New package omXplore #3347

samWieczorek · 2024-03-18T09:24:47Z

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

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

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bioc-issue-bot · 2024-03-18T09:24:51Z

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 = "samuel.wieczorek@cea.fr", 
      role = c("aut","cre"),
      comment = c(ORCID="0000-0002-5016-1203")),
  person(given = "Thomas", 
      family ="Burger",
      email = "thomas.burger@cea.fr",
      role = c("aut")),
  person(given = "Enora", 
    family = "Fremy",
    email = "enora.fremy@cea.fr", 
    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

lshep · 2024-03-21T15:46:07Z

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.

samWieczorek · 2024-03-22T10:01:19Z

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

lshep · 2024-03-27T14:31:50Z

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 ?

samWieczorek · 2024-04-02T14:04:42Z

Do not know what happened. Must be ok now.

bioc-issue-bot · 2024-04-04T14:18:45Z

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
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version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org
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bioc-issue-bot · 2024-04-04T14:27:00Z

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
git@git.bioconductor.org:packages/omXplore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-04-08T05:49:13Z

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

bioc-issue-bot · 2024-04-08T05:59:29Z

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
git@git.bioconductor.org:packages/omXplore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-04-08T06:39:51Z

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

bioc-issue-bot · 2024-04-08T06:50:18Z

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
git@git.bioconductor.org:packages/omXplore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-04-08T07:29:32Z

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

bioc-issue-bot · 2024-04-08T07:39:53Z

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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-04-08T08:14:05Z

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

bioc-issue-bot · 2024-04-08T08:23:01Z

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
git@git.bioconductor.org:packages/omXplore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-04-10T13:47:22Z

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

vjcitn · 2024-04-12T15:18:06Z

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

bioc-issue-bot · 2024-04-13T14:42:02Z

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

samWieczorek · 2024-04-13T14:42:16Z

Oupss, sorry. I have forgotten some comments. Fixed

bioc-issue-bot · 2024-04-13T14:50:49Z

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
git@git.bioconductor.org:packages/omXplore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-04-13T15:49:52Z

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

bioc-issue-bot · 2024-04-13T15:58:31Z

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
git@git.bioconductor.org:packages/omXplore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Mar 18, 2024

lshep added the 3e. pending pre-review changes review has indicated blocking concern that needs attention label Mar 21, 2024

lshep added pre-check passed pre-review performed and ready to be added to git and removed 3e. pending pre-review changes review has indicated blocking concern that needs attention labels Apr 4, 2024

bioc-issue-bot added the ERROR label Apr 4, 2024

bioc-issue-bot added OK and removed ERROR labels Apr 8, 2024

lshep added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean labels Apr 10, 2024

bioc-issue-bot assigned HelenaLC Apr 10, 2024

lshep assigned vjcitn Apr 12, 2024

bioc-issue-bot added WARNINGS and removed OK labels Apr 13, 2024

bioc-issue-bot added OK and removed WARNINGS labels Apr 13, 2024

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New package omXplore #3347

New package omXplore #3347

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New package omXplore #3347

New package omXplore #3347

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