From c201deb28c117dcdcde86b2783faafe8519199a8 Mon Sep 17 00:00:00 2001 From: bschilder <34280215+bschilder@users.noreply.github.com> Date: Sun, 10 Dec 2023 17:34:05 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20neurogen?= =?UTF-8?q?omics/rworkflows@265a77b54b4ffa82dd0d399f2bf082c214f21cf4=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/bioconductor.html | 38 ++++++++++---------- articles/depgraph.html | 32 ++++++++--------- articles/docker.html | 34 +++++++++--------- articles/repos.html | 23 ++++++------ articles/rworkflows.html | 50 +++++++++++++------------- index.html | 22 ++++++------ pkgdown.yml | 2 +- reference/construct_conda_yml.html | 2 +- reference/dt_to_desc.html | 6 ++-- reference/fill_description.html | 4 +-- reference/get_description.html | 2 +- reference/get_description_repo.html | 4 +-- reference/index.html | 2 +- reference/infer_docker_org.html | 2 +- reference/is_gha.html | 2 +- reference/use_codespace.html | 2 +- reference/use_dockerfile.html | 2 +- reference/use_issue_template.html | 4 +-- reference/use_readme.html | 2 +- reference/use_vignette_docker.html | 2 +- reference/use_vignette_getstarted.html | 2 +- reference/use_workflow.html | 2 +- 22 files changed, 120 insertions(+), 121 deletions(-) diff --git a/articles/bioconductor.html b/articles/bioconductor.html index 2e3c8d7b..ec5b668e 100644 --- a/articles/bioconductor.html +++ b/articles/bioconductor.html @@ -98,7 +98,7 @@


-Vignette updated: Nov-05-2023
+Vignette updated: Dec-10-2023

Source: vignettes/bioconductor.Rmd @@ -184,7 +184,7 @@

## runner_os: ${{ runner.os }} ## cache_version: cache-v1 ## docker_registry: ghcr.io -
## Saving yaml ==> /tmp/Rtmp5Ib4fQ/rworkflows.devel.yml
+
## Saving yaml ==> /tmp/Rtmp3Z9IRY/rworkflows.devel.yml

@@ -251,7 +251,7 @@

## runner_os: ${{ runner.os }} ## cache_version: cache-v1 ## docker_registry: ghcr.io -
## Saving yaml ==> /tmp/Rtmp5Ib4fQ/rworkflows.RELEASE_3_17.yml
+
## Saving yaml ==> /tmp/Rtmp3Z9IRY/rworkflows.RELEASE_3_17.yml

@@ -275,8 +275,8 @@

Session Info
 utils::sessionInfo()

-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-22 r85609)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -298,28 +298,28 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] rworkflows_1.0.1 BiocStyle_2.30.0
+## [1] rworkflows_1.0.1 BiocStyle_2.31.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] yulab.utils_0.1.0   sass_0.4.7          utf8_1.2.4         
-##  [4] generics_0.1.3      renv_1.0.3          stringi_1.7.12     
+##  [1] yulab.utils_0.1.0   sass_0.4.8          utf8_1.2.4         
+##  [4] generics_0.1.3      renv_1.0.3          stringi_1.8.2      
 ##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.23      
-## [10] grid_4.3.1          RColorBrewer_1.1-3  bookdown_0.36      
-## [13] fastmap_1.1.1       rprojroot_2.0.3     jsonlite_1.8.7     
-## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.5        
-## [19] scales_1.2.1        textshaping_0.3.7   jquerylib_0.1.4    
+## [10] grid_4.4.0          RColorBrewer_1.1-3  bookdown_0.37      
+## [13] fastmap_1.1.1       rprojroot_2.0.4     jsonlite_1.8.8     
+## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.6        
+## [19] scales_1.3.0        textshaping_0.3.7   jquerylib_0.1.4    
 ## [22] cli_3.6.1           rlang_1.1.2         badger_0.2.3       
 ## [25] munsell_0.5.0       cachem_1.0.8        yaml_2.3.7         
-## [28] tools_4.3.1         memoise_2.0.1       dplyr_1.1.3        
+## [28] tools_4.4.0         memoise_2.0.1       dplyr_1.1.4        
 ## [31] colorspace_2.1-0    ggplot2_3.4.4       here_1.0.1         
-## [34] vctrs_0.6.4         R6_2.5.1            lifecycle_1.0.3    
-## [37] stringr_1.5.0       fs_1.6.3            ragg_1.2.6         
-## [40] pkgconfig_2.0.3     desc_1.4.2          pkgdown_2.0.7      
-## [43] bslib_0.5.1         pillar_1.9.0        gtable_0.3.4       
-## [46] glue_1.6.2          data.table_1.14.8   systemfonts_1.0.5  
+## [34] vctrs_0.6.5         R6_2.5.1            lifecycle_1.0.4    
+## [37] stringr_1.5.1       fs_1.6.3            ragg_1.2.6         
+## [40] pkgconfig_2.0.3     desc_1.4.3          pkgdown_2.0.7      
+## [43] bslib_0.6.1         pillar_1.9.0        gtable_0.3.4       
+## [46] glue_1.6.2          data.table_1.14.10  systemfonts_1.0.5  
 ## [49] xfun_0.41           tibble_3.2.1        rvcheck_0.2.1      
 ## [52] tidyselect_1.2.0    knitr_1.45          htmltools_0.5.7    
-## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.3.1

+## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.4.0
diff --git a/articles/depgraph.html b/articles/depgraph.html index 1d01ae8b..a6576e87 100644 --- a/articles/depgraph.html +++ b/articles/depgraph.html @@ -98,7 +98,7 @@


-Vignette updated: Nov-05-2023
+Vignette updated: Dec-10-2023

Source: vignettes/depgraph.Rmd @@ -190,8 +190,8 @@

Session Info
 utils::sessionInfo()
-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-22 r85609)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -213,21 +213,21 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] data.table_1.14.8 BiocStyle_2.30.0 
+## [1] data.table_1.14.10 BiocStyle_2.31.0  
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.4         cli_3.6.1           knitr_1.45         
-##  [4] rlang_1.1.2         xfun_0.41           stringi_1.7.12     
-##  [7] purrr_1.0.2         textshaping_0.3.7   jsonlite_1.8.7     
-## [10] glue_1.6.2          rprojroot_2.0.3     htmltools_0.5.7    
-## [13] ragg_1.2.6          sass_0.4.7          rmarkdown_2.25     
-## [16] evaluate_0.23       jquerylib_0.1.4     fastmap_1.1.1      
-## [19] lifecycle_1.0.3     yaml_2.3.7          memoise_2.0.1      
-## [22] bookdown_0.36       BiocManager_1.30.22 stringr_1.5.0      
-## [25] compiler_4.3.1      fs_1.6.3            systemfonts_1.0.5  
-## [28] digest_0.6.33       R6_2.5.1            magrittr_2.0.3     
-## [31] bslib_0.5.1         tools_4.3.1         pkgdown_2.0.7      
-## [34] cachem_1.0.8        desc_1.4.2

+##  [1] vctrs_0.6.5         cli_3.6.1           knitr_1.45         
+##  [4] rlang_1.1.2         xfun_0.41           stringi_1.8.2      
+##  [7] purrr_1.0.2         textshaping_0.3.7   jsonlite_1.8.8     
+## [10] glue_1.6.2          htmltools_0.5.7     ragg_1.2.6         
+## [13] sass_0.4.8          rmarkdown_2.25      evaluate_0.23      
+## [16] jquerylib_0.1.4     fastmap_1.1.1       yaml_2.3.7         
+## [19] lifecycle_1.0.4     memoise_2.0.1       bookdown_0.37      
+## [22] BiocManager_1.30.22 stringr_1.5.1       compiler_4.4.0     
+## [25] fs_1.6.3            systemfonts_1.0.5   digest_0.6.33      
+## [28] R6_2.5.1            magrittr_2.0.3      bslib_0.6.1        
+## [31] tools_4.4.0         pkgdown_2.0.7       cachem_1.0.8       
+## [34] desc_1.4.3
diff --git a/articles/docker.html b/articles/docker.html index a51d71e4..e150edf5 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -98,7 +98,7 @@


-Vignette updated: Nov-05-2023
+Vignette updated: Dec-10-2023

Source: vignettes/docker.Rmd @@ -174,8 +174,8 @@

Session Info
 utils::sessionInfo()
-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-22 r85609)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -197,28 +197,28 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] rworkflows_1.0.1 BiocStyle_2.30.0
+## [1] rworkflows_1.0.1 BiocStyle_2.31.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] yulab.utils_0.1.0   sass_0.4.7          utf8_1.2.4         
-##  [4] generics_0.1.3      renv_1.0.3          stringi_1.7.12     
+##  [1] yulab.utils_0.1.0   sass_0.4.8          utf8_1.2.4         
+##  [4] generics_0.1.3      renv_1.0.3          stringi_1.8.2      
 ##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.23      
-## [10] grid_4.3.1          RColorBrewer_1.1-3  bookdown_0.36      
-## [13] fastmap_1.1.1       rprojroot_2.0.3     jsonlite_1.8.7     
-## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.5        
-## [19] scales_1.2.1        textshaping_0.3.7   jquerylib_0.1.4    
+## [10] grid_4.4.0          RColorBrewer_1.1-3  bookdown_0.37      
+## [13] fastmap_1.1.1       rprojroot_2.0.4     jsonlite_1.8.8     
+## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.6        
+## [19] scales_1.3.0        textshaping_0.3.7   jquerylib_0.1.4    
 ## [22] cli_3.6.1           rlang_1.1.2         badger_0.2.3       
 ## [25] munsell_0.5.0       cachem_1.0.8        yaml_2.3.7         
-## [28] tools_4.3.1         memoise_2.0.1       dplyr_1.1.3        
+## [28] tools_4.4.0         memoise_2.0.1       dplyr_1.1.4        
 ## [31] colorspace_2.1-0    ggplot2_3.4.4       here_1.0.1         
-## [34] vctrs_0.6.4         R6_2.5.1            lifecycle_1.0.3    
-## [37] stringr_1.5.0       fs_1.6.3            ragg_1.2.6         
-## [40] pkgconfig_2.0.3     desc_1.4.2          pkgdown_2.0.7      
-## [43] bslib_0.5.1         pillar_1.9.0        gtable_0.3.4       
-## [46] glue_1.6.2          data.table_1.14.8   systemfonts_1.0.5  
+## [34] vctrs_0.6.5         R6_2.5.1            lifecycle_1.0.4    
+## [37] stringr_1.5.1       fs_1.6.3            ragg_1.2.6         
+## [40] pkgconfig_2.0.3     desc_1.4.3          pkgdown_2.0.7      
+## [43] bslib_0.6.1         pillar_1.9.0        gtable_0.3.4       
+## [46] glue_1.6.2          data.table_1.14.10  systemfonts_1.0.5  
 ## [49] xfun_0.41           tibble_3.2.1        rvcheck_0.2.1      
 ## [52] tidyselect_1.2.0    knitr_1.45          htmltools_0.5.7    
-## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.3.1

+## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.4.0


diff --git a/articles/repos.html b/articles/repos.html index 635ddcbb..a7d44ad2 100644 --- a/articles/repos.html +++ b/articles/repos.html @@ -98,7 +98,7 @@


-Vignette updated: Nov-05-2023
+Vignette updated: Dec-10-2023

Source: vignettes/repos.Rmd @@ -137,8 +137,8 @@

Session Info
 utils::sessionInfo()
-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-22 r85609)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -160,15 +160,14 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.4       cli_3.6.1         knitr_1.45        rlang_1.1.2      
-##  [5] xfun_0.41         stringi_1.7.12    purrr_1.0.2       textshaping_0.3.7
-##  [9] jsonlite_1.8.7    glue_1.6.2        rprojroot_2.0.3   htmltools_0.5.7  
-## [13] ragg_1.2.6        sass_0.4.7        rmarkdown_2.25    evaluate_0.23    
-## [17] jquerylib_0.1.4   fastmap_1.1.1     yaml_2.3.7        lifecycle_1.0.3  
-## [21] memoise_2.0.1     stringr_1.5.0     compiler_4.3.1    fs_1.6.3         
-## [25] systemfonts_1.0.5 digest_0.6.33     R6_2.5.1          magrittr_2.0.3   
-## [29] bslib_0.5.1       tools_4.3.1       pkgdown_2.0.7     cachem_1.0.8     
-## [33] desc_1.4.2

+##  [1] vctrs_0.6.5       cli_3.6.1         knitr_1.45        rlang_1.1.2      
+##  [5] xfun_0.41         stringi_1.8.2     purrr_1.0.2       textshaping_0.3.7
+##  [9] jsonlite_1.8.8    glue_1.6.2        htmltools_0.5.7   ragg_1.2.6       
+## [13] sass_0.4.8        rmarkdown_2.25    evaluate_0.23     jquerylib_0.1.4  
+## [17] fastmap_1.1.1     yaml_2.3.7        lifecycle_1.0.4   memoise_2.0.1    
+## [21] stringr_1.5.1     compiler_4.4.0    fs_1.6.3          systemfonts_1.0.5
+## [25] digest_0.6.33     R6_2.5.1          magrittr_2.0.3    bslib_0.6.1      
+## [29] tools_4.4.0       pkgdown_2.0.7     cachem_1.0.8      desc_1.4.3


diff --git a/articles/rworkflows.html b/articles/rworkflows.html index 594f71e0..9badf14f 100644 --- a/articles/rworkflows.html +++ b/articles/rworkflows.html @@ -98,7 +98,7 @@


-Vignette updated: Nov-05-2023
+Vignette updated: Dec-10-2023

Source: vignettes/rworkflows.Rmd @@ -148,7 +148,7 @@

dynamic action force_new = TRUE, ## Use default save_dir in practice save_dir = tempdir()) -
## Saving yaml ==> /tmp/Rtmpuw2rzB/rworkflows.yml
+
## Saving yaml ==> /tmp/RtmpptTRhL/rworkflows.yml

static workflow @@ -165,7 +165,7 @@

static workflow force_new = TRUE, ## Use default save_dir in practice save_dir = tempdir())

-
## Saving yaml ==> /tmp/Rtmpuw2rzB/rworkflows_static.yml
+
## Saving yaml ==> /tmp/RtmpptTRhL/rworkflows_static.yml
@@ -207,7 +207,7 @@ 

 ## Use default save_dir in practice
 dockerfile <- rworkflows::use_dockerfile(save_dir = tempdir())
-
## Creating new Docker file ==> /tmp/Rtmpuw2rzB/Dockerfile
+
## Creating new Docker file ==> /tmp/RtmpptTRhL/Dockerfile

Templates @@ -225,7 +225,7 @@

README 
 ## Use default save_dir in practice
 readme <- rworkflows::use_readme(save_dir = tempdir())
-
## Creating new README file ==> /tmp/Rtmpuw2rzB/README.Rmd
+
## Creating new README file ==> /tmp/RtmpptTRhL/README.Rmd

Vignette: Get started @@ -236,7 +236,7 @@

Vignette: Get started## Use default save_dir in practice vignette1 <- rworkflows::use_vignette_getstarted(package = "mypackage", save_dir = tempdir())

-
## Creating new vignette file ==> /tmp/Rtmpuw2rzB/vignettes/mypackage.Rmd
+
## Creating new vignette file ==> /tmp/RtmpptTRhL/vignettes/mypackage.Rmd

Vignette: docker @@ -259,7 +259,7 @@

Vignette: docker## Use default save_dir in practice vignette2 <- rworkflows::use_vignette_docker(docker_org = "neurogenomics", save_dir = tempdir())

-
## Creating new vignette file ==> /tmp/Rtmpuw2rzB/vignettes/docker.Rmd
+
## Creating new vignette file ==> /tmp/RtmpptTRhL/vignettes/docker.Rmd
@@ -347,7 +347,7 @@

Using Python## runner_os: ${{ runner.os }} ## cache_version: cache-v1 ## docker_registry: ghcr.io -
## Saving yaml ==> /tmp/Rtmpuw2rzB/rworkflows.yml
+
## Saving yaml ==> /tmp/RtmpptTRhL/rworkflows.yml

Using conda @@ -460,7 +460,7 @@

Using conda## docker_registry: ghcr.io ## miniforge_variant: '' ## environment_file: /__w/rworkflows/rworkflows/myenv_conda.yml -
## Saving yaml ==> /tmp/Rtmpuw2rzB/rworkflows.yml
+
## Saving yaml ==> /tmp/RtmpptTRhL/rworkflows.yml
 ## Cleanup files
 try({file.remove(environment_file)})
@@ -472,8 +472,8 @@

Session Info
 utils::sessionInfo()

-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-22 r85609)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -495,28 +495,28 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] rworkflows_1.0.1 BiocStyle_2.30.0
+## [1] rworkflows_1.0.1 BiocStyle_2.31.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] yulab.utils_0.1.0   sass_0.4.7          utf8_1.2.4         
-##  [4] generics_0.1.3      renv_1.0.3          stringi_1.7.12     
+##  [1] yulab.utils_0.1.0   sass_0.4.8          utf8_1.2.4         
+##  [4] generics_0.1.3      renv_1.0.3          stringi_1.8.2      
 ##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.23      
-## [10] grid_4.3.1          RColorBrewer_1.1-3  bookdown_0.36      
-## [13] fastmap_1.1.1       rprojroot_2.0.3     jsonlite_1.8.7     
-## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.5        
-## [19] scales_1.2.1        textshaping_0.3.7   jquerylib_0.1.4    
+## [10] grid_4.4.0          RColorBrewer_1.1-3  bookdown_0.37      
+## [13] fastmap_1.1.1       rprojroot_2.0.4     jsonlite_1.8.8     
+## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.6        
+## [19] scales_1.3.0        textshaping_0.3.7   jquerylib_0.1.4    
 ## [22] cli_3.6.1           rlang_1.1.2         badger_0.2.3       
 ## [25] munsell_0.5.0       cachem_1.0.8        yaml_2.3.7         
-## [28] tools_4.3.1         memoise_2.0.1       dplyr_1.1.3        
+## [28] tools_4.4.0         memoise_2.0.1       dplyr_1.1.4        
 ## [31] colorspace_2.1-0    ggplot2_3.4.4       here_1.0.1         
-## [34] vctrs_0.6.4         R6_2.5.1            lifecycle_1.0.3    
-## [37] stringr_1.5.0       fs_1.6.3            ragg_1.2.6         
-## [40] pkgconfig_2.0.3     desc_1.4.2          pkgdown_2.0.7      
-## [43] bslib_0.5.1         pillar_1.9.0        gtable_0.3.4       
-## [46] glue_1.6.2          data.table_1.14.8   systemfonts_1.0.5  
+## [34] vctrs_0.6.5         R6_2.5.1            lifecycle_1.0.4    
+## [37] stringr_1.5.1       fs_1.6.3            ragg_1.2.6         
+## [40] pkgconfig_2.0.3     desc_1.4.3          pkgdown_2.0.7      
+## [43] bslib_0.6.1         pillar_1.9.0        gtable_0.3.4       
+## [46] glue_1.6.2          data.table_1.14.10  systemfonts_1.0.5  
 ## [49] xfun_0.41           tibble_3.2.1        rvcheck_0.2.1      
 ## [52] tidyselect_1.2.0    knitr_1.45          htmltools_0.5.7    
-## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.3.1

+## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.4.0
diff --git a/index.html b/index.html index 3167ccf1..59537ebb 100644 --- a/index.html +++ b/index.html @@ -102,7 +102,7 @@ Authors: Brian Schilder, Alan Murphy, Nathan Skene

-README updated: Nov-05-2023 +README updated: Dec-10-2023

Intro @@ -327,8 +327,8 @@ 

 utils::sessionInfo()
-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-22 r85609)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -353,21 +353,21 @@ 

 ## [1] rmarkdown_2.25
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] gtable_0.3.4        jsonlite_1.8.7      renv_1.0.3         
-##  [4] dplyr_1.1.3         compiler_4.3.1      BiocManager_1.30.22
-##  [7] tidyselect_1.2.0    rvcheck_0.2.1       scales_1.2.1       
+##  [1] gtable_0.3.4        jsonlite_1.8.8      renv_1.0.3         
+##  [4] dplyr_1.1.4         compiler_4.4.0      BiocManager_1.30.22
+##  [7] tidyselect_1.2.0    rvcheck_0.2.1       scales_1.3.0       
 ## [10] yaml_2.3.7          fastmap_1.1.1       here_1.0.1         
 ## [13] ggplot2_3.4.4       R6_2.5.1            generics_0.1.3     
 ## [16] knitr_1.45          yulab.utils_0.1.0   tibble_3.2.1       
-## [19] desc_1.4.2          dlstats_0.1.7       rprojroot_2.0.3    
+## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.0.4    
 ## [22] munsell_0.5.0       pillar_1.9.0        RColorBrewer_1.1-3 
 ## [25] rlang_1.1.2         utf8_1.2.4          cachem_1.0.8       
 ## [28] badger_0.2.3        xfun_0.41           fs_1.6.3           
 ## [31] memoise_2.0.1       cli_3.6.1           magrittr_2.0.3     
-## [34] rworkflows_1.0.1    digest_0.6.33       grid_4.3.1         
-## [37] lifecycle_1.0.3     vctrs_0.6.4         data.table_1.14.8  
-## [40] evaluate_0.23       glue_1.6.2          fansi_1.0.5        
-## [43] colorspace_2.1-0    tools_4.3.1         pkgconfig_2.0.3    
+## [34] rworkflows_1.0.1    digest_0.6.33       grid_4.4.0         
+## [37] lifecycle_1.0.4     vctrs_0.6.5         data.table_1.14.10 
+## [40] evaluate_0.23       glue_1.6.2          fansi_1.0.6        
+## [43] colorspace_2.1-0    tools_4.4.0         pkgconfig_2.0.3    
 ## [46] htmltools_0.5.7
diff --git a/pkgdown.yml b/pkgdown.yml index 801472a6..b9626576 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,5 +7,5 @@ articles: docker: docker.html repos: repos.html rworkflows: rworkflows.html -last_built: 2023-11-05T01:31Z +last_built: 2023-12-10T17:33Z diff --git a/reference/construct_conda_yml.html b/reference/construct_conda_yml.html index 2cc72108..12ed4ced 100644 --- a/reference/construct_conda_yml.html +++ b/reference/construct_conda_yml.html @@ -141,7 +141,7 @@

Examples

return_path = FALSE, ## Writing to temp only for example save_path=tempfile(fileext="myenv_conda.yml")) -#> Saving yaml ==> /tmp/RtmpAoNHrO/file3bf02636bf09myenv_conda.yml +#> Saving yaml ==> /tmp/RtmpTZkkPw/file4655a314999myenv_conda.yml diff --git a/reference/dt_to_desc.html b/reference/dt_to_desc.html index 9ca7dcf0..833884d7 100644 --- a/reference/dt_to_desc.html +++ b/reference/dt_to_desc.html @@ -67,13 +67,13 @@
-

data.table to desc

+

data.table to desc

Source: R/dt_to_desc.R
-

Convert data.table containing the +

Convert data.table containing the parsed DESCROPTION file data and convert each of them to to desc format.

@@ -85,7 +85,7 @@

Arguments

db
-

A data.table where each row is a different R package +

A data.table where each row is a different R package and each column is a field from the DESCROPTION file.

diff --git a/reference/fill_description.html b/reference/fill_description.html index 03529216..10dfb854 100644 --- a/reference/fill_description.html +++ b/reference/fill_description.html @@ -271,7 +271,7 @@

Examples

#> Updating: Title --> This Package Does Awesome Stuff #> Updating: Description --> MyPackageName does several awesome things. Describe thing1. Describe thing2. Describe thing3. #> Updating: Authors --> yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId) -#> Updating: Depends --> R (>= 4.3) +#> Updating: Depends --> R (>= 4.4) #> Updating: Suggests --> #> testthat, #> rmarkdown, @@ -282,7 +282,7 @@

Examples

#> Updating: biocViews --> Genetics, SystemsBiology #> Updating: URL --> https://github.com/OwnerName/MyPackageName #> Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues -#> Saving updated file: /tmp/RtmpAoNHrO/file3bf0570e5cc1DESCRIPTION +#> Saving updated file: /tmp/RtmpTZkkPw/file465569653d1aDESCRIPTION

diff --git a/reference/get_description.html b/reference/get_description.html index 7cc4c4cf..a38a909d 100644 --- a/reference/get_description.html +++ b/reference/get_description.html @@ -114,7 +114,7 @@

Arguments

db
-

A data.table of R package metadata generated by +

A data.table of R package metadata generated by biocPkgList.

diff --git a/reference/get_description_repo.html b/reference/get_description_repo.html index d5ec27e5..aba68e11 100644 --- a/reference/get_description_repo.html +++ b/reference/get_description_repo.html @@ -75,7 +75,7 @@

Get DESCRIPTION files for R repos

Get the DESCRIPTION file information in - data.table format for all R packages + data.table format for all R packages in standard R repositories (CRAN, Bioc). Can return a subset of results for specific packages as well.

@@ -99,7 +99,7 @@

Arguments

db
-

A data.table of R package metadata generated by +

A data.table of R package metadata generated by biocPkgList.

diff --git a/reference/index.html b/reference/index.html index 34a7883f..6a1d5554 100644 --- a/reference/index.html +++ b/reference/index.html @@ -103,7 +103,7 @@

All functions

dt_to_desc()

-

data.table to desc

+

data.table to desc

fill_description()

diff --git a/reference/infer_docker_org.html b/reference/infer_docker_org.html index 95876ade..5998533d 100644 --- a/reference/infer_docker_org.html +++ b/reference/infer_docker_org.html @@ -128,7 +128,7 @@

Arguments

to find DESCRIPTION files.

db
-

A data.table of R package metadata generated by +

A data.table of R package metadata generated by biocPkgList.

repo
diff --git a/reference/is_gha.html b/reference/is_gha.html index 9b246f46..08d13d86 100644 --- a/reference/is_gha.html +++ b/reference/is_gha.html @@ -105,7 +105,7 @@

Value

Examples

is_gha()
-#> Currently running on GITHUB_ACTION: __neurogenomics_rworkflows
+#> Currently running on GITHUB_ACTION: __run_22
 #> [1] TRUE
diff --git a/reference/use_codespace.html b/reference/use_codespace.html index 2de7ac05..fc278d63 100644 --- a/reference/use_codespace.html +++ b/reference/use_codespace.html @@ -145,7 +145,7 @@

Value

Examples

path <- use_codespace(save_dir=tempdir())
-#> Creating new dev container config file ==> /tmp/RtmpAoNHrO/devcontainer.json
+#> Creating new dev container config file ==> /tmp/RtmpTZkkPw/devcontainer.json
diff --git a/reference/use_dockerfile.html b/reference/use_dockerfile.html index f8cc79f8..fc217975 100644 --- a/reference/use_dockerfile.html +++ b/reference/use_dockerfile.html @@ -124,7 +124,7 @@

Value

Examples

path <- use_dockerfile(save_dir=tempdir())
-#> Creating new Docker file ==> /tmp/RtmpAoNHrO/Dockerfile
+#> Creating new Docker file ==> /tmp/RtmpTZkkPw/Dockerfile
diff --git a/reference/use_issue_template.html b/reference/use_issue_template.html index ebbc3d47..71f58e03 100644 --- a/reference/use_issue_template.html +++ b/reference/use_issue_template.html @@ -122,8 +122,8 @@

Value

Examples

path <- use_issue_template(save_dir=tempdir())
-#> Creating new Issue Template ==> /tmp/RtmpAoNHrO/bug_report.md
-#> Creating new Issue Template ==> /tmp/RtmpAoNHrO/feature_request.md
+#> Creating new Issue Template ==> /tmp/RtmpTZkkPw/bug_report.md
+#> Creating new Issue Template ==> /tmp/RtmpTZkkPw/feature_request.md
diff --git a/reference/use_readme.html b/reference/use_readme.html index 4a62b794..ba24b116 100644 --- a/reference/use_readme.html +++ b/reference/use_readme.html @@ -120,7 +120,7 @@

Value

Examples

## use default save_dir in practice
 path <- use_readme(save_dir = tempdir()) 
-#> Creating new README file ==> /tmp/RtmpAoNHrO/README.Rmd
+#> Creating new README file ==> /tmp/RtmpTZkkPw/README.Rmd
diff --git a/reference/use_vignette_docker.html b/reference/use_vignette_docker.html index 5288120f..6b159378 100644 --- a/reference/use_vignette_docker.html +++ b/reference/use_vignette_docker.html @@ -194,7 +194,7 @@

Examples

docker_org = "neurogenomics", ## use default save_dir in practice save_dir = tempdir()) -#> Creating new vignette file ==> /tmp/RtmpAoNHrO/vignettes/docker.Rmd +#> Creating new vignette file ==> /tmp/RtmpTZkkPw/vignettes/docker.Rmd diff --git a/reference/use_vignette_getstarted.html b/reference/use_vignette_getstarted.html index 4a793b43..d486da0b 100644 --- a/reference/use_vignette_getstarted.html +++ b/reference/use_vignette_getstarted.html @@ -141,7 +141,7 @@

Examples

path <- use_vignette_getstarted(package = "mypackage",
                                 ## use default save_dir in practice
                                 save_dir = tempdir())
-#> Creating new vignette file ==> /tmp/RtmpAoNHrO/vignettes/mypackage.Rmd
+#> Creating new vignette file ==> /tmp/RtmpTZkkPw/vignettes/mypackage.Rmd
diff --git a/reference/use_workflow.html b/reference/use_workflow.html index 3a608772..1353de6e 100644 --- a/reference/use_workflow.html +++ b/reference/use_workflow.html @@ -380,7 +380,7 @@

Value

Examples

path <- use_workflow(save_dir = file.path(tempdir(),".github","workflows"))
-#> Saving yaml ==> /tmp/RtmpAoNHrO/.github/workflows/rworkflows.yml
+#> Saving yaml ==> /tmp/RtmpTZkkPw/.github/workflows/rworkflows.yml