Contributions New package omXplore

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Repository: https://github.com/prostarproteomics/omXplore

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Mar 18 '24 09:03 samWieczorek

Hi @samWieczorek

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: omXplore
Type: Package
Title: Vizualization tools for 'omics' datasets with R
Version: 0.99.1
Authors@R: 
  c(person(given = "Samuel", 
      family = "Wieczorek",
      email = "[email protected]", 
      role = c("aut","cre"),
      comment = c(ORCID="0000-0002-5016-1203")),
  person(given = "Thomas", 
      family ="Burger",
      email = "[email protected]",
      role = c("aut")),
  person(given = "Enora", 
    family = "Fremy",
    email = "[email protected]", 
    role = c("ctb"))
    )
Description: This package contains a collection of functions (written as
   shiny modules) for the visualisation and the statistical analysis of omics 
   data. These plots can be displayed individually or embedded in a global 
   Shiny module.
   Additionaly, it is possible to integrate third party modules to the main
   interface of the package omXplore.
License: Artistic-2.0
Depends:
    R (>= 4.3.0), methods
Imports:
    shiny, 
    MSnbase,
    PSMatch,
    SummarizedExperiment,
    MultiAssayExperiment,
    shinyBS,
    shinyjs,
    shinyjqui,
    DT,
    RColorBrewer,
    gplots,
    highcharter,
    visNetwork,
    tibble,
    grDevices,
    stats,
    utils,
    htmlwidgets,
    vioplot,
    graphics,
    FactoMineR,
    dendextend,
    dplyr,
    factoextra,
    tidyr
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    testthat,
    Matrix,
    graph
biocViews: 
    Software,
    ShinyApps,
    MassSpectrometry,
    DataRepresentation,
    GUI,
    QualityControl
NeedsCompilation: no
Collate:
    'Infos_adjacencyMatrix.R'
    'Prostar_1x.R'
    'convert_to_mae.R'
    'doc-data.R'
    'external_apps_examples.R'
    'get_pep_prot_CC.R'
    'mae_accessors.R'
    'metacell_utils.R'
    'mod_colorLegend.R'
    'mod_explore_graphs.R'
    'modules.R'
    'omXplore_cc.R'
    'omXplore_corrmatrix.R'
    'omXplore_density.R'
    'omXplore_format_DT.R'
    'omXplore_heatmap.R'
    'omXplore_intensity.R'
    'omXplore_pca.R'
    'omXplore_plots_tracking.R'
    'omXplore_tabExplorer.R'
    'omXplore_variance.R'
    'omXplore_view_dataset.R'
    'palette.R'
    'plot_boxplot.R'
    'plot_heatmap.R'
    'plot_pca.R'
    'plot_violin.R'
    'utils.R'
    'zzz.R'
RoxygenNote: 7.3.1
Packaged: 2017-10-13 11:13:04 UTC; sw175264
Encoding: UTF-8
LazyData: false
URL: https://github.com/prostarproteomics/omXplore, https://prostarproteomics.github.io/omXplore/
BugReports: https://github.com/prostarproteomics/omXplore/issues
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr

Mar 18 '24 09:03 bioc-issue-bot

[ ] You have many additional non standard directories and listings from a base level package. Can this be cleaned up and pared down to just package code and necessities and additional material moved to a different branch?
[ ] What are the files in inst/md should these be moved to standard vignettes?
[ ] There is a single image file in inst/www is it needed or can it be condensed someplace else?
[ ] How is the data in inst/extdata used? There is no documentation on its creation. Please provide relavent informatoni in inst/script on how this data was generated and any source/licensing information.
[ ] Is the doc directory needed for pkgdown?
[ ] In the vignette can you please explain and compare how this package differs from already existing visualiztion packages for omics data that exist in Bioconductor.
[ ] Please be advised when I build the package I get the following

R CMD build omXplore 
* checking for file 'omXplore/DESCRIPTION' ... OK
* preparing 'omXplore':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'omXplore_0.99.1.tar.gz'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  'omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff'

[ ] And R CMD check

R CMD check omXplore_0.99.1.tar.gz 
* using log directory '/home/lorikern/PkgReview/PreReview/omXplore.Rcheck'
* using R Under development (unstable) (2023-10-25 r85412)
* 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 'omXplore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'omXplore' 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
  omXplore/docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package 'omXplore' 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 whether startup messages can be suppressed ... 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
Build_X_CC: no visible global function definition for ‘metadata’
Build_X_CC: no visible global function definition for ‘metadata<-’
Check_MSnSet_Consistency : <anonymous>: no visible global function
  definition for ‘experimentData’
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
  global variable ‘.colData’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘experimentData’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘metadata’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘metadata<-’
Undefined global functions or variables:
  .colData experimentData metadata metadata<-
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ...
  'addingThirdPartyPlots.Rmd' using 'UTF-8'... OK
  'omXplore.Rmd' using 'UTF-8'... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  '/home/lorikern/PkgReview/PreReview/omXplore.Rcheck/00check.log'
for details.

Mar 21 '24 15:03 lshep

I have cleand and update my package omXplore with your advices

many additional non standard directories and listings from a base level package. Can this be cleaned up and pared down to just package code and necessities and additional material moved to a different branch?

unnecessary directories and listings have been deleted

What are the files in inst/md should these be moved to standard vignettes?

Not necessary => deleted

There is a single image file in inst/www is it needed or can it be condensed someplace else?

Not necessary => deleted

How is the data in inst/extdata used? There is no documentation on its creation. Please provide relavent informatoni in inst/script on how this data was generated and any source/licensing information.

The two *.png files have been moved to inst/images

Is the doc directory needed for pkgdown?

Yes but I moved it in the gh-pages branch of omXplore

In the vignette can you please explain and compare how this package differs from already existing visualiztion packages for omics data that exist in Bioconductor.

Done (in Introduction and Features section)

Hope that these updates are sufficient. Please let me know if I have to do anything else

Mar 22 '24 10:03 samWieczorek

I'm still seeing a doc directory and _pkgdown.yml in the main branch rather than in gh-pages as indicated when I do a fresh git clone ?

Mar 27 '24 14:03 lshep

Do not know what happened. Must be ok now.

Apr 02 '24 14:04 samWieczorek

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

Apr 04 '24 14:04 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.

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): omXplore_0.99.2.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/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 04 '24 14:04 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 053cd207de0758b2c5fce050415a701a47fe3356

Apr 08 '24 05:04 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.

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): omXplore_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 [email protected]:packages/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 08 '24 05:04 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: a4f9d992d4b454a6b26c42a8517087e4def6d80b

Apr 08 '24 06:04 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.

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): omXplore_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 [email protected]:packages/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 08 '24 06:04 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 68962fab00d0652729293bf056ec9205dbd385f7

Apr 08 '24 07:04 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.

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): omXplore_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 [email protected]:packages/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 08 '24 07:04 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: a756c91d30a20129edd5d764f9b097aefb28cace

Apr 08 '24 08:04 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): omXplore_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 [email protected]:packages/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 08 '24 08:04 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.

Apr 10 '24 13:04 bioc-issue-bot

Is this really ready to go?

plot_violin.R:#' @param conds xxx
plot_violin.R:#' @param subset xxx
plot_violin.R:#' @param pal.name xxx
Prostar_1x.R:#' @title xxxx
Prostar_1x.R:#' @description xxx
utils.R:#' @title xxx
utils.R:#' @description xxx
utils.R:#' @title xxx
utils.R:#' @description xxx
utils.R:#' @return A `character(1)` with the name of the package or xxx
utils.R:#' @param width xxx
utils.R:#' @param height xxx
utils.R:#' xxxx
utils.R:#' xxxx

Apr 12 '24 15:04 vjcitn

Received a valid push on git.bioconductor.org; starting a build for commit id: 59dbd4625f43a16f3de5cd833225b5997bc370cb

Apr 13 '24 14:04 bioc-issue-bot

Oupss, sorry. I have forgotten some comments. Fixed

Apr 13 '24 14:04 samWieczorek

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: Linux (Ubuntu 22.04.3 LTS): omXplore_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 [email protected]:packages/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 13 '24 14:04 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: ad6ba1e094c1d00c8302deb256ca3b716c2a0dfe

Apr 13 '24 15:04 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): omXplore_0.99.8.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/omXplore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 13 '24 15:04 bioc-issue-bot

really sorry for delay on this. I installed and did ?SE_to_mae and saw

Description:

     The resulting object is an instance of the MultiAssayExperiment
     class. F

looks like some text is lost? Furthermore the example for SE_to_mae starts with miniACC which is not an SE but is already an MAE. What is the intention here?

Jul 11 '24 10:07 vjcitn

In the first paragraph of vignette "Bioconductor" is misspelled. When I try to follow the app code in the vignette, I see

> listPlotModules()
[1] "omXplore_cc"          "omXplore_corrmatrix"  "omXplore_density"    
[4] "omXplore_heatmap"     "omXplore_intensity"   "omXplore_pca"        
[7] "omXplore_tabExplorer" "omXplore_variance"   
> data(sub_R25)
app <- view_dataset(sub_R25)
shiny::runApp(app)

Listening on http://127.0.0.1:6128
No external module was found

and the display is

Jul 11 '24 10:07 vjcitn

@samWieczorek may we expect updates based on the above soon?

Aug 15 '24 12:08 lshep

@samWieczorek will you be working on this?

Sep 04 '24 01:09 vjcitn

Sorry, I did not see your previous message. Yes of course I still work on this. I will check all your previous messages today

Sep 04 '24 06:09 samWieczorek

About the comment of vjcitn [on Jul 11] All is normal. The message indicating "No external module found" explains that the interface only shows default plots embedded in the package omXplore ans the user did not load ant supplementary plot

Sep 04 '24 10:09 samWieczorek

Please let me know if there is anything to modify in this package so as to be in th next release

Sep 06 '24 06:09 samWieczorek

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