SVMDO

[robogeno]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/robogeno/SVMDO

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[bioc-issue-bot]

Hi @robogeno

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: SVMDO
Title: SVMDO: Identification of Tumour-discriminating mRNA Signatures
        via Support Vector Machines Supported by Disease Ontology
Version: 0.99.0
Date: 2022-10-13
Authors@R: 
    c(person(given = "Mustafa Erhan",
    family = "Özer",
    role = c("aut","cre"),
    email = "erhanozer19@marun.edu.tr"),
    person(given = "Pemra",
    family = "Özbek Sarıca",
    role = "aut",
    email = "pemra.ozbek@marmara.edu.tr"),
    person(given = "Kazım Yalçın",
    family = "Arğa",
    role = "aut",
    email = "kazim.arga@marmara.edu.tr"))      
Depends: R(>= 4.2), tcltk (>= 4.2.1), gWidgets2 (>= 1.0-9), memoise (>=
        2.0.1), gWidgets2tcltk (>= 1.0-8)
Imports: nortest (>= 1.0-4), e1071 (>= 1.7-11), BSDA (>=
        1.2.1),data.table (>= 1.14.2), sjmisc (>= 2.8.9), klaR (>=
        1.7-1), caTools (>= 1.18.2),caret (>= 6.0-93), survival (>= 3.4-0),
        DOSE (>= 3.22.1) , AnnotationDbi (>= 1.58.0), org.Hs.eg.db (>= 3.15.0),
        dplyr (>= 1.0.10),grDevices, graphics, stats, utils
Description: SVMDO is an easy-to-use GUI using disease information for detecting tumour/normal sample 
    discriminating gene sets from differentially expressed genes. Our approach is based on an 
    iterative algorithm filtering genes with disease ontology enrichment analysis and wilk’s lambda 
    criterion connected to SVM classification model construction. Along with gene set extraction, 
    SVMDO also provides individual prognostic marker detection. The algorithm is designed 
    for FPKM and RPKM normalized RNA-Seq transcriptome datasets.    
biocViews: GeneSetEnrichment, DifferentialExpression, GUI, Classification, RNASeq, Transcriptomics, Survival
NeedsCompilation: no
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Maintainer: Mustafa Erhan Özer <erhanozer19@marun.edu.tr>
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3

[robogeno]

In the "About" section of SVMDO repository page, I changed Disease Related to Disease-Associated. Is it fine to change it or do I have to wait for the moderation?

[vjcitn]

You can make any changes to the repository that you like.

[robogeno]

Do I have to resubmit the package after the changes or just add what I did into the comment section?

[lshep]

@robogeno for now you please make the change in your github repo. @vjcitn may make some pre-review comment before the package is officially in review, for responses to those please make the changes in your github rep and comment back here.

Once the package passes awaiting moderation stage, a review in progress tag will appear, and it will assigned a reviewer. At that time then you would also need to push the changes into git.bioconductor.org.

Cheers

[robogeno]

I added bug report link to the DESCRIPTION file and mentioned this update in the NEWS.md file

[robogeno]

• I changed name of vignette to vignettes due to dissapearing from the installed package
• I changed the numbering of sections in the SVMDO_guide.Rmd file
• I added two new examples about calling SVMDO GUI to the example section in the R script
• All updates were mentioned in the NEWS.md file

[robogeno]

• I updated spelling in README.md, SVMDO_guide.Rmd and DESCRIPTION files
• This update was mentioned in the NEWS.md file

[vjcitn]

  Running ‘testthat.R’
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:

  'select()' returned 1:1 mapping between keys and columns
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]

  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-prognostic_analysis.R:69'): prognostic analysis is succesful ───
  Error in `survival::coxph(survival::Surv(time = alldata1$days_to_death, 
      event = alldata1$vital_status) ~ (moduletrans[, 1]), data = alldata1)`: No (non-missing) observations
  Backtrace:
      ▆
   1. └─survival::coxph(...) at test-prognostic_analysis.R:69:4

  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
  'SVMDO_guide.Rmd' using 'UTF-8'... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

did you run R CMD check on the github repo?

[robogeno]

Yes I did, I only received an error and a warning about pdf manual because I could not install mktex properly.

@.*** MINGW64 /c/Users/Erhan/OneDrive/Belgeler/Github $ R CMD check SVMDO_0.99.0.tar.gz

• using log directory 'C:/Users/Erhan/OneDrive/Belgeler/GitHub/SVMDO.Rcheck'
• using R version 4.2.1 (2022-06-23 ucrt)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: UTF-8
• checking for file 'SVMDO/DESCRIPTION' ... OK
• this is package 'SVMDO' version '0.99.0'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'SVMDO' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... Running 'testthat.R' OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... 'SVMDO_guide.Rmd' using 'UTF-8'... OK NONE
• checking re-building of vignette outputs ... OK
• checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems.
• checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Converting parsed Rd's to LaTeX Creating pdf output from LaTeX ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -Rf C:/Users/Erhan/AppData/Local/Temp/RtmpghswWi/Rd2pdf81079375eba'
• DONE

Status: 1 ERROR, 1 WARNING

Message ID: @.***>

[robogeno]

@vjcitn I have reuploaded my test folder

Erhan özer @.***>, 12 Kas 2022 Cmt, 19:52 tarihinde şunu yazdı:

Yes I did, I only received an error and a warning about pdf manual because I could not install mktex properly.

@.*** MINGW64 /c/Users/Erhan/OneDrive/Belgeler/Github $ R CMD check SVMDO_0.99.0.tar.gz

• using log directory 'C:/Users/Erhan/OneDrive/Belgeler/GitHub/SVMDO.Rcheck'
• using R version 4.2.1 (2022-06-23 ucrt)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: UTF-8
• checking for file 'SVMDO/DESCRIPTION' ... OK
• this is package 'SVMDO' version '0.99.0'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'SVMDO' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... Running 'testthat.R' OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... 'SVMDO_guide.Rmd' using 'UTF-8'... OK NONE
• checking re-building of vignette outputs ... OK
• checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems.
• checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Converting parsed Rd's to LaTeX Creating pdf output from LaTeX ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -Rf C:/Users/Erhan/AppData/Local/Temp/RtmpghswWi/Rd2pdf81079375eba'
• DONE

Status: 1 ERROR, 1 WARNING

Message ID: @.*** com>

[robogeno]

Good night @vjcitn,

I have found and fixed a bug in one of the test scripts. I do not observe error in survival analysis anymore.

[vjcitn]

I used the updated code and the problem persisted. But there are more serious problems.

 setwd(Sys.getenv("HOME"))

  surv_object<-NULL
  tcga_sample_comb<-NULL
  st_point<-NULL
  end_point<-NULL
  exp_col_data<-NULL
  coxcoeff<-NULL

  tcga_sample_comb<-read.table("tcga_sample_comb.txt",sep="\t",header=TRUE)
  exp_col_data<-tcga_sample_comb$id
  gene_path<-system.file("extdata","top_genes_test.txt",package="SVMDO",mustWork = TRUE)
  exp_data<-data.table::fread(gene_path,sep="\t")

this indicates that your package has written a file into my HOME folder. This is not permitted. The convention is that any new data or file production occurs in a temporary folder -- R gives you tempfile() to produce paths for new file creation. Do not use setwd() to work with temporary data -- construct the full paths and work with them.

[robogeno]

@vjcitn, I have combined the test processes into a single file and got rid of the output file dependency in the code steps except the external files. I also erased the setwd(Sys.getenv("HOME")). Now all of the output files are written into a temporary file which is created by R CMD check process.

I do not receive any error.

[vjcitn]

Thanks for being so responsive. I've now checked your package and looked a little more closely at it. I am going to mark it "needs interop" because it is using files to manage information instead of using relevant Bioconductor classes like SummarizedExperiment. The use of tcltk to provide a GUI is somewhat outmoded, shiny is used to produce most GUIs in bioconductor. You could use the tcltk GUI if necessary, but it should not be limited to finding information on the user's filesystem -- it should be possible to discover and use relevant entities in the users workspace or ExperimentHub cache. Please have a look at curatedTCGAData package and its use for acquiring open TCGA data. Also be sure to expose and test functions underlying your data analysis activities. At present you export only one function to drive the GUI and that is quite non-standard. Users will want to be able to see and interact with the underlying analytical functions, and these need to be explained in the vignette and man pages.

[robogeno]

Our algorithm uses fpkm/rpkm normalized RNA-Seq datasets. I did not see these normalization forms in curatedTCGAdata package. Is it ok if I use TCGAbiolinks instead?

[vjcitn]

You can obtain data from TCGAbiolinks but please ensure that a) the user/package builder does not need to do the downloads (e.g., do it, downsample, and serialize in your package or in an ExperimentHubData package), b) you are working with SummarizedExperiment or similar data structures as much as possible.

[robogeno]

Good night @vjcitn,

Due to the illness, I could not write anything earlier.

I have added separate sections of algorithm into the package. Now whole or separate analyses can be applied. To apply separate analyses in different times, the user can save the variables in the workspace.

The recent form of algorithm does not use the output files. It creates variables in workspace and use them in the algorithm steps.

I have also updated the test section to apply the testing processes for each step in the algorithm separately.

Furthermore, I have added a test analysis section into the main screen of our algorithm. I have downsized TCGA-COAD and TCGA-LUSC expression datasets into 198 genes and loaded them into RDS objects to be called during the test analysis. To apply survival analysis, I have also loaded clinical datasets into RDS objects as well. During the test analysis, these objects can be called from the extdata folder.

[vjcitn]

Thanks for your revisions. You are not using SummarizedExperiment to organize the molecular and clinical data, and the tcltk approach does not fit with Bioconductor at this time. I will close the issue; I think you may be better off distributing your package in another way. Study the contributions.bioconductor.org and if you make revisions that are consistent with the guidelines, reopen the issue and we will have another look.

[robogeno]

Good day @vjcitn @lshep,

I have made revisions in my package.

How can I reopen the issue?

[robogeno]

@vjcitn @lshep I also accidentally opened another SVMDO issue 4 days ago.

How can I remove that issue https://github.com/Bioconductor/Contributions/issues/2884 ?

[lshep]

its already closed and had the message to continue on this issue so you are fine. Vince or I will review your changes shortly.

[robogeno]

Good day, To prevent process abort for larger input gene numbers, I have removed time limiter code section in the classification step of the script

[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.

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.

[jianhong]

Package 'SVMDO' Review

Thank you for submition your package to Bioconductor. The package passed check and build. 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.

The DESCRIPTION file

• [ ] R version need to update to 4.3.0

General package development

• [ ] NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'

R code

• [ ] NOTE: no direct slot access with @ or slot() - accessors implemented and used.
  • In file R/server.R:
    • at line 49 found ' c<-as.data.frame(c@assays@data@listData)'
    • at line 53 found ' c<-as.data.frame(c@assays@data@listData)'
    • at line 297 found ' dis_length<-length(disease_enrichment@result$Description)'
    • at line 298 found ' p_check<-(disease_enrichment@result$p.adjust[1])'
    • at line 594 found ' alldata<-as.data.frame(c@assays@data@listData)'
    • at line 598 found ' alldata<-as.data.frame(c@assays@data@listData)'
• [ ] Important: warning, message, stop instead of cat and print outside of show methods.
  • In file R/server.R:
    • at line 189 found ' print("Insufficient gene number All up/downregulated genes were selected")'
    • at line 190 found ' print("Enter a lower value of input size")'
    • at line 238 found ' print("Insufficient gene number All up/downregulated genes were selected")'
    • at line 239 found ' print("Enter a lower value of input size")'
• [ ] NOTE: :: is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::. However please note that you need to manully double check the import items when you make any change in the DESCRIPTION file during development. My recommendation is to remove one or two repeats to force the dependency check.
  • In file R/server.R:
    • at line 6 found ' def_roots <- shinyFiles::getVolumes()()'
    • at line 136 found ' dist_normal_pval<-nortest::ad.test(normal_data[[i]][1:nrow(normal_data)])$p.value'
    • at line 137 found ' dist_tumour_pval<-nortest::ad.test(tumour_data[[i]][1:nrow(tumour_data)])$p.value'
    • at line 179 found ' data.table::fwrite(complete_deg_gene_list,"complete_deg_gene_list.txt",sep = "\t")'
    • at line 198 found ' data.table::fwrite(changed_whole_data,"top_genes.txt",sep = "\t")'
    • at line 248 found ' data.table::fwrite(changed_whole_data,"top_genes.txt",sep = "\t")'
    • at line 287 found ' database_selection<-AnnotationDbi::select(org.Hs.eg.db::org.Hs.eg.db, keys = checking_data,columns = c("ENTREZID", "SYMBOL"),keytype = "SYMBOL")'
    • at line 294 found ' disease_enrichment<-DOSE::enrichDO(pop_gene_id[i],ont = "DO")'
    • at line 315 found ' if (sjmisc::str_contains(tissue_type_list$tissue_type[i],"Nor")) {'
    • at line 318 found ' if (sjmisc::str_contains(tissue_type_list$tissue_type[i],"Tum")) {'
    • at line 337 found ' data.table::fwrite(assigning_disease_filtered_gene_data,"disease_filtered_gene_data.txt",sep = "\t")'
    • at line 417 found ' elected_genes<-klaR::greedy.wilks(tissue_type ~ ., data=disease_filtered_gene_data,niveau=niv_value)'
    • at line 442 found ' spl <- caTools::sample.split(disease_filtered_gene_data$tissue_type, SplitRatio = 0.80)'
    • at line 466 found ' tuning_action<-e1071::svm(as.factor(tissue_type)~., training_set,type="C-classification",scale = FALSE, cross=10 ,gamma = g_val_selection,cost = c_val_selection,probability=TRUE)'
    • at line 477 found ' train_table<-caret::confusionMatrix(t_pred, as.factor(training_set$tissue_type))'
    • at line 478 found ' test_table<-caret::confusionMatrix(y_pred,as.factor(test_set$tissue_type))'
    • at line 636 found ' coxcoeff<- survival::coxph(survival::Surv(time= alldata1$days_to_death, event = alldata1$vital_status) ~ (moduletrans[,1]), data = alldata1)$coefficients'
    • at line 646 found ' alldata1 <- dplyr::mutate(alldata1, PI = PI$PI)'
    • at line 667 found ' surv_object <- survival::Surv(time = alldata1$days_to_death, event = alldata1$vital_status)'
    • at line 668 found ' fit1 <- survival::survfit(surv_object ~ group, data = alldata1)'
    • at line 669 found ' coxhr <- survival::coxph(surv_object ~ group, data = alldata1)'
    • at line 673 found ' data.survdiff <- survival::survdiff(surv_object ~ group, data = alldata1)'
    • at line 680 found ' if (sjmisc::str_contains(modulename,"__")) {'
• [ ] Important: 1:n is not suggested in source code. Use seq_along or seq.int instead.
  • In file R/server.R:
    • at line 61 found ' for (i in 1:ncol(c)) { '
    • at line 68 found ' for (i in 1:ncol(c)) { '
    • at line 87 found ' c<-c[,-(1:col_val_2)]'
    • at line 100 found ' i<-1:ncol(c)'
    • at line 106 found ' for(j in 1:nrow(duplicate_number)){'
    • at line 122 found ' for(i in 1:ncol(c)){'
    • at line 136 found ' dist_normal_pval<-nortest::ad.test(normal_data[[i]][1:nrow(normal_data)])$p.value'
    • at line 137 found ' dist_tumour_pval<-nortest::ad.test(tumour_data[[i]][1:nrow(tumour_data)])$p.value'
    • at line 293 found ' for (i in 1:count_gene_id) {'
    • at line 313 found ' for (i in 1:nrow(tissue_type_list)) {'
    • at line 466 found ' tuning_action<-e1071::svm(as.factor(tissue_type)~., training_set,type="C-classification",scale = FALSE, cross=10 ,gamma = g_val_selection,cost = c_val_selection,probability=TRUE)'
    • at line 622 found ' for (a in 1:length(disc_list$Names)) {'
    • at line 637 found ' PI <- data.frame()[1:nrow(moduletrans),]'
    • at line 639 found ' for (j in 1:nrow(moduletrans)) {'
    • at line 733 found ' for (i in 1:length(string_names)) {'
• [ ] NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.
  • In file R/server.R:
    • at line 61 found ' for (i in 1:ncol(c)) { '
    • at line 68 found ' for (i in 1:ncol(c)) { '
    • at line 106 found ' for(j in 1:nrow(duplicate_number)){'
    • at line 122 found ' for(i in 1:ncol(c)){'
    • at line 135 found ' for (i in start_val:ncol(normal_data)) {'
    • at line 141 found ' for (i in start_val:ncol(c)) {'
    • at line 150 found ' for(i in start_val:ncol(c)) {'
    • at line 293 found ' for (i in 1:count_gene_id) {'
    • at line 313 found ' for (i in 1:nrow(tissue_type_list)) {'
    • at line 622 found ' for (a in 1:length(disc_list$Names)) {'
    • at line 639 found ' for (j in 1:nrow(moduletrans)) {'
    • at line 733 found ' for (i in 1:length(string_names)) {'
• [ ] Important: Use file.path to replace paste
  • In file R/server.R:
    • at line 33 found ' selected_dir_val<-paste(as.character(def_roots),"/",filtered,sep = "")'
• [ ] NOTE: Avoid using '=' for assignment and use '<-' instead
  • R/server.R (line 674, column 14)
  • R/server.R (line 675, column 14)
  • R/server.R (line 676, column 15)
• [ ] Important: Please consider to add drop=FALSE to avoid the reduction of dimension for matrices and arrays. Skip this if it is data.table.
  • In file R/server.R:
    • at line 87 found ' c<-c[,-(1:col_val_2)]'
    • at line 119 found ' normal_data<-c[grep("Nor",c$tissue_type),]'
    • at line 120 found ' tumour_data<-c[grep("Tum",c$tissue_type),]'
    • at line 129 found ' normal_data_mean<-colMeans(normal_data[,start_val:ncol(normal_data)])'
    • at line 130 found ' tumour_data_mean<-colMeans(tumour_data[,start_val:ncol(tumour_data)])'
    • at line 174 found ' sorted_new_bound_form_A<-new_bound_form_A[order(-new_bound_form_A$Fold_Change),]'
    • at line 175 found ' sorted_new_bound_form_B<-new_bound_form_B[order(new_bound_form_B$Fold_Change),]'
    • at line 192 found ' max_down_genes<-sorted_new_bound_form_A[(nrow(sorted_new_bound_form_A)-(top_gene_number-1)):nrow(sorted_new_bound_form_A),]'
    • at line 193 found ' max_up_genes<-sorted_new_bound_form_B[(nrow(sorted_new_bound_form_B)-(top_gene_number-1)):nrow(sorted_new_bound_form_B),]'
    • at line 241 found ' max_down_genes<-sorted_new_bound_form_A[(nrow(sorted_new_bound_form_A)-(top_gene_number-1)):nrow(sorted_new_bound_form_A),]'
    • at line 242 found ' max_up_genes<-sorted_new_bound_form_B[(nrow(sorted_new_bound_form_B)-(top_gene_number-1)):nrow(sorted_new_bound_form_B),]'
    • at line 286 found ' colnames(changed_whole_data[,2:ncol(changed_whole_data)])<-checking_data'
    • at line 309 found ' changed_whole_data<-changed_whole_data[,-1]'
    • at line 418 found ' nameless_disease_filtered_gene_data<-disease_filtered_gene_data[,-1]'
    • at line 424 found ' try(nameless_disease_filtered_gene_data<-nameless_disease_filtered_gene_data[,..elected_val],silent = TRUE)'
    • at line 425 found ' try(nameless_disease_filtered_gene_data<-nameless_disease_filtered_gene_data[,elected_val],silent = TRUE)'
    • at line 496 found ' final_gene_list<-assign(paste0("geneset","",set_val),colnames(disease_filtered_gene_data[,-1]))'
    • at line 577 found ' tcga_sample_comb<-tcga_sample_comb[tcga_sample_comb$tissue_type=="tumour",]'
    • at line 583 found ' exp_data<-exp_data[,st_point:end_point]'
    • at line 612 found ' exp_data<-exp_data[,(names(exp_data) %in% as.factor(alldata$id))]'
    • at line 615 found ' sub_exp_data<-exp_data[exp_data$V1 %in% disc_list$Names,]'
    • at line 626 found ' module <- (sub_exp_data[a,])'
    • at line 627 found ' row.names(module) <- make.names(module[,1], unique = TRUE)'
    • at line 628 found ' module <- (module[,-1])'
    • at line 633 found ' moduletrans<-as.data.frame(moduletrans[match(alldata1$id,rownames(moduletrans)),])'
    • at line 637 found ' PI <- data.frame()[1:nrow(moduletrans),]'

      Documentation

• [ ] Important: Please include Bioconductor installation instructions using BiocManager.
  • rmd file vignettes/SVMDO_guide.Rmd
• [ ] Important: Vignette includes sessionInfo().
  • rmd file vignettes/SVMDO_guide.Rmd
• [ ] Note: Vignette includes motivation for submitting to Bioconductor as part of the abstract/intro of the main vignette.
  • rmd file vignettes/SVMDO_guide.Rmd
• [ ] Important: Please add documentation or link of documentation for the GUI usage.

shiny development

• [ ] Important: Add message and documentation for the input files.
• [ ] Important: Add message and documentation for the output files, eg 'the files were saved to ...'.
• [ ] Note: It will be better to rewrite the functions by module mode.
• [ ] Note: Please consider to rewrite the output process by load the output table by DT package and add download button to save as given format.
• [ ] Note: Please consider to add visualization funcitons.

[robogeno]

Good day @jianhong

I would like to ask about R version update in DESCRIPTION file.

The latest R version I can find in CRAN is 4.2.2

Due to being unable to update R, I get error during package building process after changing the version in DESCRIPTION :

ERROR: this R is version 4.2.2, package 'SVMDO' requires R >= 4.3

[lshep]

Bioconductor is prepping for the next spring release which coincides with the new release of R. The devel version of Bioconductor is therefore also using R-devel while the current Bioconductor release is using 4.2. All newly accepted packages are accepted to devel first and released on the next release time slot (either spring or fall)

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 32d44a3b036df518a4c0e48e888f7902cc1356c6

[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.

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.

[jianhong]

Package 'SVMDO' Review

Thank you for the updates. The package passed check and build. However I did not see your line by line answers for last comments. Please try to answer the comments line by line when you are ready for the next review. Otherwise the reviewer process will be delayed. Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

• [ ] Important: R version need to update to 4.3.0.

R code

• [ ] Important: 1:n is not suggested in source code. Use seq_along or seq.int instead.
  • In file R/server.R:
    • at line 672 found ' lap_PI_test<-lapply(seq_along(1:nrow(moduletrans)), function(b){'
    • at line 760 found ' rm_var_names<-lapply(seq_along(1:length(string_names)), function(i){'
• [ ] NOTE: Avoid using '=' for assignment and use '<-' instead
  • R/server.R (line 707, column 14)
  • R/server.R (line 708, column 14)
  • R/server.R (line 709, column 15)
• [ ] NOTE: Try to check the edge condition when using seq.int or seq_len. For example using seq.int(min(5, nrow(data))) to replace seq.int(5). Try to understand the output of seq.int(1) and seq.int(0).
  • In file R/server.R:
    • at line 71 found ' type_num_data<-seq.int(1,ncol(c))'
    • at line 77 found ' type_num_data<-seq.int(1,ncol(c))'
    • at line 81 found ' type_num_data<-seq.int(1,ncol(c))'
    • at line 162 found ' dist_normal_pval<-ad.test(normal_data[[i]][seq.int(1,ncol(normal_data))])$p.value'
    • at line 163 found ' dist_tumour_pval<-ad.test(tumour_data[[i]][seq.int(1,ncol(tumour_data))])$p.value'
    • at line 167 found ' dist_normal_pval<-ad.test(normal_data[[i]][seq.int(1,ncol(normal_data))])$p.value'
    • at line 168 found ' dist_tumour_pval<-ad.test(tumour_data[[i]][seq.int(1,ncol(tumour_data))])$p.value'
    • at line 319 found ' colnames(changed_whole_data[,seq.int(2,ncol(changed_whole_data))])<-checking_data'
    • at line 342 found ' samp_select_norm<-lapply(seq.int(1,nrow(tissue_type_list)), function(x){'
    • at line 346 found ' samp_select_tum<-lapply(seq.int(1,nrow(tissue_type_list)), function(x){'
    • at line 670 found ' PI <- data.frame()[seq.int(1,nrow(moduletrans)),]'

      Documentation

• [ ] Important: Please include Bioconductor installation instructions using BiocManager.
  • rmd file vignettes/SVMDO_guide.Rmd
• [ ] Important: Vignette includes sessionInfo().
  • rmd file vignettes/SVMDO_guide.Rmd
• [ ] Note: Vignette includes motivation for submitting to Bioconductor as part of the abstract/intro of the main vignette.
  • rmd file vignettes/SVMDO_guide.Rmd

shiny development

• [ ] Important: Add message and documentation for the input files in the shiny ui page.
• [ ] Important: Add message and documentation for the output files, eg 'the files were saved to ...' in the shiny ui page.
• [ ] Note: It will be better to rewrite the functions by module mode.
• [ ] Note: Please consider to rewrite the output process by load the output table by DT package and add download button to save as given format.
• [ ] Note: Please consider to add visualization functions.

[robogeno]

Good day @jianhong,

I apologize for not providing information about the updated sections. When I uploaded the updates to git.bioconductor.org, I only did it to check if I can do it. At that time, I did not realize that I should have added comments about updates.

I have finished most of the updates. I will provide comments about them and the recent ones that you have sent me, as soon as possible.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 26a34610a3b6676d786fcca68574d22e848a3484

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d69de4c4bec896d10d7c0cc0c9155bfda1c6b5dd

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

[robogeno]

Good day @jianhong,

I listed the latest updates in the package:

The DESCRIPTION file

• [x] R version need to update to 4.3.0

General package development

• [x] NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'

R code

• [x] NOTE: no direct slot access with @ or slot() - accessors implemented and used.

• [x] Important: warning, message, stop instead of cat and print outside of show methods.

• [x] NOTE: :: is not suggested in source code unless you can make sure all the packages are imported.

• [x] Important: 1:n is not suggested in source code. Use seq_along or seq.int instead.

• [x] NOTE: Try to check the edge condition when using seq.int or seq_len. For example using seq.int(min(5, nrow(data))) to replace seq.int(5). Try to understand the output of seq.int(1) and seq.int(0).

• [x] NOTE: Vectorize: for loops present, try to replace them by *apply functions. I have exchanged for loops with lapply function

• [x] Important: Use file.path to replace paste

• [x] NOTE: Avoid using '=' for assignment and use '<-' instead All of the ‘=’ symbols are used for arguments inside the functions. Therefore, I couldn't replace them.

• [x] Important: Please consider to add drop=FALSE to avoid the reduction of dimension for matrices and arrays. Skip this if it is data.table. They are all data tables.

Documentation:

• [x] Important: Please include Bioconductor installation instructions using BiocManager.

• [x] Note: Vignette includes motivation for submitting to Bioconductor as part of the abstract/intro of the main vignette.

• [x] Important: Vignette includes sessionInfo().

• [x] Note: Vignette includes motivation for submitting to Bioconductor as part of the abstract/intro of the main vignette.

shiny development

• [x] Important: Add message and documentation for the input files in the shiny ui page. I have added information in .Rd files about input files

• [x] Important: Add message and documentation for the output files in the shiny ui page. I have added message appearing at the download process of survival plots and final discriminative gene set indicating save location

• [x] Note: It will be better to rewrite the functions by module mode.

• [x] Note: Please consider to rewrite the output process by load the output table by DT package and add download button to save as given format. When I used DT package along with Shiny for gene set visualization, I received warning due to using dataTableOutput() function which has the same name in both packages. Therefore, I did not included DT package in algorithm. Would it still be appropriate?

• [x] Note: Please consider to add visualization functions. The recent form of GUI includes both final discriminative gene set and survival plot visualization sections.

[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/SVMDO 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: 9d7c655cb5be1814ca35016483e953d5009f85e5

[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/SVMDO 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: 8b5f9dc941b788f6e3f02a1eb2ab5f396eb033f7

[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.

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 16bfaa4c70a9ba4e5e4b266b7c4d07fb549ef60c

[robogeno]

Good day @jianhong,

• [x] Important: Please add documentation or link of documentation for the GUI usage.

In this update, I added vignette file link to the README file

[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.

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 7f46240bd89a29bca781f7097932125e7816a267

[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, 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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 0c8256d540839b38f5ee26ae228242a66e08e474

[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, 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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: c69f06bf5affba409f1a9b2f71c64d23983b1156

[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, 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.