From c5fa50683e4dedfbaa0dc150300c5726f5b96ce1 Mon Sep 17 00:00:00 2001
From: Jack Leary <j.leary@ufl.edu>
Date: Fri, 1 Dec 2023 14:45:28 -0500
Subject: [PATCH 1/3] fixed CITATION formatting

---
 inst/CITATION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/CITATION b/inst/CITATION
index 5d4b98c..68919f7 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -5,7 +5,7 @@ citEntry(
   title    = "Single Cell Linear Adaptive Expression Testing (scLANE)",
   journal  = "Zenodo",
   author   = c(person(given = c("Jack", "R."), family = "Leary"),
-               person(given = "Rhonda", family = "Bacher"))
+               person(given = "Rhonda", family = "Bacher")),
   year     = "2023",
   note     = "R package version 0.7.7",
   url      = "https://doi.org/10.5281/zenodo.10182497",

From 679b079500a96e939a5dd92dc119f0d9b730e68d Mon Sep 17 00:00:00 2001
From: Jack Leary <j.leary@ufl.edu>
Date: Wed, 6 Dec 2023 13:50:58 -0500
Subject: [PATCH 2/3] updated BiocCheck action to include BiocCheckGitClone

---
 .DS_Store                         | Bin 16388 -> 10244 bytes
 .github/workflows/bioc-check.yaml |  12 +++++-------
 .gitignore                        |   3 +++
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index 64e4768f65221a3de2f1ecd35892ca1107c9644b..ee60853be1803afc81904f8fd6a865fc39400c2f 100644
GIT binary patch
delta 288
zcmZo^U~CCcVPIfjbSh0TWMEJLGC6=4L<?{;FtBhjFh~Gt28M|$+M;Gani(j;Q0APJ
zlb;0SXe1SE7Gzq?JlVj8g_{v5%>u-X3_+V63{03O{}l_J{6RH?6C?oy9Na*);w+oh
zd7dycif>-5!^gaNpP4NqC&<)dh9ZXK&2t577&o62naemiKw=W3++-ew&zqMkUS!;?
zs2a++Sy&^Caq<qKM3{;`Nmhu-3Lq!CB0Cvq(|hL0{5F;<K+D1Q0|_RGYA^%jOAQbo
XC~h!0#b)B<ddBR@VVc6o7IXsu)hIYM

delta 1975
zcmd6o&ubGw6vy9mSDQ4k-6l;^YSk!<AXR7};tx<!E7anlm|IV2eh_~o*))w2K}f`k
z;K{gGZyqiFVD6#^p$Otl6cI0aQt{wF;G1nXGqar`R|A_#-hAKN_j&W<tu3x~i46ec
z+>KHO;5hya;loBNie~(i#&I^%vu6@{w3;{pPy`1Wa23jho4u7M?yPO5hBhZ*7%oGa
z3*7zjuAAO7KeYqr4OoRH6x+FGz3S8}Xd&TeqjWr!G+%aqlQ2OGenJt?L=Q%P7^%Hz
z2yglY;%;;l_G%@QD>}7?7YIV{)ZR5`Zmv*u3hZUiKQ*oU58j^DDN9;q7BL0X#uf3^
zi!1|0f;2yIo1`Mpf-+LI@DV~_wKh7MIhpLzJq)i=igb7X^y#!}PRP{rTgA}GWy(CG
z)F|ou#5&nG25sCZ6{sU`Yl}KaJU}CpXBP0413bhEe2lI7>#OnV_`A90@KOwR^S$JX
zc<Zitk?$cM0EBUGr5@3AXc!N{0fS`S=;Ytd2$WzM%e5?S52+BlpT0(4rB1~E`sJFB
zuhDX5u1%@~(_fR{Nn!*SwC-(Qc_F=nj+rZFrOanueeg0@=)}y=pSjL6S893YTzeWb
zSBRxWI*eBsE1g0|-%OQAJPb9gd|j-)cQh4tiEQF?9s?^>BG<~}{*hEFIaN@Zl~a<K
zk}nvOA|OppmkG7ZlLn1iqXurarK5PI2QO-g!?<{4yMiXotPxY#W7hgmCvfkJz{kE-
z{Ds`6;;?#^#A!an41&qGb97gHfgI}hC6w%BI&5VT{JIcqXV_qV8t#~VVw!0P0Bc`t
Z#Qx@utP6r$wR`l=_$l&V(1rVS{{ZuZp%wrD

diff --git a/.github/workflows/bioc-check.yaml b/.github/workflows/bioc-check.yaml
index b6e7d7c..163fbf1 100644
--- a/.github/workflows/bioc-check.yaml
+++ b/.github/workflows/bioc-check.yaml
@@ -27,16 +27,14 @@ jobs:
           install.packages("BiocManager")
           BiocManager::install("BiocCheck")
         shell: Rscript {0}
-      - name: Run BiocCheck
+      - name: Run BiocCheck & BiocCheckGitClone
         run: |
           bc_res <- BiocCheck::BiocCheck()
-          print(paste0("Errors: ", length(bc_res$error)))
-          print(paste0("Warnings: ", length(bc_res$warning)))
-          print(paste0("Notes: ", length(bc_res$note)))
-          n_errors <- length(bc_res$error)
-          Sys.setenv("BC_ERRORS" = n_errors)
+          bc_gc_res <- BiocCheck::BiocCheckGitClone()
+          n_errors <- length(bc_res$error) + length(bc_gc_res$error)
+          Sys.setenv("BC_ERRORS_TOTAL" = n_errors)
         shell: Rscript {0}
       - name: Check BiocCheck results
         run: |
-          if [[ $BC_ERRORS -gt 0 ]]; then exit 1; else echo "BiocCheck passed!"; fi
+          if [[ $BC_ERRORS_TOTAL -gt 0 ]]; then exit 1; else echo "BiocCheck passed!"; fi
         shell: bash
diff --git a/.gitignore b/.gitignore
index 48fd75c..34a89e8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,6 @@ inst/doc
 codecov.yml
 /doc/
 /Meta/
+R/.DS_Store
+.Rproj
+src/*.o

From 88a2a3c5f7912c5fd470de9281cc16fb03144702 Mon Sep 17 00:00:00 2001
From: Jack Leary <j.leary@ufl.edu>
Date: Wed, 6 Dec 2023 13:52:24 -0500
Subject: [PATCH 3/3] updated gitignore as per BiocCheckGitClone

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 34a89e8..9e95317 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ codecov.yml
 R/.DS_Store
 .Rproj
 src/*.o
+src/*.so