From 151d49c9e6ae391721271e16cc6da6aa50d7042a Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Thu, 3 Oct 2024 08:58:45 -0500
Subject: [PATCH 01/11] test pipeline

---
 .gitlab-ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9f98cb5..9115db9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -20,6 +20,7 @@ variables:
   R_PROFILE: "$R_HOME/etc/Rprofile.site"
   APT_CACHE: "$CI_PROJECT_DIR/ci/lib/apt-cache"
   CRAN: "https://rpkg.chs.usgs.gov/prod-cran/latest"
+  DEV: "https://rpkg.chs.usgs.gov/dev-gspm/latest"
   R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
   R_LIBS: "$CI_PROJECT_DIR/ci/lib"
   BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs"
@@ -104,7 +105,7 @@ pages:
     - main
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - Rscript -e 'source("deploy_simple.R")'
+    - Rscript -e 'install.packages("toxEval", repos = c(CRAN = "${CRAN}", DEV = "${DEV}")); source("deploy_simple.R")'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From 3c3e8c7232c129993c4116c7d38d1ab579d7b04c Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Thu, 3 Oct 2024 09:18:49 -0500
Subject: [PATCH 02/11] still seeing 3.1 on Shiny

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9115db9..48c1977 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -105,7 +105,7 @@ pages:
     - main
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - Rscript -e 'install.packages("toxEval", repos = c(CRAN = "${CRAN}", DEV = "${DEV}")); source("deploy_simple.R")'
+    - Rscript -e 'install.packages("toxEval", repos = c(DEV = "${DEV}")); packageVersion("toxEval"); source("deploy_simple.R")'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From 24261c9ec638eee949cd38aa2e049e45322ea899 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 11:12:21 -0500
Subject: [PATCH 03/11] add to option?

---
 .gitlab-ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 48c1977..80e9ae1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -105,7 +105,8 @@ pages:
     - main
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - Rscript -e 'install.packages("toxEval", repos = c(DEV = "${DEV}")); packageVersion("toxEval"); source("deploy_simple.R")'
+    - echo -e "options(repos=c(DEV = '$DEV'));" >> $R_PROFILE
+    - Rscript -e 'install.packages("toxEval"); packageVersion("toxEval"); source("deploy_simple.R")'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From 7214555a97047f8c0fc90eeff2060f0718b13211 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 12:05:23 -0500
Subject: [PATCH 04/11] ONLY dev

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 80e9ae1..5f4f694 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -106,7 +106,7 @@ pages:
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
     - echo -e "options(repos=c(DEV = '$DEV'));" >> $R_PROFILE
-    - Rscript -e 'install.packages("toxEval"); packageVersion("toxEval"); source("deploy_simple.R")'
+    - Rscript -e 'install.packages("toxEval", repos = '$DEV'); packageVersion("toxEval"); source("deploy_simple.R")'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From 73fabd3f741cd974301ebd92ea7a58dee24a91e9 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 14:11:32 -0500
Subject: [PATCH 05/11] curly?

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5f4f694..0bc4566 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -105,8 +105,8 @@ pages:
     - main
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - echo -e "options(repos=c(DEV = '$DEV'));" >> $R_PROFILE
-    - Rscript -e 'install.packages("toxEval", repos = '$DEV'); packageVersion("toxEval"); source("deploy_simple.R")'
+    - echo -e "options(repos=c(DEV = '${DEV}'));" >> $R_PROFILE
+    - Rscript -e 'install.packages("toxEval", repos = '${DEV}); packageVersion("toxEval"); source("deploy_simple.R")'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From 91285c8ec2dc9232ec6b7076ccc7befc3016bc88 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 14:29:29 -0500
Subject: [PATCH 06/11] missing a quote on install

---
 .gitlab-ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0bc4566..3421616 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -104,9 +104,9 @@ pages:
   only: 
     - main
   script:
-    - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - echo -e "options(repos=c(DEV = '${DEV}'));" >> $R_PROFILE
-    - Rscript -e 'install.packages("toxEval", repos = '${DEV}); packageVersion("toxEval"); source("deploy_simple.R")'
+    - echo -e "options(repos=c(DEV = '${DEV}', CRAN = '${CRAN}'));" >> $R_PROFILE
+    - Rscript -e 'install.packages("toxEval", repos = '${DEV}'); packageVersion("toxEval"); source("deploy_simple.R")'
+- Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From 2d3eef73da2ffd5739535482a7ce07729b71cbd6 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 14:38:46 -0500
Subject: [PATCH 07/11] double vs single quotes

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3421616..b0d4429 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -105,7 +105,7 @@ pages:
     - main
   script:
     - echo -e "options(repos=c(DEV = '${DEV}', CRAN = '${CRAN}'));" >> $R_PROFILE
-    - Rscript -e 'install.packages("toxEval", repos = '${DEV}'); packageVersion("toxEval"); source("deploy_simple.R")'
+    - Rscript -e 'install.packages("toxEval", repos = "${DEV}"); packageVersion("toxEval"); source("deploy_simple.R")'
 - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
   artifacts:
     paths:

From 5a052476572d378310e43b1853a81c45a6d0444a Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 14:41:23 -0500
Subject: [PATCH 08/11] indentations

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b0d4429..22ad0da 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -106,7 +106,7 @@ pages:
   script:
     - echo -e "options(repos=c(DEV = '${DEV}', CRAN = '${CRAN}'));" >> $R_PROFILE
     - Rscript -e 'install.packages("toxEval", repos = "${DEV}"); packageVersion("toxEval"); source("deploy_simple.R")'
-- Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
+    - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
   artifacts:
     paths:
       - $PAGES_OUTDIR

From c1c19d6beae3e92655285783eade572ea07e71c5 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 15:00:14 -0500
Subject: [PATCH 09/11] ?

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 22ad0da..227d9eb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -105,7 +105,7 @@ pages:
     - main
   script:
     - echo -e "options(repos=c(DEV = '${DEV}', CRAN = '${CRAN}'));" >> $R_PROFILE
-    - Rscript -e 'install.packages("toxEval", repos = "${DEV}"); packageVersion("toxEval"); source("deploy_simple.R")'
+    - Rscript -e 'install.packages("toxEval", repos = Sys.getenv("DEV")); packageVersion("toxEval"); source("deploy_simple.R")'
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
   artifacts:
     paths:

From 91d9bed4506a1b9002e6333bd3fd075ed2465a85 Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Mon, 7 Oct 2024 15:55:53 -0500
Subject: [PATCH 10/11] had a double install happening

---
 deploy_simple.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/deploy_simple.R b/deploy_simple.R
index 92075f0..00fbab0 100644
--- a/deploy_simple.R
+++ b/deploy_simple.R
@@ -2,8 +2,6 @@ library(connectapi)
 client <- connect(server = Sys.getenv("CONNECT_SERVER"),
                   api_key = Sys.getenv("CONNECT_API_KEY"))
 
-install.packages("toxEval", repos = "https://rpkg.chs.usgs.gov/prod-cran/latest")
-
 rsconnect::writeManifest(appDir = "./inst/shiny")
 bundle <- bundle_dir("./inst/shiny")
 

From 01e4fae6a53a470791ace05ae61588fb9dd0010a Mon Sep 17 00:00:00 2001
From: Laura A DeCicco <ldecicco@usgs.gov>
Date: Thu, 10 Oct 2024 15:56:07 -0500
Subject: [PATCH 11/11] move to vars

---
 .gitlab-ci.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 227d9eb..9873bdd 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,8 +19,6 @@ variables:
   _R_CHECK_DONTTEST_EXAMPLES_: "false"
   R_PROFILE: "$R_HOME/etc/Rprofile.site"
   APT_CACHE: "$CI_PROJECT_DIR/ci/lib/apt-cache"
-  CRAN: "https://rpkg.chs.usgs.gov/prod-cran/latest"
-  DEV: "https://rpkg.chs.usgs.gov/dev-gspm/latest"
   R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
   R_LIBS: "$CI_PROJECT_DIR/ci/lib"
   BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs"