Contributions loxcodeR

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Repository: https://github.com/tomsergeweber/loxcodeR

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Jun 18 '24 00:06 arnavgarg123

Hi @arnavgarg123

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: loxcodeR
Type: Package
Title: Loxcode Tools
Version: 0.99.1
Authors@R: c(person("Stephen", "Zhang", email = "[email protected]", role = c("aut")),
  person("Arnav", "Garg", email = "[email protected]", role = c("cre", "aut"), comment= c(ORCID = "0009-0007-7156-5382")), 
  person("Tom","Weber", email = "[email protected]", role = c("cph", "aut")))
Description: A system to explore and visualise Loxcodes. This is a Web application to visualise and analyse different aspects of a Loxcode. The app can be used to manipulate and extract meaningful insights from experiment data. The app has Pdf and Web page based report creation to present data analysed in the application.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
LinkingTo: 
    Rcpp
Imports:
    Rcpp,
    dplyr,
    rlang,
    tidyr,
    ggplot2,
    readxl,
    stats,
    ggbeeswarm,
    scatterpie,
    grid,
    methods,
    utils,
    magrittr,
    comprehenr,
    plyr,
    shiny,
    pals
Suggests: 
    knitr,
    rmarkdown,
    qpdf,
    ggthemes,
    matrixStats,
    devtools,
    viridis,
    dygraphs,
    htmlwidgets,
    digest,
    bit,
    flexdashboard,
    highcharter,
    scatterD3,
    VennDiagram,
    reshape,
    tidyverse,
    plotly,
    gridExtra,
    testthat (>= 3.0.0)
URL: https://github.com/tomsergeweber/LoxCodeR2024
BugReports: https://github.com/tomsergeweber/LoxCodeR2024/issues
VignetteBuilder: knitr
RoxygenNote: 7.3.1
biocViews: Software, Visualization, Genetics
Config/testthat/edition: 3

Jun 18 '24 00:06 bioc-issue-bot

I'm getting errors when checking locally. Please investigate

 R CMD check loxcodeR_0.99.1.tar.gz 
* using log directory '/home/lorikern/PkgReview/PreReview/loxcodeR.Rcheck'
* using R version 4.4.0 Patched (2024-04-30 r86503)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file 'loxcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'loxcodeR' version '0.99.1'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'loxcodeR' can be installed ... OK
* used C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   7.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
gatherpairs: ... may be used in an incorrect context
* checking Rd files ... NOTE
checkRd: (-1) run_markov.Rd:26: Lost braces; missing escapes or markup?
    26 | For example, starting from the unrecombined cassette, an interaction (0, 12) yields the 1-element cassette {13}
       |                                                                                                            ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'loxcodeR-Ex.R' failed
The error most likely occurred in:

> ### Name: barcode_table
> ### Title: Generate bar code table
> ### Aliases: barcode_table barcode_table,loxcode_experiment-method
> 
> ### ** Examples
> 
> # Load required packages
> library(loxcodeR)
> 
> # Example usage
> # Assume lox, code_set, and count_matrix are defined
> lox <- readRDS("~/Desktop/loxcodeR/LoxcodeR_app/data-2024-05-20.rds")
Warning in gzfile(file, "rb") :
  cannot open compressed file '/home/lorikern/Desktop/loxcodeR/LoxcodeR_app/data-2024-05-20.rds', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: readRDS -> gzfile
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Class:   simpleError/error/condition
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-codeset_table.R:2:5
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─base::readRDS("~/Desktop/temp22/temp221/loxcodeR/LoxcodeR_app/data-2024-05-20.rds")
   8.   └─base::gzfile(file, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
File ../Docs/FirstPage.png not found in resource path
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 4 NOTEs

Jun 25 '24 13:06 lshep

Hey Ishep,

I have made the changes and these errors should now be resolved. Can you please try again?

Thanks

Jul 05 '24 04:07 arnavgarg123

Please make sure to have an inst/script directory that describes how the data in inst/extdata was created. This can be text, pseudo-code, or code but should minimally contain licensing/source information and be enough information for someone to reproduce the data.

Please rename the vignette to something more informative. my-vignette is too generic and can result in naming conflicts with other packages. We strongly suggest using the name of the package.

Currently the vignette is not appropriate for Bioconductor. The package must contain runnable code to describe the functionality of the package. You may keep this current vignette with the graphics but you should also contain a vignette that has code chunks that are run.

Jul 09 '24 16:07 lshep

Hey Ishep,

I made the above changes and added code chunks that run in the existing vignette. Can you please have a look again?

Thanks

Jul 21 '24 22:07 arnavgarg123

inst/script/DataCreation.md is an empty file? Please update

When I try to build the package I get the following ERROR

R CMD build loxcodeR 
* checking for file 'loxcodeR/DESCRIPTION' ... OK
* preparing 'loxcodeR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘loxcodeR.Rmd’ using rmarkdown

Quitting from lines 249-253 [unnamed-chunk-1] (loxcodeR.Rmd)
Error: processing vignette 'loxcodeR.Rmd' failed with diagnostics:
could not find function "exp_table"
--- failed re-building ‘loxcodeR.Rmd’

SUMMARY: processing the following file failed:
  ‘loxcodeR.Rmd’

Error: Vignette re-building failed.
Execution halted

Aug 05 '24 15:08 lshep

I am sorry about that. Could you please have a look at it again? Thanks

Aug 14 '24 05:08 arnavgarg123

There are some references to a Desktop readRDS("~/Desktop/loxcodeR/LoxcodeR_app/data-2024-05-20.rds") which likely should be updated to a system.file provided?

Aug 20 '24 14:08 lshep

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

Aug 21 '24 13:08 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): loxcodeR_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 [email protected]:packages/loxcodeR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 21 '24 13:08 bioc-issue-bot

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

Sep 03 '24 15:09 bioc-issue-bot

@arnavgarg123 - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

[ ] REQUIRED: There are files within the package that exceed the 5MB size limit.
[ ] REQUIRED: The Installation instructions should also include how to install the package from Bioconductor.

DESCRIPTION

[ ] REQUIRED: Update R version dependency from 3.5.0 to 4.4.0.
[ ] REQUIRED: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependences. For more information, reach out to the Bioconductor community and/or consider a CRAN submission.

Vignette

[ ] REQUIRED: There should be an installation section that demonstrates to the user how to install the package from Bioconductor.

Man pages

[ ] REQUIRED: Use accessors; don't access S4 class slots via @ in examples.

R code

[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 361 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for lin indents. There are 643 lines that are not.

Best, Kayla

Oct 12 '24 22:10 Kayla-Morrell

@arnavgarg123 may we expected updates soon that address reviewer comments?

Dec 03 '24 14:12 lshep

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

Thank you for your interest in Bioconductor.

Jan 14 '25 19:01 bioc-issue-bot

Dear @arnavgarg123 ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

Feb 20 '25 16:02 bioc-issue-bot

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

Feb 20 '25 16:02 bioc-issue-bot

@arnavgarg123 - Please push a version bump of the package and address the comments in my initial review from October.

Best, Kayla

Apr 02 '25 13:04 Kayla-Morrell

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

Thank you for your interest in Bioconductor.

May 30 '25 11:05 bioc-issue-bot

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loxcodeR

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