From 0b89c5c1c93933290a0fefd711860b37b70f4a97 Mon Sep 17 00:00:00 2001 From: jwokaty Date: Wed, 7 Aug 2024 14:40:56 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20jwokaty/?= =?UTF-8?q?bedbaser@2b29376add731af7109ed623dfefca7a2a9237ce=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- articles/bedbaser.html | 12 +++++------ articles/index.html | 2 +- authors.html | 4 ++-- index.html | 2 +- news/index.html | 4 ++-- pkgdown.yml | 8 ++++---- reference/BEDbase-class.html | 4 ++-- reference/bb_bed_text_search.html | 4 ++-- reference/bb_beds_in_bedset.html | 4 ++-- reference/bb_example.html | 4 ++-- reference/bb_list_beds.html | 4 ++-- reference/bb_list_bedsets.html | 4 ++-- reference/bb_metadata.html | 4 ++-- reference/bb_to_granges.html | 7 +++---- reference/bb_to_grangeslist.html | 34 +++++++++++-------------------- reference/bedbaser-package.html | 4 ++-- reference/bedbaser.html | 4 ++-- reference/index.html | 2 +- 19 files changed, 51 insertions(+), 62 deletions(-) diff --git a/404.html b/404.html index 509e70b..5a31f1d 100644 --- a/404.html +++ b/404.html @@ -91,7 +91,7 @@

Page not found (404)

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.0.9000.

diff --git a/articles/bedbaser.html b/articles/bedbaser.html index 08a0435..3486f80 100644 --- a/articles/bedbaser.html +++ b/articles/bedbaser.html @@ -76,7 +76,7 @@

J Wokaty

- Source: vignettes/bedbaser.Rmd + Source: vignettes/bedbaser.Rmd @@ -520,11 +520,11 @@

SessionInfo()sessionInfo() 
## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 24.04 LTS
+## Running under: Ubuntu 22.04.4 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
-## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
+## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
 ## 
 ## locale:
 ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
@@ -534,7 +534,7 @@ 
SessionInfo()##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 ## 
-## time zone: America/New_York
+## time zone: UTC
 ## tzcode source: system (glibc)
 ## 
 ## attached base packages:
@@ -618,7 +618,7 @@ 
SessionInfo()## [101] Rcpp_1.0.13                 dbplyr_2.5.0               
 ## [103] png_0.1-8                   XML_3.99-0.17              
 ## [105] rapiclient_0.1.5            parallel_4.4.1             
-## [107] pkgdown_2.1.0               readr_2.1.5                
+## [107] pkgdown_2.1.0.9000          readr_2.1.5                
 ## [109] blob_1.2.4                  prettyunits_1.2.0          
 ## [111] bitops_1.0-8                txdbmaker_1.1.1            
 ## [113] VariantAnnotation_1.51.0    purrr_1.0.2                
@@ -642,7 +642,7 @@ 
SessionInfo()
   

-
Site built with pkgdown 2.1.0.

+
Site built with pkgdown 2.1.0.9000.

 
 
       
diff --git a/articles/index.html b/articles/index.html
index 1fd165e..47838ee 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -65,7 +65,7 @@ 
All vignettes

 
 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/authors.html b/authors.html
index 53cb2c5..aa64e45 100644
--- a/authors.html
+++ b/authors.html
@@ -63,7 +63,7 @@ 
Authors and Citation

     

     

       
Citation

-      Source: DESCRIPTION
+      Source: DESCRIPTION
     

     

 
@@ -91,7 +91,7 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/index.html b/index.html
index 1c5428f..c06f3dc 100644
--- a/index.html
+++ b/index.html
@@ -129,7 +129,7 @@ 
Developers

 
 

   

-
Site built with pkgdown 2.1.0.

+
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/news/index.html b/news/index.html
index 2f8823a..b838a43 100644
--- a/news/index.html
+++ b/news/index.html
@@ -47,7 +47,7 @@
   

     

       
Changelog 

-      Source: NEWS.md
+      Source: NEWS.md
     

 
     

@@ -68,7 +68,7 @@ 
bedbaser 0.99.
 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

diff --git a/pkgdown.yml b/pkgdown.yml
index 57cd8f2..9e92ee2 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,6 @@
-pandoc: 3.1.3
-pkgdown: 2.1.0
-pkgdown_sha: ~
+pandoc: '3.2'
+pkgdown: 2.1.0.9000
+pkgdown_sha: 1d40a80e6b3564a6d7da0ce467b0a4570aa5665e
 articles:
   bedbaser: bedbaser.html
-last_built: 2024-08-07T13:56Z
+last_built: 2024-08-07T14:39Z
diff --git a/reference/BEDbase-class.html b/reference/BEDbase-class.html
index c97986b..2499e91 100644
--- a/reference/BEDbase-class.html
+++ b/reference/BEDbase-class.html
@@ -47,7 +47,7 @@
   

     

     
BEDbase class

-    Source: R/bedbase-class.R
+    Source: R/bedbase-class.R
     
     

 
@@ -69,7 +69,7 @@ 
BEDbase class

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_bed_text_search.html b/reference/bb_bed_text_search.html
index dc7fba2..be146b8 100644
--- a/reference/bb_bed_text_search.html
+++ b/reference/bb_bed_text_search.html
@@ -47,7 +47,7 @@
   

     

     
Search BED files by text

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -123,7 +123,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_beds_in_bedset.html b/reference/bb_beds_in_bedset.html
index 28662ea..69257cb 100644
--- a/reference/bb_beds_in_bedset.html
+++ b/reference/bb_beds_in_bedset.html
@@ -47,7 +47,7 @@
   

     

     
Get BEDs associated with BEDset

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -111,7 +111,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_example.html b/reference/bb_example.html
index 1a6dad2..589ffc4 100644
--- a/reference/bb_example.html
+++ b/reference/bb_example.html
@@ -47,7 +47,7 @@
   

     

     
Get the example BED file or BEDset with metadata

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -525,7 +525,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_list_beds.html b/reference/bb_list_beds.html
index b761173..bb1e59b 100644
--- a/reference/bb_list_beds.html
+++ b/reference/bb_list_beds.html
@@ -47,7 +47,7 @@
   

     

     
List BEDs

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -123,7 +123,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_list_bedsets.html b/reference/bb_list_bedsets.html
index b90cfbd..3902449 100644
--- a/reference/bb_list_bedsets.html
+++ b/reference/bb_list_bedsets.html
@@ -47,7 +47,7 @@
   

     

     
List BEDsets

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -117,7 +117,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_metadata.html b/reference/bb_metadata.html
index 73e526e..5ab10f1 100644
--- a/reference/bb_metadata.html
+++ b/reference/bb_metadata.html
@@ -48,7 +48,7 @@
   

     

     
Get metadata for a BED file or BEDset

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -400,7 +400,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bb_to_granges.html b/reference/bb_to_granges.html
index bc2c7b5..e00c5c6 100644
--- a/reference/bb_to_granges.html
+++ b/reference/bb_to_granges.html
@@ -47,7 +47,7 @@
   

     

     
Create a GRanges object given a BED id

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -100,11 +100,10 @@ 
Examples

     
api <- bedbaser()
 ex_bed <- bb_example(api, "bed")
 bb_to_granges(api, ex_bed$id)
-#> 
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> GRanges object with 4675 ranges and 2 metadata columns:
 #>          seqnames            ranges strand |           name        V5
 #>             <Rle>         <IRanges>  <Rle> |    <character> <numeric>
@@ -136,7 +135,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

diff --git a/reference/bb_to_grangeslist.html b/reference/bb_to_grangeslist.html
index a512fd7..510a84a 100644
--- a/reference/bb_to_grangeslist.html
+++ b/reference/bb_to_grangeslist.html
@@ -47,7 +47,7 @@
   

     

     
Create a GRangesList object given a BEDset id

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -85,56 +85,46 @@ 
Examples

     
api <- bedbaser()
 id <- "lola_hg38_ucsc_features"
 bb_to_grangeslist(api, id)
-#> 
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
-#> 
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> 'getOption("repos")' replaces Bioconductor standard repositories, see
 #> 'help("repositories", package = "BiocManager")' for details.
 #> Replacement repositories:
-#>     CRAN: https://cloud.r-project.org
+#>     CRAN: https://p3m.dev/cran/__linux__/jammy/latest
 #> GRangesList object of length 10:
 #> [[1]]
 #> GRanges object with 28633 ranges and 0 metadata columns:
@@ -171,7 +161,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

diff --git a/reference/bedbaser-package.html b/reference/bedbaser-package.html
index 412e301..455eb9f 100644
--- a/reference/bedbaser-package.html
+++ b/reference/bedbaser-package.html
@@ -47,7 +47,7 @@
   

     

     
bedbaser: A BEDbase client

-    Source: R/bedbaser-package.R
+    Source: R/bedbaser-package.R
     
     

 
@@ -80,7 +80,7 @@ 
Author

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/bedbaser.html b/reference/bedbaser.html
index 378f9b1..cf0cb8f 100644
--- a/reference/bedbaser.html
+++ b/reference/bedbaser.html
@@ -49,7 +49,7 @@
   

     

     
An R client for BEDbase

-    Source: R/bedbaser.R
+    Source: R/bedbaser.R
     
     

 
@@ -120,7 +120,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
diff --git a/reference/index.html b/reference/index.html
index 423f536..d2f0641 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -106,7 +106,7 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.1.0.9000.