search

Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

tidysbml #3319

Closed veronicapaparozzi closed 1 month ago

veronicapaparozzi commented 8 months 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 8 months ago

Hi @veronicapaparozzi

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: tidysbml
Type: Package
Title: Extract SBML's data into dataframes
Version: 0.99.0
Authors@R: person("Veronica", "Paparozzi", role = c("aut", "cre"), email = "veronicapaparozzi1@gmail.com")
Author: Veronica Paparozzi [aut, cre]
Maintainer: Veronica Paparozzi <veronicapaparozzi1@gmail.com>
Description: Starting from one SBML file, it is possible to extract its information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the 'notes' subelement and one set of columns for the content of the 'annotation' subelement. 
License: CC BY 4.0
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: 
  xml2,
  methods
Suggests: 
    rmarkdown,
    knitr,
    BiocStyle
biocViews: GraphAndNetwork, Network, Pathways, Software
VignetteBuilder: knitr
vjcitn commented 8 months ago

Thanks for this submission. Please provide some scientific context in the vignette. It would be great to show how information organized using SBML can be used with existing Bioconductor workflow or annotation processes. This would really help fit the package into the ecosystem. At present the package software focuses on xml transformation.

veronicapaparozzi commented 7 months ago

Thanks for the feedback. I have updated vignette file with required info. If I understand correctly from submission instructions, at this stage the version bump is not required, so I have not made changes in Description file. Please let me know if any adjustment is required. Thank you.

lshep commented 7 months ago

We recommend the vignette have a more distinct name (like your package name). Something generic like introduction can have naming conflicts depending on package load order. For instance just doing library of your package and doing a vignette("introduction") actually pulls up cowplot vignette without explicitly stating your package 

> library(tidysbml)
> vignette("introduction")
starting httpd help server ... done
Warning message:
vignette 'introduction' found more than once,
using the one found in '/home/lorikern/R-Libraries/R4.4-Bioc3.19/cowplot/doc'

You also don't show any examples still that use Bioconductor structures or packages? Unless I missed it?

veronicapaparozzi commented 6 months ago

Dear @lshep, I apologise for delayed reply. I’ve renamed the vignette file adding the package name. About interoperability examples, I've previously inserted at the beginning of the vignette a very short description of interoperability, just quoting the packages name, but your last answer suggest me that maybe it is not enough. Currently I am close to finish an article which describes the package and its applications. In particular, I’ve described some use cases of workflows in R to enable tidysbml output (R dataframes) as input to use other R packages. Specially, I show the R commands to run for:

I suppose that these cases can be used for interoperability examples as well (please correct me if I’m wrong), but only one document can incorporate them. Thus I have some questions:

Many thanks for your patience and availability.

lshep commented 6 months ago

Yes those examples (in particular RCy3 and biomaRt as Bioconductor packages) are suitable. We prefer to have some executed code in the vignette in a similar example to ensure runnable code/examples perform as advertised. If you could add examples showing how to incorporate with RCy3 and boimaRt that would be sufficient.

lshep commented 4 months ago

May we expected updates soon?

veronicapaparozzi commented 4 months ago

Yes, by tomorrow or at the latest the day after tomorrow I will update the package with the requested changes.

veronicapaparozzi commented 4 months ago

Dear @lshep, I've completed the changes discussed: I've update the vignette inserting two example of interoperability (with RCy3 and biomaRt). I've also put an additional file in external data.

bioc-issue-bot commented 4 months ago

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 up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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 4 months ago

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: "skipped, 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: 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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

veronicapaparozzi commented 4 months ago

The error is due to execution of RCy3 function while Cytoscape is not running. I've tried to fix the issue inserting eval=FALSE in the respective chunk, but I cannot fetch or push to Bioconductor git since I lost the passphrase. Should I create another SSH key or there is another way to solve the connection issue? Thank you in advance.

vjcitn commented 4 months ago

@lshep can you help here with ssh problem?

lshep commented 4 months ago

We can not help with ssh key passphrases as they are created locally and known only by the creator. Yes you should create a new ssh key and put it in your BiocCredentials account

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4d17ab7652a3d9f0508a804ae6f6cbe3073c4989

bioc-issue-bot commented 3 months ago

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: macOS 12.7.1 Monterey: tidysbml_0.99.1.tar.gz Linux (Ubuntu 22.04.3 LTS): tidysbml_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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cc17e5c5bd64b305ca354acd6652ed6eb6f6a626

bioc-issue-bot commented 3 months ago

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: "skipped, 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: 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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a82f6c51feff6f69c509e6ce635be513f634e94f

bioc-issue-bot commented 3 months ago

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: macOS 12.7.1 Monterey: tidysbml_0.99.3.tar.gz Linux (Ubuntu 22.04.3 LTS): tidysbml_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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0543b2002954c7c7266d2289f374f5f6c06f910c

bioc-issue-bot commented 3 months ago

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: macOS 12.7.1 Monterey: tidysbml_0.99.4.tar.gz Linux (Ubuntu 22.04.3 LTS): tidysbml_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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0efd11aba5814413f791444bda99d14d83732c82

bioc-issue-bot commented 3 months ago

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: "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.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: tidysbml_0.99.5.tar.gz Linux (Ubuntu 22.04.3 LTS): tidysbml_0.99.5.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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f7ca18d2481553179208d17afd981f02f370cec5

bioc-issue-bot commented 3 months ago

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: "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.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: tidysbml_0.99.6.tar.gz Linux (Ubuntu 22.04.3 LTS): tidysbml_0.99.6.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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

veronicapaparozzi commented 3 months ago

I have added in Suggests the RCy3 and biomaRt packages (that I use in Vignette for examples of interoperability), yet the warning persists.

lshep commented 3 months ago

Thank you. We can proceed with this warning as you show interoperability in the vignette with the mentioned Bioconductor packages. I will assign a reviewer shortly.

bioc-issue-bot commented 3 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

jianhong commented 3 months ago

Package 'tidysbml' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

R code

veronicapaparozzi commented 2 months ago

Dear @jianhong, many thanks for your detailed revision. I am about to finish to address your points and I will provide update soon, before that, I would like to ask you some help now, in order to address all the changes at once.

For this point:

I am creating a new function to validate the SBML file given in input. I've found xml schema for SBML Level 1 and Level 2, and using the xml_validate function from the xml2 package I've successfully validated all the related versions. For SBML Level 3, the schema files are different, in particular only .rng schema are available, containing multiple files with relative dependences. I am encountering issues in this validation, because the xml_validate function returns error saying that the file (the one from which start all the dependencies) is not a schema. I've followed instruction from http://sbml.org/documents/elaborations/using-rng-schemas/ to save correctly the files in a local directory, but I stll cannot address this point. Could you provide any help to solve this error and be able to validate in R the SBML Level 3?

Thank you in advance for your support and, once again, for your valuable feedbacks. Any further help would be really appreciated.

jianhong commented 2 months ago

Did you tired to use Trang to convert the rng file to dtd or xml file?

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7a7d5dbf7eb02b6e5575d3b39febe323115950f8

veronicapaparozzi commented 2 months ago

Dear @jianhong, I've submitted the new package's version. In the following, I've ticked all addressed points, with comments where needed, and commented the others.

Package 'tidysbml' Review

The DESCRIPTION file

  • [x] Important: Depends field is not found in DESCRIPTION.
  • [x] Important: R version is not clear in DESCRIPTION.
  • [x] NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION.
  • [ ] Important: No Bioconductor dependencies detected (Imports or Depends).

As said in previous revisions steps, no Bioconductor packages are required in Depends field for package functioning. However, the package incorporates well with other Bioconductor packages in order to perform applications on bioinformatics tasks. This is outlined in Vignette, where examples are shown, and, also, in the related publication whose submission is currently ongoing (it will be added in CITATION once completed).

The NAMESPACE file

  • [x] Important: Function names use camelCase or snake_case and do not include ..

    • in line 4 export(as_df.annotation)
    • in line 5 export(as_df.attributes)
    • in line 6 export(as_df.notes)

General package development

This point has been addressed only partially, namely I've added a function 'sbml_validate()' which performs validation for SBML up to level 2 version 5. Regarding Level 3, thank you for the suggestion of using Trang, I've tried it now (all versions available in the project site), but issues occurred. In particular, it returns errors due to the presence of external references as they are not supported. To address this issue, I've installed also Jing (trying all available versions) to 'simplify' the original .rng and then pass it to Trang, but also in this case it returns errors, due to conflicts with ID-types in some of the .rng documents: /Users/veronica/Downloads/jing-20091111/bin/sbml-core/sbml-simple-types.rng:104:16: error: conflicting ID-types for attribute "id" of element "exponentiale" from namespace "http://www.w3.org/1998/Math/MathML"

  • [ ] Note: S4 object oriented programming is suggested for xml converted objects.

The purpose of this package is to enable management of SBML information by exploiting the grammar developed in the tidyverse for manipulations. To this aim, an S3 object like a data frame is the final object of interest.

R code

  • [x] 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 be aware that you will need to manually double-check the imported items if you make any changes to the DESCRIPTION file during development. My suggestion is to remove one repetitions to trigger the dependency check.

I'm not sure if I've understood correctly the suggestion: I tried to remove one repetition (when the related function was not imported in namespace using @importFrom command) and then the check() function returned a NOTE saying that there is no visible global function defined with that name. Therefore I have reinserted the repetition. After, I tried to remove one repetition in another function (where the @importFrom is present) and, as expected, no new NOTE appeared. Did I understood well and should keep this elimination, or should I change and return to have all the repetitions?

  • [x] NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.

    • In file R/as_df.annotation.R:

    • at line 13 found ' for(p in seq_along(list_creator[[descriptor_content_idx]])){'

    • at line 24 found ' for(q in seq_along(list_creator[[descriptor_content_idx]][[p]])){'

    • at line 59 found ' for(m in seq_along(list_app)){'

    • at line 108 found ' for (i in seq_len(len)) {'

    • at line 109 found ' for(j in seq_along(names(sbml_list_listOf[[i]]))){'

    • at line 116 found ' for(k in seq_along(sbml_list_listOf[[i]][[j]])){'

    • at line 122 found ' for(n_descr in seq_along(sbml_list_listOf[[i]][[j]][[k]])){'

    • at line 127 found ' for(l in seq_along(list_temp)){'

    • In file R/as_df.attributes.R:

    • at line 26 found ' for (i in seq_along(sbml_list_listOf)) {'

    • at line 27 found ' for(j in seq_along(names(attributes(sbml_list_listOf[[i]])))){'

    • In file R/as_df.notes.R:

    • at line 57 found ' for(l in seq_along(names(list_notes))){'

    • at line 99 found ' for (i in seq_len(len)) {'

    • at line 100 found ' for(j in seq_along(names(sbml_list_listOf[[i]]))){'

    • In file R/as_dfs.R:

    • at line 35 found ' for (i in seq_along(vec_names_model)) {'

    • In file R/as_subdf.R:

    • at line 39 found ' for (i in seq_len(len)) {'

    • at line 40 found ' for(j in seq_along(names(sbml_list_listOf[[i]]))){'

    • at line 47 found ' for(k in seq_along(sbml_list_listOf[[i]][[j]])){'

    • at line 52 found ' for(l in seq_along(names(attributes(list_speciesref)))){'

    • at line 66 found ' for (l in seq_along(list_speciesref)) {'

    • at line 78 found ' for(m in seq_along(list_speciesref[[l]])){'

    • at line 84 found ' for(n_descr in seq_along(names(list_speciesref[[l]][[m]]))){'

    • at line 89 found ' for(n in seq_along(list_descr)){'

I've substituted some of the for loops that have been detected. For the others (in as_df.attributes, as_df.annotation, as_subdf) the replacement requires code reengineering and I think I should change the functions' rationale. Since in this way no performances issues are detected I'm keeping the remaining for loops as they are.

  • [x] Important: Remove unused code.

    • In file R/as_df.notes.R:

    • at line 47 found 'as_value.notes <- function(list_notes){ # , vec_notes_i){ # I think you cannot have multiple notes elements within on entity'

Correct, each entity may contain maximum one notes element. Indeed, here the index is to identify the entity: vec_notes_i is the notes value reported for i-th entity, but which may still contain multiple paragraphs. Anyway, I've simplified the code in this .R file by removing one function.

  • [x] NOTE: Avoid using '=' for assignment and use '<-' instead. Please user styler package to reformat your package.

    • R/as_df.annotation.R (line 18, column 27)
    • R/as_df.annotation.R (line 99, column 6)
    • R/as_df.annotation.R (line 185, column 7)
    • R/as_df.notes.R (line 93, column 6)
    • R/as_df.notes.R (line 97, column 12)
    • R/as_subdf.R (line 22, column 6)
    • R/as_subdf.R (line 48, column 12)
    • R/as_subdf.R (line 150, column 10)
    • R/as_subdf.R (line 152, column 32)
    • R/as_subdf.R (line 165, column 63)
    • R/as_subdf.R (line 166, column 12)
    • R/as_subdf.R (line 173, column 12)
  • [x] To avoid the * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions in BioCheck, could you please change the word error to other word in
    • R/as_df.notes.R (line 12, column 50)

  • [x] NOTE: Functional programming: code repetition.

    • repetition in as_df.annotation, as_df.attributes, as_df.notes, as_subdf, and as_value.notes

    • in as_df.annotation

      • line 1:{
      • line 2: if (missing(sbml_list_listOf))
      • line 3: stop("no argument inserted. You must provide one list in input.")
      • line 4: if (!typeof(sbml_list_listOf) == "list")
      • line 5: stop("argument is not a list")
      • line 6: len = length(sbml_list_listOf)
      • line 7: if (!len)
      • line 8: stop("Empty output : list of length 0 inserted")
      • line 9: if (length(unique(names(sbml_list_listOf))) != 1 && !unique(names(sbml_list_listOf)) %in%
      • line 10: c("species", "reaction", "compartment"))
      • line 11: stop("invalid format for list in input : it must contain only one type of element, that is either 'species','reaction' or 'compartment' type")
      • line 12: vec_names_attr <- c()
      • line 13: vec_annotation <- c()
      • line 14: vec_colname_annotation <- c()
      • line 15: vec_colname_ann_final <- c()
      • line 16: for (i in seq_len(len)) {
      • line 17: for (j in seq_along(names(sbml_list_listOf[[i]]))) {
      • line 18: if (names(sbml_list_listOf[[i]])[j] == "annotation") {
      • line 30: for (l in seq_along(list_temp)) {
      • line 31: name_descriptor <- names(list_temp)[l]
      • line 32: name_coldescriptor <- paste("annotation",
      • line 33: name_descriptor, "__", sep = "")
      • line 34: name_col_tosearch <- substr(name_col_descriptor,
      • line 35: 1, nchar(name_col_descriptor) -
      • line 36: 1)
      • line 37: name_col_tosave <- substr(name_col_descriptor,
      • line 38: 1, nchar(name_col_descriptor) -
      • line 39: 2)
      • line 40: if (!name_col_descriptor %in% vec_colname_annotation) {
      • line 41: assign(name_col_descriptor, rep(NA,
      • line 42: length(sbml_list_listOf)))
      • line 43: vec_colname_ann_final <- c(vec_colname_ann_final,
      • line 44: name_col_tosave)
      • line 45: vec_colname_annotation <- c(vec_colname_annotation,
      • line 46: name_col_descriptor)
      • line 47: vec_names_descriptor <- c(vec_names_descriptor,
      • line 48: name_col_descriptor)
      • line 49: }
      • line 50: else if (!name_col_descriptor %in%
      • line 51: vec_names_descriptor) {
      • line 52: vec_names_descriptor <- c(vec_names_descriptor,
      • line 53: name_col_descriptor)
      • line 54: }
      • line 55: else {
      • line 56: string_tosearch <- paste("^",
      • line 57: name_col_tosearch, ".+", sep = "")
      • line 58: number <- sum(grepl(string_tosearch,
      • line 59: vec_names_descriptor))
      • line 60: name_new_col <- paste(name_col_tosearch,
      • line 61: number, sep = "")
      • line 62: if (name_new_col %in% vec_colname_annotation) {
      • line 63: vec_names_descriptor <- c(vec_names_descriptor,
      • line 64: name_new_col)
      • line 65: }
      • line 66: else {
      • line 67: assign(name_new_col, rep(NA,
      • line 68: length(sbml_list_listOf)))
      • line 69: vec_colname_ann_final <- c(vec_colname_ann_final,
      • line 70: name_new_col)
      • line 71: vec_colname_annotation <- c(vec_colname_annotation,
      • line 72: name_new_col)
      • line 73: vec_names_descriptor <- c(vec_names_descriptor,
      • line 74: name_new_col)
      • line 75: }
      • line 76: name_col_descriptor <- name_new_col
      • line 77: }
      • line 78: list_temp1 <- list_temp[[l]]
      • line 79: vec_app <- get(name_col_descriptor)
      • line 82: vec_app[i] <- as_value.annotation(list_temp1,
      • line 83: vec_app[i])
      • line 84: }
      • line 85: assign(name_col_descriptor, vec_app)
      • line 86: }
      • line 87: }
      • line 88: }
      • line 90: else {
      • line 91: warning("Extraction of 'annotation' is not totally available for '",
      • line 92: names(sbml_list_listOf)[i], " ", i,
      • line 93: "': found element '", names(sbml_list_listOf[[i]][[j]])[k],
      • line 94: "' different from 'RDF' within the input list")
      • line 95: }
      • line 96: }
      • line 97: }
      • line 103: length(vec_colname_annotation)) {
      • line 104: vec_colname_ann_final <- sort(vec_colname_ann_final)
      • line 105: vec_colname_annotation <- sort(vec_colname_annotation)
      • line 106: df = data.frame(lapply(seq_along(vec_colname_annotation),
      • line 107: function(n_col) get(vec_colname_annotation[n_col])))
      • line 109: df
      • line 110: }
      • line 111: else {
      • line 112: message("Empty annotation's columns for '", unique(names(sbml_list_listOf)),
      • line 113: "' elements")
      • line 114: c()
      • line 115: }

    • in as_df.attributes

      • line 1:{
      • line 2: if (missing(sbml_list_listOf))
      • line 3: stop("no argument inserted. You must provide one list in input.")
      • line 4: if (!typeof(sbml_list_listOf) == "list")
      • line 5: stop("argument is not a list")
      • line 6: if (!length(sbml_list_listOf))
      • line 7: stop("empty output. List of length 0 inserted.")
      • line 8: if (length(unique(names(sbml_list_listOf))) != 1 && !unique(names(sbml_list_listOf)) %in%
      • line 9: c("species", "reaction", "compartment"))
      • line 10: stop("invalid format for list in input : it must contain only one type of element, that is either 'species','reaction' or 'compartment' type")
      • line 11: vec_names_attr <- c()
      • line 12: for (i in seq_along(sbml_list_listOf)) {

    • in as_df.notes

      • line 1:{
      • line 2: if (missing(sbml_list_listOf))
      • line 3: stop("no argument inserted. You must provide one list in input.")
      • line 4: if (!typeof(sbml_list_listOf) == "list")
      • line 5: stop("argument is not a list")
      • line 6: len = length(sbml_list_listOf)
      • line 7: if (!len > 0)
      • line 8: stop("empty output. List in input must have length greater than 0.")
      • line 9: if (length(unique(names(sbml_list_listOf))) != 1 && !unique(names(sbml_list_listOf)) %in%
      • line 10: c("species", "reaction", "compartment"))
      • line 11: stop("invalid format for list in input : it must contain only one type of element, that is either 'species','reaction' or 'compartment' type")
      • line 12: vec_notes = rep(NA, len)
      • line 13: for (i in seq_len(len)) {
      • line 14: for (j in seq_along(names(sbml_list_listOf[[i]]))) {
      • line 15: if (names(sbml_list_listOf[[i]])[j] == "notes") {
      • line 23: df
      • line 24: }
      • line 25: else {
      • line 26: message("Empty notes' column for '", unique(names(sbml_list_listOf)),
      • line 27: "' elements")
      • line 28: c()
      • line 29: }

    • in as_subdf

      • line 1:{
      • line 2: if (missing(sbml_list_listOf))
      • line 3: stop("no argument inserted. You must provide one list in input.")
      • line 4: if (!typeof(sbml_list_listOf) == "list")
      • line 5: stop("argument is not a list")
      • line 6: len = length(sbml_list_listOf)
      • line 7: if (!len)
      • line 8: stop("Empty output : list of length 0 inserted")
      • line 17: vec_names_attr <- c()
      • line 18: vec_annotation <- c()
      • line 19: vec_colname_annotation <- c()
      • line 20: vec_colname_ann_final <- c()
      • line 61: for (n in seq_along(list_descr)) {
      • line 62: name_descriptor <- names(list_descr)[n]
      • line 63: name_coldescriptor <- paste("annotation",
      • line 64: name_descriptor, "__",
      • line 65: sep = "")
      • line 66: name_col_tosearch <- substr(name_col_descriptor,
      • line 67: 1, nchar(name_col_descriptor) -
      • line 68: 1)
      • line 69: name_col_tosave <- substr(name_col_descriptor,
      • line 70: 1, nchar(name_col_descriptor) -
      • line 71: 2)
      • line 72: if (!name_col_descriptor %in%
      • line 73: vec_colname_annotation) {
      • line 74: assign(name_col_descriptor,
      • line 75: rep(NA, length(sbml_list_listOf)))
      • line 76: vec_colname_ann_final <- c(vec_colname_ann_final,
      • line 77: name_col_tosave)
      • line 78: vec_colname_annotation <- c(vec_colname_annotation,
      • line 79: name_col_descriptor)
      • line 80: vec_names_descriptor <- c(vec_names_descriptor,
      • line 81: name_col_descriptor)
      • line 82: }
      • line 83: else if (!name_col_descriptor %in%
      • line 84: vec_names_descriptor) {
      • line 85: vec_names_descriptor <- c(vec_names_descriptor,
      • line 86: name_col_descriptor)
      • line 87: }
      • line 88: else {
      • line 89: string_tosearch <- paste("^",
      • line 90: name_col_tosearch,
      • line 91: ".+", sep = "")
      • line 92: number <- sum(grepl(string_tosearch,
      • line 93: vec_names_descriptor))
      • line 94: name_new_col <- paste(name_col_tosearch,
      • line 95: number, sep = "")
      • line 96: if (name_new_col %in%
      • line 97: vec_colname_annotation) {
      • line 98: vec_names_descriptor <- c(vec_names_descriptor,
      • line 99: name_new_col)
      • line 100: }
      • line 101: else {
      • line 102: assign(name_new_col,
      • line 103: rep(NA, length(sbml_list_listOf)))
      • line 104: vec_colname_ann_final <- c(vec_colname_ann_final,
      • line 105: name_new_col)
      • line 106: vec_colname_annotation <- c(vec_colname_annotation,
      • line 107: name_new_col)
      • line 108: vec_names_descriptor <- c(vec_names_descriptor,
      • line 109: name_new_col)
      • line 110: }
      • line 111: name_col_descriptor <- name_new_col
      • line 112: }
      • line 113: list_tmp <- list_descr[[n]]
      • line 114: vec_tmp <- get(name_col_descriptor)
      • line 115: vec_tmp[r] <- as_value.annotation(list_tmp,
      • line 116: vec_tmp[r])
      • line 117: assign(name_col_descriptor,
      • line 118: vec_tmp)
      • line 119: }
      • line 120: }
      • line 124: warning("Extraction of 'annotation' for nested dataframe is not totally available for '",
      • line 125: names(sbml_list_listOf)[i],
      • line 126: " ", i, "': found element '",
      • line 127: names(sbml_list_listOf[[i]][[j]])[k],
      • line 128: "' different from 'RDF' within the input list")
      • line 129: }
      • line 130: }
      • line 131: }
      • line 164: if (length(vec_colname_annotation)) {
      • line 165: vec_colname_ann_final <- sort(vec_colname_ann_final)
      • line 166: vec_colname_annotation <- sort(vec_colname_annotation)
      • line 167: subdf = data.frame(subdf, lapply(seq_along(vec_colname_annotation),
      • line 168: function(n_colannotation) {

    • in as_value.notes

      • line 1:{
      • line 2: if (missing(list_notes))
      • line 3: stop("no argument inserted. You must provide one list in input.")
      • line 4: if (!typeof(list_notes) == "list")
      • line 5: stop("argument is not a list")
      • line 6: if (length(list_notes) == 0) {

Thank you for the notification. Many repetitions have been removed.

Documentation

  • [x] Important: Vignette should have an Installation section.

    • rmd file vignettes/tidysbml-introduction.Rmd

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

    • rmd file vignettes/tidysbml-introduction.Rmd

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

    • rmd file vignettes/tidysbml-introduction.Rmd

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

    • rmd file vignettes/tidysbml-introduction.Rmd
  • [x] Important: when first using an abbreviation or acronym in writing, spelling out the full term and including the abbreviation in parentheses are suggested.
bioc-issue-bot commented 2 months ago

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 22.04.3 LTS): tidysbml_0.99.7.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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0a8602d60cc9557afdafb3478fd026b35ce8ddc9

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3afc293f4c0a633b297858ea8098619449e93e39

bioc-issue-bot commented 2 months ago

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 22.04.3 LTS): tidysbml_0.99.9.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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jianhong commented 2 months ago

Package 'tidysbml' 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 consider; Important: must be addressed.

The DESCRIPTION file

R code

General package development

bioc-issue-bot commented 1 month ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8741976fa528f5810ca1630511ec81a4ef75f421

bioc-issue-bot commented 1 month ago

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): tidysbml_0.99.10.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/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

veronicapaparozzi commented 1 month ago

Dear @jianhong, thanks for this second review, all the points have been addressed.

bioc-issue-bot commented 1 month ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

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

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("tidysbml"). The package 'landing page' will be created at

https://bioconductor.org/packages/tidysbml

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.