."
Resolution:
While I understand the recommendation, refactoring these functions would compromise their readability and maintainability. Therefore, I request an exception for this note.
e. Line Indentation
Issue:
"Consider multiples of 4 spaces for line indents; 605 lines (27%) are not."
Resolution:
Aligning all lines to use multiples of 4 spaces across 605 lines is a significant effort and may not be feasible in the current timeline. I will consider improving this in future updates.

I have addressed all actionable items, resolved errors, and clarified why specific notes cannot be resolved at this time. Please let me know if further adjustments are required for the package's acceptance.
Thank you for your time and consideration.

Best regards,
Harpreet Kaur, Ph.D

[lshep]

Can you please do a version bump and push to git.bioconductor.org to trigger a new build report

[hks5august]

Hello,
I have updated the version of the package.

Thank You

Harpreet Kaur, Ph.D

[lshep]

You need to push to git.bioconductor.org to trigger a new build report. See the previous comment #3518 (comment)

[hks5august]

Hi,
I was trying push my updated package with command "git push bioconductor main". But I am getting following error.

"FATAL: W any hks5august/CPSM hks5august DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists. "

I have checked i have permission of "R and W" for CPSM with Bioctedentials
I have also make sure ssh key is added.

I am unable to understand above issue.

Thank You

Harpreet Kaur, Ph.D

[lshep]

Please share git remote -v so we can make sure the remotes are set up correctly and that a remote called bioconductor exists (we normally recommend calling this upstream). Next Bioconductor does not have a main branch. We have releases and devel branch. https://contributions.bioconductor.org/git-version-control.html . See section 21.5.1 particularly step 5 that shows how to push from a differently named branch

[hks5august]

git remote -v

bioconductor git@git.bioconductor.org:hks5august/CPSM.git (fetch)
bioconductor git@git.bioconductor.org:hks5august/CPSM.git (push)
origin git@github.com:hks5august/CPSM.git (fetch)
origin git@github.com:hks5august/CPSM.git (push)

[lshep]

and the branch you are on locally is called main git branch ? if so then it should be something do a git fetch --all and then git push bioconductor main:devel

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f9f657b51245c5039c5b72c44f3f5df1c188f1ab

[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 24.04.1 LTS): CPSM_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/CPSM 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: dc4e3774401758a4df4c7dc1d0e815fc18df777e

[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 24.04.1 LTS): CPSM_0.99.2.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/CPSM 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: 0b74789b02021f74b7bf857dc430a9f0d464db65

[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 24.04.1 LTS): CPSM_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/CPSM 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: 511690277553cc33d202e9fc3f081b492fe83763

[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 24.04.1 LTS): CPSM_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/CPSM to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hks5august]

Dear Bioconductor Team,

Thank you for your detailed feedback on the CPSM package submission. After carefully reviewing the identified issues in the build report, I have made the necessary updates and addressed them accordingly. Below is a summary of the build report of updated version of the package and concerns raised and the actions taken to resolve them:

BiocCheck v1.43.2 Results
Outcome:
0 ERRORS | 0 WARNINGS | 0 NOTES

R CMD CHECK Results
Outcome:
All checks passed successfully with 0 errors, 0 warnings, and 0 notes.

BiocCheck ('CPSM_0.99.4.tar.gz') Results
Outcome:
BiocCheck v1.43.2 results:
0 ERRORS | 0 WARNINGS | 4 NOTES

Details on Unresolved Notes
Note: Avoid redundant 'stop' and 'warn' in signal conditions.
Response:
I have thoroughly reviewed the code to ensure proper usage of these functions. This note appears generic, and no redundant usage of stop or warn was identified. Therefore, no further action is required.

Note: Avoid 'suppressWarnings'/'suppressMessages' if possible (found 2 times).
Response:
The use of suppressWarnings and suppressMessages is critical in the identified cases to prevent irrelevant output from interfering with the package's functionality. Unfortunately, there are no suitable alternatives for these scenarios.

Note: The recommended function length is 50 lines or less. There are 7 functions greater than 50 lines.
Response:
While I understand the recommendation, refactoring these functions would compromise their readability and maintainability. Given their current design, I kindly request an exception for this note.

Note: Consider multiples of 4 spaces for line indents; 569 lines (26%) are not.
Response:
Aligning all lines to use multiples of 4 spaces across 369 lines would require considerable effort and is not feasible in the current timeline. However, I will prioritize addressing this in future updates to enhance code formatting consistency.

Summary
I have addressed all actionable items, resolved errors, and provided detailed justifications for the notes that remain unresolved. Please let me know if additional adjustments are required to facilitate the acceptance of the CPSM package.

Thank you for your time and consideration.

Best regards,
Harpreet Kaur, Ph.D