From a3a16a10b48700916127bb07db98da4171743c5d Mon Sep 17 00:00:00 2001
From: Greg Finak <greg.finak@gmail.com>
Date: Mon, 4 Jan 2021 16:34:50 -0800
Subject: [PATCH 1/2] Delete .travis.yml

---
 .travis.yml | 70 -----------------------------------------------------
 1 file changed, 70 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index ada6190..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,70 +0,0 @@
-# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
-
-language: r
-sudo: required
-
-matrix:
-  include:
-   - os: linux
-     r: release
-   - os: linux
-     r: devel
-     env: R_CODECOV=true
-
-cache: 
-  packages: TRUE
-
-before_install:
-  - R -e 'install.packages("devtools")'
-
-r_packages:
-  - data.table
-  - shiny
-  - shinythemes
-  - MASS
-  - methods
-  - stats
-  - utils
-  - graphics
-  - grDevices
-  - tools
-  - magrittr
-  - rmarkdown
-  - robustbase
-  - ggplot2
-
-r_github_packages:
-  - jrowen/rhandsontable
-  - rlbarter/superheat
-  - yihui/knitr
-  - r-lib/covr
-  - r-lib/testthat
-  - r-lib/vdiffr
-  - r-lib/pkgdown
-  - rstudio/shinytest
-  
-use_bioc: true
-
-bioc_packages:
-  - BiocGenerics
-  - RProtoBufLib
-  - flowCore
-  - ncdfFlow
-  - cytolib
-  - flowWorkspace
-  
-warnings_are_errors: false
-
-after_success:
-  -  if [[ "${R_CODECOV}" ]]; then R -e 'covr::codecov()'; fi
-  
-env:
- global:
-   - CRAN: http://cran.rstudio.com
-   - BIOC_USE_DEVEL="FALSE"
-
-addons:
-  apt:
-    packages:
-      - libhdf5-dev
-  

From 7220446233fd325530b46fa856f0bbeef91daf8c Mon Sep 17 00:00:00 2001
From: Greg Finak <gfinak@fredhutch.org>
Date: Mon, 11 Jan 2021 14:11:24 -0800
Subject: [PATCH 2/2] conditional eval of a section when no model is fit in
 COMPASS

---
 DESCRIPTION |  2 +-
 R/COMPASS.R | 17 +++++++++--------
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f8a5613..bfbb94a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: COMPASS
 Type: Package
 Title: Combinatorial Polyfunctionality Analysis of Single Cells
-Version: 1.29.4
+Version: 1.29.5
 Date: 2014-07-11
 Author: Lynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)
 Authors@R: c( person("Lynn", "Lin", role="aut", email="llin@fhcrc.org"),
diff --git a/R/COMPASS.R b/R/COMPASS.R
index e1d7abf..2283c81 100644
--- a/R/COMPASS.R
+++ b/R/COMPASS.R
@@ -450,25 +450,26 @@ COMPASS <- function(data, treatment, control, subset=NULL,
 
   ## go to the model fitting processes
   if(run_model_or_return_data=="run_model"){
-  output <- list(
-    fit=.COMPASS.discrete(n_s=n_s, n_u=n_u, categories=categories,
-      iterations=iterations, replications=replications, verbose=verbose, init_with_fisher=init_with_fisher, ...),
-    data=list(n_s=n_s, n_u=n_u, counts_s=counts_s, counts_u=counts_u,
-      categories=categories, meta=data$meta, sample_id=data$sample_id,
-      individual_id=data$individual_id)
-  )
+    output <- list(
+        fit=.COMPASS.discrete(n_s=n_s, n_u=n_u, categories=categories,
+        iterations=iterations, replications=replications, verbose=verbose, init_with_fisher=init_with_fisher, ...),
+        data=list(n_s=n_s, n_u=n_u, counts_s=counts_s, counts_u=counts_u,
+        categories=categories, meta=data$meta, sample_id=data$sample_id,
+        individual_id=data$individual_id)
+    )
   }else{
 	output<-list(fit="No model was fitted");
   }
-
   if (keep_original_data) {
     output$orig <- data
   }
 
+if(run_model_or_return_data == "run_model"){
   ## Compute the posterior ps-pu; log(ps)-log(pu)
   vmessage("Computing the posterior difference in proportions, posterior log ratio...")
   output$fit$posterior <- compute_posterior(output)
   vmessage("Done!")
+}
 
   ## Filter metadata
   ..iid.. <- iid