loxcodeR

[arnavgarg123]

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

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

Confirm the following by editing each check box to '[x]'

• I understand that by submitting my package to Bioconductor,
  the package source and all review commentary are visible to the
  general public.

• I have read the Bioconductor Package Submission
  instructions. My package is consistent with the Bioconductor
  Package Guidelines.

• I understand Bioconductor Package Naming Policy and acknowledge
  Bioconductor may retain use of package name.

• I understand that a minimum requirement for package acceptance
  is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS.
  Passing these checks does not result in automatic acceptance. The
  package will then undergo a formal review and recommendations for
  acceptance regarding other Bioconductor standards will be addressed.

• My package addresses statistical or bioinformatic issues related
  to the analysis and comprehension of high throughput genomic data.

• I am committed to the long-term maintenance of my package. This
  includes monitoring the support site for issues that users may
  have, subscribing to the bioc-devel mailing list to stay aware
  of developments in the Bioconductor community, responding promptly
  to requests for updates from the Core team in response to changes in
  R or underlying software.

• I am familiar with the Bioconductor code of conduct and
  agree to abide by it.

I am familiar with the essential aspects of Bioconductor software
management, including:

• The 'devel' branch for new packages and features.
• The stable 'release' branch, made available every six
  months, for bug fixes.
• Bioconductor version control using Git
  (optionally via GitHub).

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]

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

[lshep]

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