robogeno commented 1 year ago

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bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a9f56517d562bbae3d2f7c51da83d95599d95f84

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

robogeno commented 1 year ago

Good Day @jianhong @lshep,

I changed GUI title section from SVMDO-trial to SVMDO in R/runApp file.

After pushing the update, this error appeared in the build report section of nebbiolo1 BUILD SRC output. I did not change anything in rmd file for this update. Do you have any suggestion?

Error running filter pandoc-citeproc: Could not find executable pandoc-citeproc Error: processing vignette 'SVMDO_guide.Rmd' failed with diagnostics: pandoc document conversion failed with error 83 --- failed re-building SVMDO_guide.Rmd

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e782abdba77c25c2561693d39b75fa2ac9e76fcf

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

robogeno commented 1 year ago

Good Day @jianhong @lshep,

I fixed the error by removing citation style section and applying citation by hand in vignette file

jianhong commented 1 year ago

Package 'SVMDO' Review

The package passed check and build. It is in pretty good shape now. I saw multiple modules. Great job! However there are still somethings need to be improved. 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.

R code

[ ] Important: system2 instead of system.
- In file R/deg_server.R:
  - at line 20 found ' c_path<-system.file("extdata","coad_exp_sum.rds",package="SVMDO",mustWork = TRUE)'
  - at line 26 found ' c_path<-system.file("extdata","lusc_exp_sum.rds",package="SVMDO",mustWork = TRUE)'
- In file R/directory_selection_server.R:
  - at line 10 found ' osSystem <- Sys.info()["sysname"]'
  - at line 11 found ' if (osSystem == "Linux") {'
  - at line 37 found ' if (osSystem == "Linux") {'
- In file R/survival_analysis_server.R:
  - at line 51 found ' c_path<-system.file("extdata","coad_clinic_sum.rds",package="SVMDO",mustWork = TRUE)'
  - at line 55 found ' c_path<-system.file("extdata","lusc_clinic_sum.rds",package="SVMDO",mustWork = TRUE)'
[ ] NOTE: Avoid using '=' for assignment and use '<-' instead Found in files:
- R/survival_analysis_server.R (line 136, column 14)
- R/survival_analysis_server.R (line 137, column 14)
- R/survival_analysis_server.R (line 138, column 15)
[ ] NOTE: Functional programming: code repetition.
- repetition in innerServer_3 and innerServer_5
  - in innerServer_3
    - line 147: if (nrow(sorted_new_bound_form_A) < top_gene_number |
    - line 148: nrow(sorted_new_bound_form_B) < top_gene_number) {
    - line 149: message_val_2 <- 1
    - line 150: max_down_genes <- sorted_new_bound_form_A
    - line 151: max_up_genes <- sorted_new_bound_form_B
    - line 152: message("Insufficient gene number All up/downregulated genes were selected")
    - line 153: message("Enter a lower value of input size")
    - line 154: }
    - line 155: else {
    - line 156: max_down_genes <- sorted_new_bound_form_A[seq.int((nrow(sorted_new_bound_form_A) -
    - line 157: (top_gene_number - 1)), nrow(sorted_new_bound_form_A)),
    - line 158: ]
    - line 159: max_up_genes <- sorted_new_bound_form_B[seq.int((nrow(sorted_new_bound_form_B) -
    - line 160: (top_gene_number - 1)), nrow(sorted_new_bound_form_B)),
    - line 161: ]
    - line 162: }
    - line 163: top_combined_genes <- rbind(max_down_genes, max_up_genes)
    - line 164: rownames(top_combined_genes) <- top_combined_genes[,
    - line 165: 1]
    - line 166: changed_whole_data <- subset(c, select = top_combined_genes$Genes)
    - line 167: assign("top_genes_test", changed_whole_data, envir = .GlobalEnv)
    - line 168: message_val_2 <- 1
    - line 169: }
    - line 170: else {
    - line 172: }
    - line 173: if (!is.null(message_val)) {
    - line 174: showModal(modalDialog(title = "DEG Analysis Result",
    - line 175: "Process Completed", easyClose = TRUE, footer = NULL))
    - line 176: }
    - line 177: if (!is.null(message_val_2)) {
    - line 178: showModal(modalDialog(title = "Test Data-Based DEG Analysis Result",
    - line 179: "Process Completed", easyClose = TRUE, footer = NULL))
    - line 180: }
  - in innerServer_5
    - line 7: if (nrow(sorted_new_bound_form_A) < top_gene_number |
    - line 8: nrow(sorted_new_bound_form_B) < top_gene_number) {
    - line 9: message_val_2 <- 1
    - line 10: max_down_genes <- sorted_new_bound_form_A
    - line 11: max_up_genes <- sorted_new_bound_form_B
    - line 12: message("Insufficient gene number All up/downregulated genes were selected")
    - line 13: message("Enter a lower value of input size")
    - line 14: }
    - line 15: else {
    - line 16: max_down_genes <- sorted_new_bound_form_A[seq.int((nrow(sorted_new_bound_form_A) -
    - line 17: (top_gene_number - 1)), nrow(sorted_new_bound_form_A)),
    - line 18: ]
    - line 19: max_up_genes <- sorted_new_bound_form_B[seq.int((nrow(sorted_new_bound_form_B) -
    - line 20: (top_gene_number - 1)), nrow(sorted_new_bound_form_B)),
    - line 21: ]
    - line 22: }
    - line 23: top_combined_genes <- rbind(max_down_genes, max_up_genes)
    - line 24: rownames(top_combined_genes) <- top_combined_genes[,
    - line 25: 1]
    - line 26: changed_whole_data <- subset(total_exp_dataset, select = top_combined_genes$Genes)
    - line 27: assign("top_genes", changed_whole_data, envir = .GlobalEnv)
    - line 28: message_val <- 1
    - line 29: }
    - line 30: else {
    - line 33: }
    - line 34: if (!is.null(message_val)) {
    - line 35: showModal(modalDialog(title = "Top Gene Selection Result",
    - line 36: "Process Completed", easyClose = TRUE, footer = NULL))
    - line 37: }
- repetition in innerServer_3 and innerServer_8
  - in innerServer_3
    - line 7: if (rval_sel == "COAD") {
    - line 8: c_path <- system.file("extdata", "coad_exp_sum.rds",
    - line 9: package = "SVMDO", mustWork = TRUE)
    - line 10: c <- readRDS(c_path)
    - line 11: c <- assay(c)
    - line 14: }
    - line 15: else if (rval_sel == "LUSC") {
    - line 16: c_path <- system.file("extdata", "lusc_exp_sum.rds",
    - line 17: package = "SVMDO", mustWork = TRUE)
    - line 18: c <- readRDS(c_path)
    - line 19: c <- assay(c)
    - line 178: showModal(modalDialog(title = "Test Data-Based DEG Analysis Result",
    - line 179: "Process Completed", easyClose = TRUE, footer = NULL))
    - line 180: }
    - line 181: })
  - in innerServer_8
    - line 36: if (rval_sel == "COAD") {
    - line 37: c_path <- system.file("extdata", "coad_clinic_sum.rds",
    - line 38: package = "SVMDO", mustWork = TRUE)
    - line 39: c <- readRDS(c_path)
    - line 40: alldata <- assay(c)
    - line 41: }
    - line 42: else if (rval_sel == "LUSC") {
    - line 43: c_path <- system.file("extdata", "lusc_clinic_sum.rds",
    - line 44: package = "SVMDO", mustWork = TRUE)
    - line 45: c <- readRDS(c_path)
    - line 46: alldata <- assay(c)
    - line 137: }
    - line 138: showModal(modalDialog(title = "Survival Analysis Result",
    - line 139: "Process Completed", easyClose = TRUE, footer = NULL))
    - line 140: })
    - line 141: }
- repetition in innerServer_9 and plot_list_server
  - in innerServer_9
    - line 41: }
    - line 42: if (!is.null(ls(pattern = "fit1_", envir = .GlobalEnv))) {
    - line 43: fitlist <- ls(pattern = "fit1", envir = .GlobalEnv)
    - line 44: modulenamelist <- ls(pattern = "modulename", envir = .GlobalEnv)
    - line 45: plist <- ls(pattern = "^p", envir = .GlobalEnv)
    - line 46: hrlist <- ls(pattern = "hr", envir = .GlobalEnv)
    - line 47: assign("fit_list", fit_list, envir = .GlobalEnv)
    - line 48: assign("modulename_list", modulename_list, envir = .GlobalEnv)
    - line 49: assign("hr_list", hr_list, envir = .GlobalEnv)
    - line 50: assign("p_list", p_list, envir = .GlobalEnv)
  - in plot_list_server
    - line 4: if (length(ls(pattern = "^fit1_", envir = .GlobalEnv)) >
    - line 5: 0) {
    - line 6: fitlist <- ls(pattern = "^fit1", envir = .GlobalEnv)
    - line 7: modulenamelist <- ls(pattern = "modulename", envir = .GlobalEnv)
    - line 8: plist <- ls(pattern = "^p", envir = .GlobalEnv)
    - line 9: hrlist <- ls(pattern = "^hr", envir = .GlobalEnv)
    - line 10: assign("fit_list", fit_list, envir = .GlobalEnv)
    - line 11: assign("modulename_list", modulename_list, envir = .GlobalEnv)
    - line 12: assign("hr_list", hr_list, envir = .GlobalEnv)
    - line 13: assign("p_list", p_list, envir = .GlobalEnv)
[ ] NOTE: About repeat loop, to avoid deep load, please consider to add the loop counter as force stoper.

Documentation

[ ] Important: replace the section How to install R and RStudio GUI by documentation from [Rstudio](https://posit.co/download/rstudio-desktop/) in Vignette
[ ] Note: To make my message clear, I attached a figure here. Please add documentation at the red labels.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d98de698eb91c20d799ef436eeaf9ccab852675a

robogeno commented 1 year ago

Good day @jianhong,

I listed the latest updates in the package:

[x] Important: system2 instead of system. I could not implement system2. Therefore, I used find.package() function to detect package location to be able to call test datasets.
[ ] NOTE: Avoid using '=' for assignment and use '<-' instead ‘=’ symbol was used for function arguments. Therefore, I could not remove them
[x] NOTE: Functional programming: code repetition.
[ ] NOTE: About repeat loop, to avoid deep load, please consider to add the loop counter as force stoper. In the classification server script, duration of repeat loop changes based on the increase in the user-defined top gene number after differential expression analysis. It is also affected from computer performance. Therefore, if I add a loop counter, it can lead to a problem in working with large gene number. Can I keep it in this form?
[x] Important: replace the section How to install R and RStudio GUI by documentation from Rstudio in Vignette
[x] Note: To make my message clear, I attached a figure here. Please add documentation at the red labels. I added messages about steps and a documentation link to GUI. I also removed “result” word from the dialogs to prevent any misunderstanding about showing any result in GUI other than final gene list and survival plots.

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2ec1340f70b6634486598fb7f3e455e92a0c80de

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.

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bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 28f8fd732eda26154b877617d41a3749057a7f10

robogeno commented 1 year ago

Good day @jianhong,

In this update, I added recent figures of SVMDO GUI into the vignette folder

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

robogeno commented 1 year ago

Good day @lshep,

Are you the new reviewer for my package?

lshep commented 1 year ago

yes I have taken over the review. I'm sorry for the delay. I hope to have any feedback for you within the next day.

lshep commented 1 year ago

Please see additional comments below:

README

[ ] Please include Bioconductor installation instructions

inst

[ ] Please include an inst/scripts directory that describes how the data in inst/extdata was generated. This can be code, psuedocode, or text but mimimally should contain source and licensing information. A user should be able to have an idea of how to recreate the objects from these scripts.

man

[ ] Please have a package level man page ?SVMDO that describes the package and maybe where to start or main functions

vignette/shiny

[ ] I am unclear of how to test this with test data. Have you provided the necessary files to run a dummy example for the shiny app? According to your vignette, this is a txt file but from the test section it appears to take rda files with format of SummarizedExperiments. This should be explained and emphasized in the vignette and the documentation updated to state that SummarizedExperiments can be used and what data they should contain. If this is the case, your filter for only txt files should also probably be updated to show all files. I'm curious as to why your browsers also all start at the home directory. It feels more appropriate to start in whatever the users working directory is.
[ ] I would explain that you have to click to get rid of the messages that appear to return to the analysis section and to be able to continue on with another section
[ ] For download, minimally you should give the user the option of where to download. ideally, what to name the file. A user may want to Choose Directory where files are but save to a different folder/subfolder/results folder etc.
[ ] I agree with the previous comment that the messages could be more informative if they are suppose to continue with an analysis step or jump to the results tab.

I look forward to your comments. Cheers,

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c2b948484e1b96eaec1f9f64d23d55ea577513bb

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

robogeno commented 1 year ago

Good day @lshep,

I listed the latest updates in the package:

[x] Including Bioconductor installation instructions into README file
[x] Including an inst/scripts directory that describes how the data in inst/extdata was generated
[x] I have provided test datasets as dummy examples for the shiny app. In this update I emphasized it in vignette and package level man page
[x] I changed the output directory to be only used for downloading gene sets and survival plots. The package will function in user's working directory. Furthermore, final gene set list can be now named before download process. I kept the automatic naming process of individual survival plots.
[x] I added a package level man page that can called with ?SVMDO
[x] I added information about how to get rid of message boxes appearing after each process
[x] I added information in the analysis screen about the analyses that users can jump to the result tab after applying them. Furthermore, I added information in message boxes of classification and survival analyses about checking the result tab

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 174146ebe73f4ec2e12342351021ae6784c01cce

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5aa723e90049976d0b48cd124fcb5474cfc1ce56

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.

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 50be8b5ae059d47f8d994c35b069501545393114

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7f52ba91a6676dc89512beeb4c09a0b14ea3bfab

bioc-issue-bot commented 1 year ago

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bioc-issue-bot commented 1 year ago

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lshep commented 1 year 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/robogeno.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

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for working with this repository. See especially

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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

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(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("SVMDO"). The package 'landing page' will be created at

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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.

robogeno commented 1 year ago

Good day @lshep,

My package is not in nightly devel build list. Is it ok if I remove a section in my vignette file before it appears?

lshep commented 1 year ago

You can update your package at any time. I added to the daily build list today and it should appear tomorrow. If you push changes before 2 PM ET today, changes should be reflected. Cheers,

robogeno commented 1 year ago

Good day @lshep,

My package passed Multiple platform build/check process. Yet, the landing page link opens an empty page in bioconductor. When will my package have a landing page?

lshep commented 1 year ago

It should be there today. I will investigate tho and look into any issues that may be causing it.

robogeno commented 1 year ago

The link is active now. Yet, build section says error, the recent version is "0.99.23" not "0.99.22" and vignette file is not in the Documentation section

lshep commented 1 year ago

so 0.99.22 was built likely the day before. 0.99.23 was reflected in today's report and is just propagating now. Once the 0.99.23 officially propagates then the landing page will update (later today -- likely in the next hour or two)

robogeno commented 1 year ago

Good day @lshep,

In the build report, SVMDO windows server build bin is NA. Is there anything I can do to fix the anomaly? I cannot click on NA.

lshep commented 1 year ago

No the NA is on our end and I don't think it prevented the new version from propagating as it is available for download on the landing pages http://bioconductor.org/packages/3.17/bioc/html/SVMDO.html Cheers

robogeno commented 1 year ago

Good day @lshep,

In my build check report of 0.99.23 version, there was a warning about NEWS file. Furthermore, NEWS file link in package page was sending me a blank page with a text saying "NULL".

I updated my package. Warning about NEWS file disappeared. Yet, NEWS link in my package page still opens a page with a text saying "NULL"

lshep commented 1 year ago

http://bioconductor.org/packages/3.17/bioc/news/SVMDO/NEWS is not "NULL" maybe this was transient?

robogeno commented 1 year ago

Good day @lshep,

You are right. It was probably propagating the latest update.

robogeno commented 1 year ago

Good day @lshep,

In BioC 3.18 build/check, kunpeng2 linux ARM64 system reports this error:

ERROR: dependencies ‘klaR’, ‘org.Hs.eg.db’ are not available for package ‘SVMDO’

Is it going to be fixed by itself?

lshep commented 1 year ago

I see this has been answered on bioc-devel mailing list too but yes it should clear up on its own

Bioconductor / Contributions

SVMDO #2848

Package 'SVMDO' Review

R code

Documentation