CRAN submission

reconverse · Mar 11, 2021 · c8478cd · c8478cd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: reportfactory
 Title: Lightweight Infrastructure for Handling Multiple R Markdown Documents
-Version: 0.1.3.9000
+Version: 0.2.0
 Authors@R: c(
   person("Thibaut", "Jombart", role = "aut", email = "[email protected]"),
   person("Amy", "Gimma", role = "ctb", email = "[email protected]"),
@@ -11,8 +11,8 @@ Description: Provides an infrastructure for handling multiple R Markdown
   reports, including automated curation and time-stamping of outputs,
   parameterisation and provision of helper functions to manage dependencies.
 License: MIT + file LICENSE
-URL: https://github.com/reconhub/reportfactory
-BugReports: https://github.com/reconhub/reportfactory/issues
+URL: https://github.com/reconverse/reportfactory
+BugReports: https://github.com/reconverse/reportfactory/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# reportfactory (development version)
+# reportfactory 0.2.0
 
 ## Bug fixes
 * Fixes (#74) where files generated within the Rmd were not being copied

diff --git a/README.Rmd b/README.Rmd
@@ -14,9 +14,9 @@ knitr::opts_chunk$set(
 ```
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/reconhub/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconhub/reportfactory/actions)
-[![Codecov test coverage](https://codecov.io/gh/reconhub/reportfactory/branch/master/graph/badge.svg)](https://codecov.io/gh/reconhub/reportfactory?branch=master)
-[![R build status](https://github.com/reconhub/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconhub/reportfactory/actions)
+[![R-CMD-check](https://github.com/reconverse/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconverse/reportfactory/actions)
+[![Codecov test coverage](https://codecov.io/gh/reconverse/reportfactory/branch/master/graph/badge.svg)](https://codecov.io/gh/reconverse/reportfactory?branch=master)
+[![R build status](https://github.com/reconverse/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconverse/reportfactory/actions)
 <!-- badges: end -->
 
 # Welcome to reportfactory!
@@ -29,11 +29,11 @@ unreleased version.  For those already using {reportfactory} in their pipelines
 you can obtain the old version using the {remotes} package:
 
 ```{r installold, eval = FALSE}
-remotes::install_github("reconhub/reportfactory@old_version")
+remotes::install_github("reconverse/reportfactory@old_version")
 ``` 
 
 You can also download it directly from
-https://github.com/reconhub/reportfactory/releases/tag/old_version.
+https://github.com/reconverse/reportfactory/releases/tag/old_version.
 
 You can install the current version of the package from 
 [CRAN](https://cran.r-project.org/) with:
@@ -48,7 +48,7 @@ The development version can be installed from [GitHub](https://github.com/) with
 if (!require(remotes)) {
   install.packages("remotes")
 }
-remotes::install_github("reconhub/reportfactory", build_vignettes = TRUE)
+remotes::install_github("reconverse/reportfactory", build_vignettes = TRUE)
 ```
 
 ## reportfactory in a nutshell 
@@ -58,7 +58,7 @@ remotes::install_github("reconhub/reportfactory", build_vignettes = TRUE)
 in well-organised, timestamped folders. This is illustrated in the figure below:
 
 <br>
-<img src="https://github.com/reconhub/reportfactory/raw/master/artwork/workflow.png" width="100%" alt="workflow">
+<img src="https://github.com/reconverse/reportfactory/raw/master/artwork/workflow.png" width="100%" alt="workflow">
 <br>
 
 There a few key principles it adheres to:
@@ -84,7 +84,7 @@ There a few key principles it adheres to:
 To install the development version of the package, use:
 
 ```{r install2, eval = FALSE}
-remotes::install_github("reconhub/reportfactory")
+remotes::install_github("reconverse/reportfactory")
 ```
 
 

diff --git a/README.md b/README.md
@@ -3,11 +3,11 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/reconhub/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconhub/reportfactory/actions)
+[![R-CMD-check](https://github.com/reconverse/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconverse/reportfactory/actions)
 [![Codecov test
-coverage](https://codecov.io/gh/reconhub/reportfactory/branch/master/graph/badge.svg)](https://codecov.io/gh/reconhub/reportfactory?branch=master)
+coverage](https://codecov.io/gh/reconverse/reportfactory/branch/master/graph/badge.svg)](https://codecov.io/gh/reconverse/reportfactory?branch=master)
 [![R build
-status](https://github.com/reconhub/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconhub/reportfactory/actions)
+status](https://github.com/reconverse/reportfactory/workflows/R-CMD-check/badge.svg)](https://github.com/reconverse/reportfactory/actions)
 <!-- badges: end -->
 
 # Welcome to reportfactory\!
@@ -20,11 +20,11 @@ their pipelines you can obtain the old version using the {remotes}
 package:
 
 ``` r
-remotes::install_github("reconhub/reportfactory@old_version")
+remotes::install_github("reconverse/reportfactory@old_version")
 ```
 
 You can also download it directly from
-<https://github.com/reconhub/reportfactory/releases/tag/old_version>.
+<https://github.com/reconverse/reportfactory/releases/tag/old_version>.
 
 You can install the current version of the package from
 [CRAN](https://cran.r-project.org/) with:
@@ -40,7 +40,7 @@ The development version can be installed from
 if (!require(remotes)) {
   install.packages("remotes")
 }
-remotes::install_github("reconhub/reportfactory", build_vignettes = TRUE)
+remotes::install_github("reconverse/reportfactory", build_vignettes = TRUE)
 ```
 
 ## reportfactory in a nutshell
@@ -51,7 +51,7 @@ storing outputs in well-organised, timestamped folders. This is
 illustrated in the figure below:
 
 <br>
-<img src="https://github.com/reconhub/reportfactory/raw/master/artwork/workflow.png" width="100%" alt="workflow">
+<img src="https://github.com/reconverse/reportfactory/raw/master/artwork/workflow.png" width="100%" alt="workflow">
 <br>
 
 There a few key principles it adheres to:
@@ -77,7 +77,7 @@ There a few key principles it adheres to:
 To install the development version of the package, use:
 
 ``` r
-remotes::install_github("reconhub/reportfactory")
+remotes::install_github("reconverse/reportfactory")
 ```
 
 ## Quick start
@@ -133,8 +133,8 @@ Use `list_ouputs()` to view the report outputs.
 
 ``` r
 list_outputs()
-#> [1] "example_report/2021-03-08_T09-16-24/example_report.html"
-#> [2] "example_report/2021-03-08_T09-16-24/example_report.Rmd"
+#> [1] "example_report/2021-03-11_T09-55-40/example_report.html"
+#> [2] "example_report/2021-03-11_T09-55-40/example_report.Rmd"
 ```
 
 `compile_reports()` can also be used to pass a set of parameters to use
@@ -151,10 +151,10 @@ compile_reports(
 #>       - with parameters: grouped_plot = FALSE
 #> All done!
 list_outputs()
-#> [1] "example_report/2021-03-08_T09-16-24/example_report.html"         
-#> [2] "example_report/2021-03-08_T09-16-24/example_report.Rmd"          
-#> [3] "example_report/regional/2021-03-08_T09-16-25/example_report.html"
-#> [4] "example_report/regional/2021-03-08_T09-16-25/example_report.Rmd"
+#> [1] "example_report/2021-03-11_T09-55-40/example_report.html"         
+#> [2] "example_report/2021-03-11_T09-55-40/example_report.Rmd"          
+#> [3] "example_report/regional/2021-03-11_T09-55-41/example_report.html"
+#> [4] "example_report/regional/2021-03-11_T09-55-41/example_report.Rmd"
 ```
 
 Note that reports can also be an integer or a logical vector, in which
@@ -172,7 +172,7 @@ the `factory_overview()` function:
 
 ``` r
 factory_overview()
-#> /tmp/RtmpWSy7OS/my_factory
+#> /tmp/Rtmp1gxZ7u/my_factory
 #> ├── README.md
 #> ├── data
 #> │   ├── clean
@@ -181,11 +181,11 @@ factory_overview()
 #> ├── factory_config
 #> ├── outputs
 #> │   └── example_report
-#> │       ├── 2021-03-08_T09-16-24
+#> │       ├── 2021-03-11_T09-55-40
 #> │       │   ├── example_report.Rmd
 #> │       │   └── example_report.html
 #> │       └── regional
-#> │           └── 2021-03-08_T09-16-25
+#> │           └── 2021-03-11_T09-55-41
 #> │               ├── example_report.Rmd
 #> │               └── example_report.html
 #> ├── report_sources

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,12 +1,12 @@
 ## Reason for update
-* minor bugfix/workflow improvement.
-* resolves a failing test I noticed on the macos checks.
+* Important bug fix and minor workflow improvement
 
 ## Tested on
-* Fedora 33, local R installation, R 4.0.3 (2020-10-10)
-* win-builder, R Under development (unstable) (2021-02-13 r80000)
+* Fedora 33, R Under development (unstable) (2021-03-10 r80084)
+* win-builder, R Under development (unstable) (2021-03-10 r80084)
 
 ### R CMD check results for above environments
+Status: OK
 0 errors | 0 warnings | 0 note