From 459bcd90f7027d6ed449679ab47136b891097f48 Mon Sep 17 00:00:00 2001 From: kevinrue Date: Tue, 1 Oct 2024 14:42:32 +0000 Subject: [PATCH] Built site for iSEEindex@1.3.1: 923404e --- 404.html | 18 +- CODE_OF_CONDUCT.html | 18 +- CONTRIBUTING.html | 18 +- SUPPORT.html | 18 +- articles/header.html | 339 ++++++++-------- articles/iSEEindex.html | 363 +++++++++--------- articles/index.html | 18 +- articles/resources.html | 191 +++++---- authors.html | 30 +- index.html | 24 +- news/index.html | 24 +- pkgdown.yml | 7 +- reference/Rplot001.png | Bin 1011 -> 0 bytes reference/iSEEindex-package.html | 20 +- reference/iSEEindex.html | 46 +-- reference/iSEEindexHttpsResource-class.html | 32 +- .../iSEEindexLocalhostResource-class.html | 34 +- reference/iSEEindexRcallResource-class.html | 34 +- reference/iSEEindexResource-class.html | 46 ++- reference/iSEEindexResource-generics.html | 38 +- reference/iSEEindexS3Resource-class.html | 38 +- reference/index.html | 18 +- sitemap.xml | 84 ++-- 23 files changed, 702 insertions(+), 756 deletions(-) delete mode 100644 reference/Rplot001.png diff --git a/404.html b/404.html index c932dc3..c069436 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • iSEEindex - + @@ -19,7 +19,7 @@ - +
@@ -48,7 +48,7 @@
  • @@ -79,7 +79,7 @@
    • - +
    @@ -107,16 +107,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 8e0e159..08c0b8c 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -1,9 +1,9 @@ -NA • iSEEindexNA • iSEEindex - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -92,15 +92,15 @@

    NA

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 004dae6..94cf812 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,9 +1,9 @@ -Contributing to iSEEindex • iSEEindexContributing to iSEEindex • iSEEindex - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -108,15 +108,15 @@

    Code of Conduct
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/SUPPORT.html b/SUPPORT.html index 1e40837..152af33 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -1,9 +1,9 @@ -Getting help with iSEEindex • iSEEindexGetting help with iSEEindex • iSEEindex - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -98,15 +98,15 @@

    What happens next? -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/header.html b/articles/header.html index fd25eff..71389de 100644 --- a/articles/header.html +++ b/articles/header.html @@ -6,21 +6,20 @@ Adding a custom header and footer to the landing page • iSEEindex - + - - +
    @@ -49,7 +48,7 @@
  • @@ -80,7 +79,7 @@
    • - +
    @@ -94,9 +93,9 @@

    Kevin Oxford
    -

    27 March 2024

    +

    1 October 2024

    - Source: vignettes/header.Rmd + Source: vignettes/header.Rmd
    @@ -109,7 +108,7 @@

    Exampleif (interactive()) { shiny::runApp(app, port = 1234) }

    -

    +

    Reproducibility

    -

    The iSEEindex +

    The iSEEindex package (Rue-Albrecht and Marini, 2024) was made possible thanks to:

    -

    This package was developed using biocthis.

    +

    This package was developed using biocthis.

    Code for creating the vignette

     ## Create the vignette
@@ -240,155 +239,155 @@ 
    Reproducibilitylibrary("knitr")
 knit("header.Rmd", tangle = TRUE)

    Date the vignette was generated.

    -
    #> [1] "2024-03-27 09:38:59 UTC"
    +
    #> [1] "2024-10-01 14:42:14 UTC"

    Wallclock time spent generating the vignette.

    -
    #> Time difference of 7.486 secs
    +
    #> Time difference of 7.623 secs

    R session information.

    #> ─ Session info ───────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
-#>  version  R Under development (unstable) (2024-03-24 r86185)
-#>  os       Ubuntu 22.04.4 LTS
+#>  version  R version 4.4.1 (2024-06-14)
+#>  os       Ubuntu 22.04.5 LTS
 #>  system   x86_64, linux-gnu
 #>  ui       X11
 #>  language en
 #>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-03-27
-#>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
+#>  date     2024-10-01
+#>  pandoc   3.4 @ /usr/bin/ (via rmarkdown)
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 #> 
 #>  [1] /__w/_temp/Library
 #>  [2] /usr/local/lib/R/site-library
@@ -399,16 +398,16 @@ 
    Reproducibility
 
    Bibliography
 
    
-
    This vignette was generated using BiocStyle
-(Oleś, 2023) with knitr (Xie,
-2023) and rmarkdown
+
    This vignette was generated using BiocStyle
+(Oleś, 2024) with knitr (Xie,
+2024) and rmarkdown
 (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.
    
 
    Citations made with RefManageR
 (McLean, 2017).
    
 
    
 [1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.26. 2024. URL:
+for R. R package version 2.28. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 
    
 
    
@@ -419,9 +418,9 @@ 
    Bibliography10.21105/joss.00338.
 
    
 
    
-[3]
+[3]
 A. Oleś. BiocStyle: Standard styles for vignettes and other
-Bioconductor documents. R package version 2.31.0. 2023. DOI:
+Bioconductor documents. R package version 2.33.1. 2024. DOI:
 10.18129/B9.bioc.BiocStyle.
 URL:
 https://bioconductor.org/packages/BiocStyle.
@@ -437,7 +436,7 @@ 
    Bibliography[5]
 K. Rue-Albrecht and F. Marini. iSEEindex: iSEE extension for a
 landing page to a custom collection of data sets. R package version
-1.1.2. 2024. URL:
+1.3.1. 2024. URL:
 https://github.com/iSEE/iSEEindex.
 
    
 
    
@@ -449,13 +448,13 @@ 
    Bibliography[7]
 H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session
-Information. R package version 1.2.2. 2021. URL:
-https://CRAN.R-project.org/package=sessioninfo.
+Information. R package version 1.2.2, https://r-lib.github.io/sessioninfo/. 2021. URL:
+https://github.com/r-lib/sessioninfo#readme.
 
    
 
    
-[8]
+[8]
 Y. Xie. knitr: A General-Purpose Package for Dynamic Report
-Generation in R. R package version 1.45. 2023. URL:
+Generation in R. R package version 1.48. 2024. URL:
 https://yihui.org/knitr/.
 
    
 
@@ -464,9 +463,7 @@ 
    Bibliography
 
-        
-
    + @@ -479,16 +476,16 @@

    Bibliography

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/iSEEindex.html b/articles/iSEEindex.html index 17e241e..41c44bd 100644 --- a/articles/iSEEindex.html +++ b/articles/iSEEindex.html @@ -6,21 +6,20 @@ Introduction to iSEEindex • iSEEindex - + - - +
    @@ -49,7 +48,7 @@
  • @@ -80,7 +79,7 @@
    • - +
    @@ -93,9 +92,9 @@

    Kevin Oxford
    -

    27 March 2024

    +

    1 October 2024

    - Source: vignettes/iSEEindex.Rmd + Source: vignettes/iSEEindex.Rmd
    @@ -109,10 +108,10 @@

    Basics

    Install iSEEindex

    R is an open-source statistical environment which can be -easily modified to enhance its functionality via packages. iSEEindex +easily modified to enhance its functionality via packages. iSEEindex is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install -iSEEindex +iSEEindex by using the following commands in your R session:

     if (!requireNamespace("BiocManager", quietly = TRUE)) {
@@ -127,13 +126,13 @@ 
    Install iSEEindex
 
    Required knowledge
 
    
-
    iSEEindex
+
    iSEEindex
 is based on many other packages and in particular those that have
 implemented the infrastructure needed for dealing with omics data and
-interactive visualisation. That is, packages like SummarizedExperiment,
-SingleCellExperiment,
-iSEE
-and shiny.
    
+interactive visualisation. That is, packages like SummarizedExperiment,
+SingleCellExperiment,
+iSEE
+and shiny.
    
 
    If you are asking yourself the question “Where do I start using
 Bioconductor?” you might be interested in this
 blog post.
    
@@ -158,7 +157,7 @@ 
    Asking for help
 
    Citing iSEEindex
 
    
-
    We hope that iSEEindex
+
    We hope that iSEEindex
 will be useful for your research. Please use the following information
 to cite the package and the overall approach. Thank you!
    @@ -207,11 +206,11 @@

    Quick start to using iSEEindexif (interactive()) { shiny::runApp(app, port = 1234) }

    -

    +

    Let’s break down this example step by step, to illustrate the -functionality and flexibility of iSEEindex.

    -

    First, we load the iSEEindex -and BiocFileCache +functionality and flexibility of iSEEindex.

    +

    First, we load the iSEEindex +and BiocFileCache packages, to access their functionality.

    Next, we use the BiocFileCache::BiocFileCache() function, to create a persistent on-disk cache of files that the app can @@ -240,7 +239,7 @@

    Quick start to using iSEEindex?iSEEindex, for the argument FUN.initial.

    Then, we pass the BiocFileCache object and the two custom functions defined above to the -iSEEindex::iSEEindex() function, to create an iSEE +iSEEindex::iSEEindex() function, to create an iSEE application that incorporates a landing page offering users the choice of data sets and initial configurations fetched by the custom functions.

    @@ -250,16 +249,16 @@

    Quick start to using iSEEindex

    Reproducibility

    -

    The iSEEindex +

    The iSEEindex package (Rue-Albrecht and Marini, 2024) was made possible thanks to:

    -

    This package was developed using biocthis.

    +

    This package was developed using biocthis.

    Code for creating the vignette

     ## Create the vignette
@@ -285,155 +284,155 @@ 
    Reproducibilitylibrary("knitr")
 knit("iSEEindex.Rmd", tangle = TRUE)

    Date the vignette was generated.

    -
    #> [1] "2024-03-27 09:39:09 UTC"
    +
    #> [1] "2024-10-01 14:42:26 UTC"

    Wallclock time spent generating the vignette.

    -
    #> Time difference of 7.376 secs
    +
    #> Time difference of 7.772 secs

    R session information.

    #> ─ Session info ───────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
-#>  version  R Under development (unstable) (2024-03-24 r86185)
-#>  os       Ubuntu 22.04.4 LTS
+#>  version  R version 4.4.1 (2024-06-14)
+#>  os       Ubuntu 22.04.5 LTS
 #>  system   x86_64, linux-gnu
 #>  ui       X11
 #>  language en
 #>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-03-27
-#>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
+#>  date     2024-10-01
+#>  pandoc   3.4 @ /usr/bin/ (via rmarkdown)
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 #> 
 #>  [1] /__w/_temp/Library
 #>  [2] /usr/local/lib/R/site-library
@@ -444,16 +443,16 @@ 
    Reproducibility
 
    Bibliography
 
    
-
    This vignette was generated using BiocStyle
-(Oleś, 2023) with knitr (Xie,
-2023) and rmarkdown
+
    This vignette was generated using BiocStyle
+(Oleś, 2024) with knitr (Xie,
+2024) and rmarkdown
 (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.
    
 
    Citations made with RefManageR
 (McLean, 2017).
    
 
    
 [1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.26. 2024. URL:
+for R. R package version 2.28. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 
    
 
    
@@ -464,9 +463,9 @@ 
    Bibliography10.21105/joss.00338.
 
    
 
    
-[3]
+[3]
 A. Oleś. BiocStyle: Standard styles for vignettes and other
-Bioconductor documents. R package version 2.31.0. 2023. DOI:
+Bioconductor documents. R package version 2.33.1. 2024. DOI:
 10.18129/B9.bioc.BiocStyle.
 URL:
 https://bioconductor.org/packages/BiocStyle.
@@ -482,7 +481,7 @@ 
    Bibliography[5]
 K. Rue-Albrecht and F. Marini. iSEEindex: iSEE extension for a
 landing page to a custom collection of data sets. R package version
-1.1.2. 2024. URL:
+1.3.1. 2024. URL:
 https://github.com/iSEE/iSEEindex.
 
    
 
    
@@ -494,13 +493,13 @@ 
    Bibliography[7]
 H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session
-Information. R package version 1.2.2. 2021. URL:
-https://CRAN.R-project.org/package=sessioninfo.
+Information. R package version 1.2.2, https://r-lib.github.io/sessioninfo/. 2021. URL:
+https://github.com/r-lib/sessioninfo#readme.
 
    
 
    
-[8]
+[8]
 Y. Xie. knitr: A General-Purpose Package for Dynamic Report
-Generation in R. R package version 1.45. 2023. URL:
+Generation in R. R package version 1.48. 2024. URL:
 https://yihui.org/knitr/.
 
    
 
@@ -509,9 +508,7 @@ 
    Bibliography
 
-        
-
+      
 
 
 
@@ -524,16 +521,16 @@ 
    Bibliography
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.1.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
diff --git a/articles/index.html b/articles/index.html
index 680311c..1bef924 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,9 +1,9 @@
 
-Articles • iSEEindexArticles • iSEEindex
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -82,15 +82,15 @@ 
    All vignettes
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/articles/resources.html b/articles/resources.html
index a57fca6..74afd40 100644
--- a/articles/resources.html
+++ b/articles/resources.html
@@ -6,21 +6,20 @@
 
 
 Implementing custom iSEEindex resources • iSEEindex
-
+
 
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -49,7 +48,7 @@
 
  • 
   
   
@@ -80,7 +79,7 @@
 
    • 
 
 
-      
+
 
       
    
   
    
@@ -93,9 +92,9 @@ 
    Kevin
 Oxford
    
       
                   
-            
    27 March 2024
    
+            
    1 October 2024
    
       
-      Source: vignettes/resources.Rmd
+      Source: vignettes/resources.Rmd
       
 
     
    
@@ -108,34 +107,34 @@ 
    iSEEindex resources
 
    Overview
 
    
-
    iSEEindex
+
    iSEEindex
 imports data sets and initial app configurations from files. Each of
 those files is represented by a Uniform Resource Identifier (URI) in the
 lists of metadata returned by the functions supplied to the
 FUN.datasets and FUN.initial arguments of
 iSEEindex().
    
-
    iSEEindex
+
    iSEEindex
 requires each URI to contain a scheme component (Wikipedia
 ),
 to identify the type of resource and invoke the associated method for
 accessing it.
    
-
    This system allows iSEEindex
+
    This system allows iSEEindex
 users to use both standard and custom schemes in the URI of their
 resources, to fetch files from virtually any logical or physical
 resource, local or remote.
    
-
    In this vignette, we describe the implementation of iSEEindex
+
    In this vignette, we describe the implementation of iSEEindex
 resources, using built-in classes of resources as examples.
    
 
    
 
    
 
    Implementation
 
    
-
    Given a scheme <scheme>, iSEEindex
+
    Given a scheme <scheme>, iSEEindex
 automatically attempts to create an object of class
 iSEEindex<Scheme>Resource that contains the class
 iSEEindexResource. For instance, the scheme
 https produces an object of class
 iSEEindexHttpsResource.
    
-
    iSEEindex
+
    iSEEindex
 provides a range of built-in iSEEindexResource sub-classes,
 described in dedicated sections below.
    
 
    The raw value of the URI (including the scheme component) is always
@@ -145,9 +144,9 @@ 
    Implementationprecache().
    
 
    On first use, precache() processes the raw value of the
 URI, downloads the resource file locally using custom code if necessary,
-caches the file using BiocFileCache,
+caches the file using BiocFileCache,
 and returns the path to the cached file.
    
-
    In subsequent uses, BiocFileCache
+
    In subsequent uses, BiocFileCache
 is used to fetch the cached file directly.
    
 
    
 
@@ -172,10 +171,10 @@ 
    Structure
 
    Caching
 
    
-
    The BiocFileCache
+
    The BiocFileCache
 package can handle HTTPS perfectly well.
    
 
    In this instance, the precache() function has no other
-job than to cache the file located at the given URI using BiocFileCache.
    
+job than to cache the file located at the given URI using BiocFileCache.
    
 
 
 
    
@@ -197,12 +196,12 @@ 
    Structure
 
    Caching
 
    
-
    Now, while the BiocFileCache
+
    Now, while the BiocFileCache
 package can perfectly well handle local files, it does not know how to
 deal with the custom scheme localhost.
    
 
    In this instance, the precache() function has for only
 job to remove the localhost:// prefix from the URI, and
-cache the file located at the resulting file path using BiocFileCache.
    
+cache the file located at the resulting file path using BiocFileCache.
    
 
    
 
 
    
@@ -228,12 +227,12 @@ 
    CachingInternet
-Assigned Numbers Authority (IANA). As such, the BiocFileCache
+Assigned Numbers Authority (IANA). As such, the BiocFileCache
 package cannot possibly know how to handle that custom scheme.
    
 
    In this instance, the precache() function has the job to
 remove the rcall:// prefix from the URI, evaluate the
 remainder of the URI as R code, and cache the file located at the
-resulting file path using BiocFileCache.
    
+resulting file path using BiocFileCache.
    
 
    
 
 
    
@@ -255,27 +254,27 @@ 
    StructureCaching
 
    
 
    Now, while the scheme s3 is recognised by the AWS Command Line Interface, the
-BiocFileCache
+BiocFileCache
 package does not know how to deal with it.
    
 
    In this instance, the precache() function has the job to
 parse the URI for information that is passed to the paws.storage
-package to download the file, which is then cached using BiocFileCache.
    
+package to download the file, which is then cached using BiocFileCache.
    
 
    
 
 
 
    
 
    Reproducibility
 
    
-
    The iSEEindex
+
    The iSEEindex
 package (Rue-Albrecht and Marini, 2024) was made possible thanks to:
    
 
-
    This package was developed using biocthis.
    
+
    This package was developed using biocthis.
    
 
    Code for creating the vignette
    
 
     ## Create the vignette
@@ -301,70 +300,68 @@ 
    Reproducibilitylibrary("knitr")
 knit("resources.Rmd", tangle = TRUE)
    
 
    Date the vignette was generated.
    
-
    #> [1] "2024-03-27 09:39:12 UTC"
    
+
    #> [1] "2024-10-01 14:42:29 UTC"
    
 
    Wallclock time spent generating the vignette.
    
-
    #> Time difference of 0.574 secs
    
+
    #> Time difference of 0.589 secs
    
 
    R session information.
    
 
    #> ─ Session info ───────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
-#>  version  R Under development (unstable) (2024-03-24 r86185)
-#>  os       Ubuntu 22.04.4 LTS
+#>  version  R version 4.4.1 (2024-06-14)
+#>  os       Ubuntu 22.04.5 LTS
 #>  system   x86_64, linux-gnu
 #>  ui       X11
 #>  language en
 #>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-03-27
-#>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
+#>  date     2024-10-01
+#>  pandoc   3.4 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────
 #>  package     * version date (UTC) lib source
-#>  backports     1.4.1   2021-12-13 [1] CRAN (R 4.4.0)
-#>  bibtex        0.5.1   2023-01-26 [1] CRAN (R 4.4.0)
-#>  BiocManager   1.30.22 2023-08-08 [2] CRAN (R 4.4.0)
-#>  BiocStyle   * 2.31.0  2023-10-24 [1] Bioconductor
-#>  bookdown      0.38    2024-03-04 [1] CRAN (R 4.4.0)
-#>  bslib         0.6.2   2024-03-22 [2] CRAN (R 4.4.0)
-#>  cachem        1.0.8   2023-05-01 [2] CRAN (R 4.4.0)
-#>  cli           3.6.2   2023-12-11 [2] CRAN (R 4.4.0)
-#>  desc          1.4.3   2023-12-10 [2] CRAN (R 4.4.0)
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-#>  generics      0.1.3   2022-07-05 [1] CRAN (R 4.4.0)
-#>  glue          1.7.0   2024-01-09 [2] CRAN (R 4.4.0)
-#>  htmltools     0.5.8   2024-03-25 [2] CRAN (R 4.4.0)
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-#>  lubridate     1.9.3   2023-09-27 [1] CRAN (R 4.4.0)
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-#>  stringi       1.8.3   2023-12-11 [2] CRAN (R 4.4.0)
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-#>  xfun          0.43    2024-03-25 [2] CRAN (R 4.4.0)
-#>  xml2          1.3.6   2023-12-04 [2] CRAN (R 4.4.0)
-#>  yaml          2.3.8   2023-12-11 [2] CRAN (R 4.4.0)
+#>  backports     1.5.0   2024-05-23 [1] RSPM (R 4.4.0)
+#>  bibtex        0.5.1   2023-01-26 [1] RSPM (R 4.4.0)
+#>  BiocManager   1.30.25 2024-08-28 [2] CRAN (R 4.4.1)
+#>  BiocStyle   * 2.33.1  2024-06-12 [1] Bioconductor 3.20 (R 4.4.0)
+#>  bookdown      0.40    2024-07-02 [1] RSPM (R 4.4.0)
+#>  bslib         0.8.0   2024-07-29 [2] RSPM (R 4.4.0)
+#>  cachem        1.1.0   2024-05-16 [2] RSPM (R 4.4.0)
+#>  cli           3.6.3   2024-06-21 [2] RSPM (R 4.4.0)
+#>  desc          1.4.3   2023-12-10 [2] RSPM (R 4.4.0)
+#>  digest        0.6.37  2024-08-19 [2] RSPM (R 4.4.0)
+#>  evaluate      1.0.0   2024-09-17 [2] RSPM (R 4.4.0)
+#>  fastmap       1.2.0   2024-05-15 [2] RSPM (R 4.4.0)
+#>  fontawesome   0.5.2   2023-08-19 [2] RSPM (R 4.4.0)
+#>  fs            1.6.4   2024-04-25 [2] RSPM (R 4.4.0)
+#>  generics      0.1.3   2022-07-05 [1] RSPM (R 4.4.0)
+#>  glue          1.8.0   2024-09-30 [2] RSPM (R 4.4.0)
+#>  htmltools     0.5.8.1 2024-04-04 [2] RSPM (R 4.4.0)
+#>  htmlwidgets   1.6.4   2023-12-06 [2] RSPM (R 4.4.0)
+#>  httr          1.4.7   2023-08-15 [1] RSPM (R 4.4.0)
+#>  jquerylib     0.1.4   2021-04-26 [2] RSPM (R 4.4.0)
+#>  jsonlite      1.8.9   2024-09-20 [2] RSPM (R 4.4.0)
+#>  knitr         1.48    2024-07-07 [2] RSPM (R 4.4.0)
+#>  lifecycle     1.0.4   2023-11-07 [2] RSPM (R 4.4.0)
+#>  lubridate     1.9.3   2023-09-27 [1] RSPM (R 4.4.0)
+#>  magrittr      2.0.3   2022-03-30 [2] RSPM (R 4.4.0)
+#>  pkgdown       2.1.1   2024-09-17 [2] RSPM (R 4.4.0)
+#>  plyr          1.8.9   2023-10-02 [1] RSPM (R 4.4.0)
+#>  R6            2.5.1   2021-08-19 [2] RSPM (R 4.4.0)
+#>  ragg          1.3.3   2024-09-11 [2] RSPM (R 4.4.0)
+#>  Rcpp          1.0.13  2024-07-17 [2] RSPM (R 4.4.0)
+#>  RefManageR  * 1.4.0   2022-09-30 [1] RSPM (R 4.4.0)
+#>  rlang         1.1.4   2024-06-04 [2] RSPM (R 4.4.0)
+#>  rmarkdown     2.28    2024-08-17 [2] RSPM (R 4.4.0)
+#>  sass          0.4.9   2024-03-15 [2] RSPM (R 4.4.0)
+#>  sessioninfo * 1.2.2   2021-12-06 [2] RSPM (R 4.4.0)
+#>  stringi       1.8.4   2024-05-06 [2] RSPM (R 4.4.0)
+#>  stringr       1.5.1   2023-11-14 [2] RSPM (R 4.4.0)
+#>  systemfonts   1.1.0   2024-05-15 [2] RSPM (R 4.4.0)
+#>  textshaping   0.4.0   2024-05-24 [2] RSPM (R 4.4.0)
+#>  timechange    0.3.0   2024-01-18 [1] RSPM (R 4.4.0)
+#>  xfun          0.47    2024-08-17 [2] RSPM (R 4.4.0)
+#>  xml2          1.3.6   2023-12-04 [2] RSPM (R 4.4.0)
+#>  yaml          2.3.10  2024-07-26 [2] RSPM (R 4.4.0)
 #> 
 #>  [1] /__w/_temp/Library
 #>  [2] /usr/local/lib/R/site-library
@@ -375,16 +372,16 @@ 
    Reproducibility
 
    Bibliography
 
    
-
    This vignette was generated using BiocStyle
-(Oleś, 2023) with knitr (Xie,
-2023) and rmarkdown
+
    This vignette was generated using BiocStyle
+(Oleś, 2024) with knitr (Xie,
+2024) and rmarkdown
 (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.
    
 
    Citations made with RefManageR
 (McLean, 2017).
    
 
    
 [1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.26. 2024. URL:
+for R. R package version 2.28. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 
    
 
    
@@ -395,9 +392,9 @@ 
    Bibliography10.21105/joss.00338.
 
    
 
    
-[3]
+[3]
 A. Oleś. BiocStyle: Standard styles for vignettes and other
-Bioconductor documents. R package version 2.31.0. 2023. DOI:
+Bioconductor documents. R package version 2.33.1. 2024. DOI:
 10.18129/B9.bioc.BiocStyle.
 URL:
 https://bioconductor.org/packages/BiocStyle.
@@ -413,7 +410,7 @@ 
    Bibliography[5]
 K. Rue-Albrecht and F. Marini. iSEEindex: iSEE extension for a
 landing page to a custom collection of data sets. R package version
-1.1.2. 2024. URL:
+1.3.1. 2024. URL:
 https://github.com/iSEE/iSEEindex.
 
    
 
    
@@ -425,13 +422,13 @@ 
    Bibliography[7]
 H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session
-Information. R package version 1.2.2. 2021. URL:
-https://CRAN.R-project.org/package=sessioninfo.
+Information. R package version 1.2.2, https://r-lib.github.io/sessioninfo/. 2021. URL:
+https://github.com/r-lib/sessioninfo#readme.
 
    
 
    
-[8]
+[8]
 Y. Xie. knitr: A General-Purpose Package for Dynamic Report
-Generation in R. R package version 1.45. 2023. URL:
+Generation in R. R package version 1.48. 2024. URL:
 https://yihui.org/knitr/.
 
    
 
@@ -440,9 +437,7 @@ 
    Bibliography
 
-        
-
    
+      
 
 
 
@@ -455,16 +450,16 @@ 
    Bibliography
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.1.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
diff --git a/authors.html b/authors.html
index 7c0bc5b..31bc6be 100644
--- a/authors.html
+++ b/authors.html
@@ -1,9 +1,9 @@
 
-Authors and Citation • iSEEindexAuthors and Citation • iSEEindex
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
       
    
-        
    Authors
    
+        
    Authors and Citation
    
       
    
 
-      
+
       
    • 
           
      Kevin Rue-Albrecht. Author, maintainer. 
           
      
@@ -77,27 +77,27 @@ 
      Authors
      
           
      
         
      • 
         
    • 
-          
      Denali Therapeutics. Funder. 
+          
      Denali Therapeutics. Funder.
           
      
         
      • 
       
    
     
    
     
    
       
    Citation
    
-      Source: DESCRIPTION
+      Source: DESCRIPTION
     
    
     
    
 
 
     
    Rue-Albrecht K, Marini F (2024).
 iSEEindex: iSEE extension for a landing page to a custom collection of data sets.
-R package version 1.1.2, https://github.com/iSEE/iSEEindex. 
+R package version 1.3.1, https://github.com/iSEE/iSEEindex.
 
    
     
    @Manual{,
   title = {iSEEindex: iSEE extension for a landing page to a custom collection of data sets},
   author = {Kevin Rue-Albrecht and Federico Marini},
   year = {2024},
-  note = {R package version 1.1.2},
+  note = {R package version 1.3.1},
   url = {https://github.com/iSEE/iSEEindex},
 }
    
 
@@ -112,15 +112,15 @@ 
    Citation
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/index.html b/index.html
index c4c1a5d..dbd2ccd 100644
--- a/index.html
+++ b/index.html
@@ -6,25 +6,21 @@
 
 
 iSEE extension for a landing page to a custom collection of data sets • iSEEindex
-
+
 
 
 
 
 
 
-
+
 
 
 
-    
+
 
     
    
       
    
 
@@ -53,7 +49,7 @@
 
  • 
   
   
@@ -84,7 +80,7 @@
 
    • 
 
 
-      
+
 
       
    
   
    
@@ -263,16 +259,16 @@ 
    Dev status
    
 
 
    
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.1.
    
 
    
 
       
 
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/news/index.html b/news/index.html
index 6aa7304..3ebb335 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,9 +1,9 @@
 
-Changelog • iSEEindexChangelog • iSEEindex
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
       
    Changelog 
    
-      Source: NEWS.md
+      Source: NEWS.md
     
    
 
+    
    
+
    iSEEindex 1.3.1
    
+
    • Version bump to rebuild classes derived from DotPlot.
      • 
+
    
     
    
 
    iSEEindex 1.1.1
    
 
    • Add possibility to customise the title of the app.
      • 
@@ -138,15 +142,15 @@ 
      iSEEindex 0.9
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/pkgdown.yml b/pkgdown.yml
index c5a7c34..2035c19 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,8 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: '3.4'
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   header: header.html
   iSEEindex: iSEEindex.html
   resources: resources.html
-last_built: 2024-03-27T09:38Z
-
+last_built: 2024-10-01T14:41Z
diff --git a/reference/Rplot001.png b/reference/Rplot001.png
deleted file mode 100644
index 17a358060aed2a86950757bbd25c6f92c08c458f..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1011
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U7`aXvEC5;V>FVdQ&MBb@00SN#Z2$lO

diff --git a/reference/iSEEindex-package.html b/reference/iSEEindex-package.html
index 381d1fe..04f58fa 100644
--- a/reference/iSEEindex-package.html
+++ b/reference/iSEEindex-package.html
@@ -1,5 +1,5 @@
 
-iSEEindex: iSEE extension for a landing page to a custom collection of data sets — iSEEindex-package • iSEEindexiSEEindex: iSEE extension for a landing page to a custom collection of data sets — iSEEindex-package • iSEEindex
 
 
-    
+
 
     
    
       
    
 
@@ -35,7 +35,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    iSEEindex: iSEE extension for a landing page to a custom collection of data sets
    
-    Source: R/iSEEindex-package.R
+    Source: R/iSEEindex-package.R
     
     
    
 
@@ -103,15 +103,15 @@ 
    Author
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/iSEEindex.html b/reference/iSEEindex.html
index d60f50d..229e40c 100644
--- a/reference/iSEEindex.html
+++ b/reference/iSEEindex.html
@@ -1,11 +1,11 @@
 
-iSEEindex App — iSEEindex • iSEEindexiSEEindex App — iSEEindex • iSEEindex
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
     
    iSEEindex App
    
-    Source: R/iSEEindex.R
+    Source: R/iSEEindex.R
     
     
    
 
@@ -87,55 +87,55 @@ 
    iSEEindex App
    
 
     
    
     
    Arguments
    
-    
    bfc
    
+
+
+
    bfc
    
 
    An BiocFileCache() object.
    
 
 
-
    FUN.datasets
    
+
    FUN.datasets
    
 
    A function that returns a list of metadata for
 available data sets.
    
 
 
-
    FUN.initial
    
+
    FUN.initial
    
 
    A function that returns a list of metadata for
 available initial configuration states.
    
 
 
-
    default.add
    
+
    default.add
    
 
    Logical scalar indicating whether a default
 initial configuration should be added as a choice in the Shiny selectizeInput().
 See iSEEindex().
    
 
 
-
    default.position
    
+
    default.position
    
 
    Character scalar indicating whether the default
 initial configuration should be added as the "first" or "last" option
 in the Shiny selectizeInput().
    
 
 
-
    app.title
    
+
    app.title
    
 
    Character string to specify the desired title to be displayed
 in the main window of the dashboard. Defaults to NULL, which displays some
 info on the versions of the iSEEindex and iSEE packages.
    
 
 
-
    body.header
    
+
    body.header
    
 
    UI element to display above the main landing page body.
    
 
 
-
    body.footer
    
+
    body.footer
    
 
    UI element to display below the main landing page body.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    An iSEE::iSEE() app with a custom landing page using a BiocFileCache() to cache a selection of data sets.
    
+    
    An iSEE::iSEE() app with a custom landing page using a BiocFileCache() to cache a selection of data sets.
    
     
    
     
    
     
    Data Sets
    
-    
+
 
 
    The function passed to the argument FUN.datasets must return a list that contains metadata about the available data sets.
    
 
    For each data set, required metadata are:
    
@@ -173,7 +173,7 @@ 
    Data Sets
    
     
    
     
    
     
    Initial Configurations
    
-    
+
 
 
    The function passed to the argument FUN.initial must return a list that contains metadata about the available initial configurations, or NULL in the absence of any custom initial configuration (default settings will be applied to all data sets.).
    
 
    For each initial configuration, required metadata are:
    
@@ -260,15 +260,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/iSEEindexHttpsResource-class.html b/reference/iSEEindexHttpsResource-class.html
index ae4791f..a0617ec 100644
--- a/reference/iSEEindexHttpsResource-class.html
+++ b/reference/iSEEindexHttpsResource-class.html
@@ -1,11 +1,11 @@
 
-The iSEEindexHttpsResource class — iSEEindexHttpsResource-class • iSEEindexThe iSEEindexHttpsResource class — iSEEindexHttpsResource-class • iSEEindex
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    The iSEEindexHttpsResource class
    
-    Source: R/iSEEindexResource-class.R
+    Source: R/iSEEindexResource-class.R
     
     
    
 
@@ -78,15 +78,15 @@ 
    The iSEEindexHttpsResource class
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    List of metadata. See Details.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    The constructor function iSEEindexHttpsResource() returns an object of object of class iSEEindexHttpsResource.
    
+    
    The constructor function iSEEindexHttpsResource() returns an object of object of class iSEEindexHttpsResource.
    
     
    
     
    
     
    Details
    
@@ -98,13 +98,13 @@ 
    Details
    
 
    
     
    
     
    Slot overview
    
-    
+
 
 
    This class inherits all slots from its parent class iSEEindexResource.
    
     
    
     
    
     
    Supported methods
    
-    
+
 
 
    In the following code snippets, x is an instance of a iSEEindexHttpsResource class.
 Refer to the documentation for each method for more details on the remaining arguments.
    
@@ -134,15 +134,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/iSEEindexLocalhostResource-class.html b/reference/iSEEindexLocalhostResource-class.html
index b58a883..6cdf7b8 100644
--- a/reference/iSEEindexLocalhostResource-class.html
+++ b/reference/iSEEindexLocalhostResource-class.html
@@ -1,11 +1,11 @@
 
-The iSEEindexLocalhostResource class — iSEEindexLocalhostResource-class • iSEEindexThe iSEEindexLocalhostResource class — iSEEindexLocalhostResource-class • iSEEindex
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    The iSEEindexLocalhostResource class
    
-    Source: R/iSEEindexResource-class.R
+    Source: R/iSEEindexResource-class.R
     
     
    
 
@@ -78,15 +78,15 @@ 
    The iSEEindexLocalhostResource class
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    List of metadata. See Details.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    The constructor function iSEEindexLocalhostResource() returns an object of object of class iSEEindexLocalhostResource.
    
+    
    The constructor function iSEEindexLocalhostResource() returns an object of object of class iSEEindexLocalhostResource.
    
     
    
     
    
     
    Details
    
@@ -98,13 +98,13 @@ 
    Details
    
 
    
     
    
     
    Slot overview
    
-    
+
 
 
    This class inherits all slots from its parent class iSEEindexResource.
    
     
    
     
    
     
    Supported methods
    
-    
+
 
 
    In the following code snippets, x is an instance of a iSEEindexLocalhostResource class.
 Refer to the documentation for each method for more details on the remaining arguments.
    
@@ -112,7 +112,7 @@ 
    Supported methods
    
 
    
     
    
     
    Absolute and relative paths
    
-    
+
 
 
 
    Absolute and relative paths are both supported.
    
@@ -150,15 +150,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/iSEEindexRcallResource-class.html b/reference/iSEEindexRcallResource-class.html
index e0d89af..fed9bf5 100644
--- a/reference/iSEEindexRcallResource-class.html
+++ b/reference/iSEEindexRcallResource-class.html
@@ -1,11 +1,11 @@
 
-The iSEEindexRcallResource class — iSEEindexRcallResource-class • iSEEindexThe iSEEindexRcallResource class — iSEEindexRcallResource-class • iSEEindex
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    The iSEEindexRcallResource class
    
-    Source: R/iSEEindexResource-class.R
+    Source: R/iSEEindexResource-class.R
     
     
    
 
@@ -78,15 +78,15 @@ 
    The iSEEindexRcallResource class
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    List of metadata. See Details.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    The constructor function iSEEindexRcallResource() returns an object of object of class iSEEindexRcallResource.
    
+    
    The constructor function iSEEindexRcallResource() returns an object of object of class iSEEindexRcallResource.
    
     
    
     
    
     
    Details
    
@@ -98,7 +98,7 @@ 
    Details
    
 
    
     
    
     
    URI format
    
-    
+
 
 
    The URI must contain valid R code, once the prefix rcall:// is removed.
 The code must return the path to an existing file on the local filesystem.
    
@@ -107,13 +107,13 @@ 
    URI format
    
     
    
     
    
     
    Slot overview
    
-    
+
 
 
    This class inherits all slots from its parent class iSEEindexResource.
    
     
    
     
    
     
    Supported methods
    
-    
+
 
 
    In the following code snippets, x is an instance of a iSEEindexRcallResource class.
 Refer to the documentation for each method for more details on the remaining arguments.
    
@@ -148,15 +148,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/iSEEindexResource-class.html b/reference/iSEEindexResource-class.html
index a17ee90..db00f2e 100644
--- a/reference/iSEEindexResource-class.html
+++ b/reference/iSEEindexResource-class.html
@@ -1,9 +1,9 @@
 
-The iSEEindexResource class — iSEEindexResource-class • iSEEindexThe iSEEindexResource class — iSEEindexResource-class • iSEEindex
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    The iSEEindexResource class
    
-    Source: R/iSEEindexResource-class.R
+    Source: R/iSEEindexResource-class.R
     
     
    
 
@@ -69,53 +69,51 @@ 
    The iSEEindexResource class
    
     
    
 
     
    
-    
    # S4 method for iSEEindexResource
+    
    # S4 method for class 'iSEEindexResource'
 show(object)
 
-# S4 method for iSEEindexResource
+# S4 method for class 'iSEEindexResource'
 precache(x, bfc, id, ...)
    
     
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    An iSEEindexResource object.
    
 
 
-
    x
    
+
    x
    
 
    An iSEEindexResource object.
    
 
 
-
    bfc
    
+
    bfc
    
 
    A BiocFileCache() object.
    
 
 
-
    id
    
+
    id
    
 
    A data set identifier as a character scalar.
    
 
 
-
    ...
    
+
    ...
    
 
    additional arguments passed to and from other methods.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    show() returns NULL after displaying a summary of the object.
    
-
-
+    
    show() returns NULL after displaying a summary of the object.
    
 
    precache() throws an error if no method is found for the derived class.
    
     
    
     
    
     
    Slot overview
    
-    
+
 
 
    • uri, a character scalar specifying the URI of a resource.
      • 
 
    
     
    
     
    Supported methods
    
-    
+
 
 
    In the following code snippets, x is an instance of a iSEEindexResource class.
 Refer to the documentation for each method for more details on the remaining arguments.
    
@@ -152,15 +150,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/iSEEindexResource-generics.html b/reference/iSEEindexResource-generics.html
index 0073a71..8ba3487 100644
--- a/reference/iSEEindexResource-generics.html
+++ b/reference/iSEEindexResource-generics.html
@@ -1,9 +1,9 @@
 
-Generics for iSEEindexResources Objects — iSEEindexResource-generics • iSEEindexGenerics for iSEEindexResources Objects — iSEEindexResource-generics • iSEEindex
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Generics for iSEEindexResources Objects
    
-    Source: R/iSEEindexResource-class.R
+    Source: R/iSEEindexResource-class.R
     
     
    
 
@@ -74,31 +74,31 @@ 
    Generics for iSEEindexResources Objects
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    An iSEEindexResource object.
    
 
 
-
    bfc
    
+
    bfc
    
 
    A BiocFileCache() object.
    
 
 
-
    id
    
+
    id
    
 
    A data set identifier as a character scalar.
    
 
 
-
    ...
    
+
    ...
    
 
    additional arguments passed to and from other methods.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    precache() returns the file path to the cached copy of a resource fetched from a given URI.
    
+    
    precache() returns the file path to the cached copy of a resource fetched from a given URI.
    
     
    
     
    
     
    Preparing and caching resources
    
-    
+
 
 
    precache(x, bfc, id, ...) retrieves and caches a resource from an URI, caches it, and returns the path to the cached file.
    
     
    
@@ -117,7 +117,7 @@ 
    Examples
    
 ))
 precache(x, bfc, "ID0")
 #>                                                            BFC1 
-#> "/tmp/RtmpYFtrVe/1f7c4a27545d_ReprocessedAllenData_config_01.R" 
+#> "/tmp/RtmpG1bWSV/16bf24945d47_ReprocessedAllenData_config_01.R"
    @@ -132,15 +132,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/iSEEindexS3Resource-class.html b/reference/iSEEindexS3Resource-class.html index d45e51e..32ebee4 100644 --- a/reference/iSEEindexS3Resource-class.html +++ b/reference/iSEEindexS3Resource-class.html @@ -1,5 +1,5 @@ -The iSEEindexS3Resource class — iSEEindexS3Resource-class • iSEEindexThe iSEEindexS3Resource class — iSEEindexS3Resource-class • iSEEindex - +
    @@ -35,7 +35,7 @@
    • - +

    The iSEEindexS3Resource class

    - Source: R/iSEEindexResource-class.R + Source: R/iSEEindexResource-class.R
    @@ -82,15 +82,15 @@

    The iSEEindexS3Resource class

    Arguments

    -
    x
    + + +
    x

    List of metadata. See Details.

    Value

    - - -

    The constructor function iSEEindexS3Resource() returns an object of object of class iSEEindexS3Resource.

    +

    The constructor function iSEEindexS3Resource() returns an object of object of class iSEEindexS3Resource.

    Details

    @@ -102,7 +102,7 @@

    Details

    Slot overview

    - +

    This class inherits all slots from its parent class iSEEindexResource.

    Furthermore, this class defines the additional slot(s) below:

    region
    @@ -112,7 +112,7 @@

    Slot overview

    Supported methods

    - +

    In the following code snippets, x is an instance of a iSEEindexS3Resource class. Refer to the documentation for each method for more details on the remaining arguments.

    @@ -124,7 +124,7 @@

    Supported methods

    URI format

    - +

    The URI must correspond to an existing file in an AWS S3 compatible cloud storage system.

    @@ -134,7 +134,7 @@

    URI format

    Pre-caching

    - +

    Additional arguments to the precache(x, ..., temp_dir = tempdir()):

    temp_dir
    @@ -146,7 +146,7 @@

    Pre-caching

    AWS Credentials and region settings

    - +

    For detailed information, please consult the paws R package documentation.

    @@ -208,15 +208,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/index.html b/reference/index.html index 1ea4292..5cb14d2 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • iSEEindexPackage index • iSEEindex - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -107,15 +107,15 @@

    All functions
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/sitemap.xml b/sitemap.xml index aeda668..1052966 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,63 +1,23 @@ - - - - /404.html - - - /CODE_OF_CONDUCT.html - - - /CONTRIBUTING.html - - - /SUPPORT.html - - - /articles/header.html - - - /articles/iSEEindex.html - - - /articles/index.html - - - /articles/resources.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/iSEEindex-package.html - - - /reference/iSEEindex.html - - - /reference/iSEEindexHttpsResource-class.html - - - /reference/iSEEindexLocalhostResource-class.html - - - /reference/iSEEindexRcallResource-class.html - - - /reference/iSEEindexResource-class.html - - - /reference/iSEEindexResource-generics.html - - - /reference/iSEEindexS3Resource-class.html - - - /reference/index.html - + +/404.html +/CODE_OF_CONDUCT.html +/CONTRIBUTING.html +/SUPPORT.html +/articles/header.html +/articles/iSEEindex.html +/articles/index.html +/articles/resources.html +/authors.html +/index.html +/news/index.html +/reference/iSEEindex-package.html +/reference/iSEEindex.html +/reference/iSEEindexHttpsResource-class.html +/reference/iSEEindexLocalhostResource-class.html +/reference/iSEEindexRcallResource-class.html +/reference/iSEEindexResource-class.html +/reference/iSEEindexResource-generics.html +/reference/iSEEindexS3Resource-class.html +/reference/index.html +