169 bug calling appendix fix echo (#170)

* update to remove message before appendix * updated session info page to extract packages from gh workflow * check if publish works * update wordlist * deploy only on main
pharmaverse · May 15, 2024 · 7531768 · 7531768
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diff --git a/inst/WORDLIST.txt b/inst/WORDLIST.txt
@@ -729,3 +729,6 @@ ropensci
 Rucki
 runiverse
 thecoatlessprofessor
+strsplit
+yaml
+YAML
diff --git a/posts/2023-06-27__hackathon_app/index.qmd b/posts/2023-06-27__hackathon_app/index.qmd
@@ -381,7 +381,7 @@ From our perspective, the application provided a great added value to the hackat
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-06-27_admiral/valuelevel/derive_param_computed.qmd b/posts/2023-06-27_admiral/valuelevel/derive_param_computed.qmd
@@ -99,7 +99,7 @@ diffdf(adex_expected, adex_admiral, keys = c("USUBJID", "PARAMCD"))
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-06-27_hackathon_writeup/index.qmd b/posts/2023-06-27_hackathon_writeup/index.qmd
@@ -182,7 +182,7 @@ Please reach out to [Edoardo Mancini (product owner)](mailto:edoardo.mancini@roc
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-06-28_welcome/index.qmd b/posts/2023-06-28_welcome/index.qmd
@@ -77,7 +77,7 @@ Step 4: Poke us to do a review!
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-07-09_falcon/falcon.qmd b/posts/2023-07-09_falcon/falcon.qmd
@@ -44,7 +44,7 @@ In addition, while currently all templates were built using {rtables}, {tern}, {
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-07-10_blanks_and_nas/blanks_and_nas.qmd b/posts/2023-07-10_blanks_and_nas/blanks_and_nas.qmd
@@ -74,7 +74,7 @@ list_all_templates()
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-07-14_code_sections/code_sections.qmd b/posts/2023-07-14_code_sections/code_sections.qmd
@@ -91,7 +91,7 @@ Code sections are an easy way to navigate long scripts and foster good commentin
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd b/posts/2023-07-20_cross_company_dev/cross_industry_dev.qmd
@@ -141,7 +141,7 @@ The [{admiral}](https://github.com/pharmaverse/admiral) project serves as a test
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-07-24_rounding/rounding.qmd b/posts/2023-07-24_rounding/rounding.qmd
@@ -214,7 +214,7 @@ If you spot an issue or have different opinions, please don't hesitate to raise
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-08-08_study_day/study_day.qmd b/posts/2023-08-08_study_day/study_day.qmd
@@ -78,7 +78,7 @@ If you want to get `--DT` or `--DTM` variables using `admiral` then check out [`
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-08-14_rhino_submission_2/rhino_submission_2.qmd b/posts/2023-08-14_rhino_submission_2/rhino_submission_2.qmd
@@ -207,7 +207,7 @@ https://doi.org/10.1177/17407745221123244
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-09-26_date_functions_and_imputation/date_functions_and_imputation.qmd b/posts/2023-09-26_date_functions_and_imputation/date_functions_and_imputation.qmd
@@ -317,7 +317,7 @@ For an even more detailed treatment of this topic, users are once again invited
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-10-10_pharmaverse_story/pharmaverse_story.qmd b/posts/2023-10-10_pharmaverse_story/pharmaverse_story.qmd
@@ -93,7 +93,7 @@ After all, even though we live together as a community, we still have our own un
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-10-30_floating_point/floating_point.qmd b/posts/2023-10-30_floating_point/floating_point.qmd
@@ -349,7 +349,7 @@ I.e. `.Machine$double.eps / 1.8` is still detectable, while `.Machine$double.eps
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-11-27_higher_order/higher_order.qmd b/posts/2023-11-27_higher_order/higher_order.qmd
@@ -285,7 +285,7 @@ The three higher order functions available in [{admiral}](https://pharmaverse.gi
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-12-18_admiral_1_0/admiral_1_0.qmd b/posts/2023-12-18_admiral_1_0/admiral_1_0.qmd
@@ -283,7 +283,7 @@ knitr::include_graphics("wayback.png")
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2023-12-20_p_k__examples/p_k__examples.qmd b/posts/2023-12-20_p_k__examples/p_k__examples.qmd
@@ -187,7 +187,7 @@ Happy exploring!
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-01-04_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.qmd b/posts/2024-01-04_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.qmd
@@ -47,7 +47,7 @@ Here's to a 2024 full of progress and collaboration!
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-02-13_teal_on_cran/teal_on_cran.qmd b/posts/2024-02-13_teal_on_cran/teal_on_cran.qmd
@@ -56,7 +56,7 @@ Feel free to explore the `teal` website [here](https://insightsengineering.githu
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-02-14_iscr_conference/iscr_conference.qmd b/posts/2024-02-14_iscr_conference/iscr_conference.qmd
@@ -80,7 +80,7 @@ The power of technology coupled with domain expertise can make us deliver qualit
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-03-01_admiral_filter_functions/admiral_filter_functions.qmd b/posts/2024-03-01_admiral_filter_functions/admiral_filter_functions.qmd
@@ -219,7 +219,7 @@ However, remember Uncle Ben's maxim:  _"with great power comes great responsibil
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-03-04_inside_the__phar.../inside_the__pharmaverse.qmd b/posts/2024-03-04_inside_the__phar.../inside_the__pharmaverse.qmd
@@ -130,7 +130,7 @@ And, if not – let us know!
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-03-11_tips_for__first_.../tips_for__first__time__contributors.qmd b/posts/2024-03-11_tips_for__first_.../tips_for__first__time__contributors.qmd
@@ -178,7 +178,7 @@ blog)](contributors.png){fig-align="center"}
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-03-29_xportr_0_4_0/xportr_0_4_0.qmd b/posts/2024-03-29_xportr_0_4_0/xportr_0_4_0.qmd
@@ -136,7 +136,7 @@ As we look towards the future, embracing diverse data formats and technologies w
 This blog contains opinions that are of the authors alone and do not necessarily reflect the strategy of their respective organizations.
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message = FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-04-08_tmc_cran/tmc_cran.qmd b/posts/2024-04-08_tmc_cran/tmc_cran.qmd
@@ -56,7 +56,7 @@ And not to forget our wonderful users for your continued support and enthusiasm.
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-04-15_de-_mystifying__.../de-_mystifying__r__programming_in__clinical__trials.qmd b/posts/2024-04-15_de-_mystifying__.../de-_mystifying__r__programming_in__clinical__trials.qmd
@@ -164,7 +164,7 @@ value and potential of open-source tools in tackling complex challenges.
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-04-29_appsilon_and__sa.../appsilon_and__sanofi_joins_the_pharmaverse_council!.qmd b/posts/2024-04-29_appsilon_and__sa.../appsilon_and__sanofi_joins_the_pharmaverse_council!.qmd
@@ -61,7 +61,7 @@ On behalf of the council, Ari Siggaard Knoph
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/posts/2024-05-08_tlg_catalog_webr/tlg_catalog_webr.qmd b/posts/2024-05-08_tlg_catalog_webr/tlg_catalog_webr.qmd
@@ -59,7 +59,7 @@ Happy learning!
 
 <!--------------- appendices go here ----------------->
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, message=FALSE}
 source("appendix.R")
 insert_appendix(
   repo_spec = "pharmaverse/blog",

diff --git a/session_info.qmd b/session_info.qmd
@@ -1,9 +1,30 @@
 ---
 title: "Session Info"
-description: "This page displays the session information for the site."
+description: "List of all packages (and package versions) required to render all blog posts."
 ---
 
+
+```{r, include = FALSE, eval = TRUE, message = FALSE}
+# Read the contents of the publish.yml file
+publish_yml <- readLines(".github/workflows/publish.yml")
+
+
+# Convert the YAML content to a list
+publish_list <- yaml::yaml.load(publish_yml)
+
+# Extract the package names from the list
+package_names <- publish_list$jobs$`build-deploy`$steps[[4]]$with$packages
+
+# Split the package names into a vector
+package_names <- strsplit(package_names, "\n")[[1]]
+
+
+# Load all the packages
+for (package in package_names) {
+  library(package, character.only = TRUE)
+}
+```
+
 ```{r}
-library(sessioninfo)
 session_info()
 ```