From 2258b79448b1bcb65259e53e0e8b58b624dc80b8 Mon Sep 17 00:00:00 2001
From: Jack Leary <j.leary@ufl.edu>
Date: Wed, 13 Dec 2023 12:30:36 -0500
Subject: [PATCH] removing files that shouldnt be tracked for BiocCheck

---
 .DS_Store                                     | Bin 10244 -> 0 bytes
 .Rbuildignore                                 |   5 -----
 .gitignore                                    |   1 +
 R/.DS_Store                                   | Bin 6148 -> 0 bytes
 R/{GetResultsDE.R => getResultsDE.R}          |   0
 R/{ModelLRT.R => modelLRT.R}                  |   0
 codecov.yml                                   |  20 ------------------
 inst/.DS_Store                                | Bin 6148 -> 0 bytes
 inst/rmarkdown/.DS_Store                      | Bin 6148 -> 0 bytes
 inst/rmarkdown/templates/.DS_Store            | Bin 6148 -> 0 bytes
 .../templates/Bacher_Group_HTML/.DS_Store     | Bin 6148 -> 0 bytes
 scLANE.Rproj                                  |  20 ------------------
 12 files changed, 1 insertion(+), 45 deletions(-)
 delete mode 100644 .DS_Store
 delete mode 100644 .Rbuildignore
 delete mode 100644 R/.DS_Store
 rename R/{GetResultsDE.R => getResultsDE.R} (100%)
 rename R/{ModelLRT.R => modelLRT.R} (100%)
 delete mode 100644 codecov.yml
 delete mode 100644 inst/.DS_Store
 delete mode 100644 inst/rmarkdown/.DS_Store
 delete mode 100644 inst/rmarkdown/templates/.DS_Store
 delete mode 100644 inst/rmarkdown/templates/Bacher_Group_HTML/.DS_Store
 delete mode 100644 scLANE.Rproj

diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
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diff --git a/.Rbuildignore b/.Rbuildignore
deleted file mode 100644
index b46f55f..0000000
--- a/.Rbuildignore
+++ /dev/null
@@ -1,5 +0,0 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^\.github$
-^doc$
-^Meta$
diff --git a/.gitignore b/.gitignore
index ed47a3d..be6819e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+scLANE.Rproj
 .Rproj.user
 .Rhistory
 .RData
diff --git a/R/.DS_Store b/R/.DS_Store
deleted file mode 100644
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GIT binary patch
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diff --git a/R/GetResultsDE.R b/R/getResultsDE.R
similarity index 100%
rename from R/GetResultsDE.R
rename to R/getResultsDE.R
diff --git a/R/ModelLRT.R b/R/modelLRT.R
similarity index 100%
rename from R/ModelLRT.R
rename to R/modelLRT.R
diff --git a/codecov.yml b/codecov.yml
deleted file mode 100644
index bb2358a..0000000
--- a/codecov.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-comment: false
-language: R
-sudo: false
-token: 22c87571-03cf-4f2e-a913-0bdf858e606b
-cache: packages
-after_success:
-- Rscript -e 'covr::codecov()'
-
-coverage:
-  status:
-    project:
-      default:
-        target: auto
-        threshold: 1%
-        informational: true
-    patch:
-      default:
-        target: auto
-        threshold: 1%
-        informational: true
diff --git a/inst/.DS_Store b/inst/.DS_Store
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diff --git a/inst/rmarkdown/.DS_Store b/inst/rmarkdown/.DS_Store
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diff --git a/inst/rmarkdown/templates/.DS_Store b/inst/rmarkdown/templates/.DS_Store
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diff --git a/scLANE.Rproj b/scLANE.Rproj
deleted file mode 100644
index 497f8bf..0000000
--- a/scLANE.Rproj
+++ /dev/null
@@ -1,20 +0,0 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source