Merge pull request #37 from USCbiostats/master

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USCbiostats · Mar 1, 2020 · 2a2311b · 2a2311b
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diff --git a/.travis.yml b/.travis.yml
@@ -13,6 +13,10 @@ jobs:
     os: osx
   - r: devel
     os: linux
+  - r: oldrel
+    os: linux
+  - r: oldrel
+    os: osx
 
 osx_image: xcode10.2
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: xrnet
 Type: Package
 Title: Hierarchical Regularized Regression
-Version: 0.1.6
+Version: 0.1.7
 Authors@R: c(
   person("Garrett", "Weaver", email = "gmweaver.usc@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9918-8386")),
   person("Juan Pablo", "Lewinger", email = "lewinger@usc.edu", role = c("ctb", "ths"))
@@ -21,7 +21,6 @@ Suggests:
     rmarkdown,
     testthat,
     Matrix,
-    glmnet,
     doParallel
 LinkingTo: 
     Rcpp,
@@ -34,5 +33,5 @@ Imports:
     bigmemory,
     methods
 Depends:
-    R (>= 3.6)
+    R (>= 3.5)
 SystemRequirements: C++11 
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# xrnet 0.1.7
+
+* Patched release to fix tests on Solaris OS and removed test dependency on glmnet
+
 # xrnet 0.1.6
 
 * First release to CRAN

diff --git a/README.Rmd b/README.Rmd
@@ -14,10 +14,11 @@ knitr::opts_chunk$set(
 )
 ```
 
-[![Build Status](https://travis-ci.org/USCbiostats/xrnet.svg?branch=development)](https://travis-ci.org/USCbiostats/xrnet)
-[![Build status](https://ci.appveyor.com/api/projects/status/6pr8hlc4wg9vjcxd?svg=true)](https://ci.appveyor.com/project/gmweaver/xrnet)
-[![codecov](https://codecov.io/gh/USCbiostats/xrnet/branch/development/graph/badge.svg)](https://codecov.io/gh/USCbiostats/xrnet)
+[![Travis Build Status](https://travis-ci.org/USCbiostats/xrnet.svg?branch=development)](https://travis-ci.org/USCbiostats/xrnet)
+[![Appveyor Build status](https://ci.appveyor.com/api/projects/status/6pr8hlc4wg9vjcxd?svg=true)](https://ci.appveyor.com/project/gmweaver/xrnet)
+[![codecov](https://codecov.io/gh/USCbiostats/xrnet/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/xrnet)
 [![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.01761/status.svg)](https://doi.org/10.21105/joss.01761)
 
 # Introduction
 
@@ -37,7 +38,15 @@ Note that our model allows for the predictor coefficients, beta, to shrink towar
 
 This package extends the coordinate descent algorithm of Friedman et al. 2010 (used in the R package **glmnet**) to allow for this variable-specific generalization and to fit the model described above. Currently, we allow for continuous and binary outcomes, but plan to extend to other outcomes (i.e. survival) in the next release.  
 
-# Setup
+# Installation
+
+#### From CRAN
+
+```{r, eval = FALSE}
+install.packages("xrnet")
+```
+
+#### From Github (most up-to-date)
 
 1. OS-specific prerequisites
     + *Windows*: Install [RTools](https://cran.r-project.org/bin/windows/Rtools/) (not an R package)
@@ -53,17 +62,12 @@ devtools::install_github("USCbiostats/xrnet")
 devtools::install_github("USCbiostats/xrnet", ref = "development")
 ```
 
-4. Load the package 
-
-```{r load-package}
-library(xrnet)
-```
-
 # A First Example
 
-As an example of how you might use xrnet, we have provided a small set of simulated external data variables (ext), predictors (x), and a continuous outcome variable (y). First, load the example data:
+As an example of how you might use xrnet, we have provided a small set of simulated external data variables (ext), predictors (x), and a continuous outcome variable (y). First, load the package and the example data:
 
 ```{r load-data}
+library(xrnet)
 data(GaussianExample)
 ```
 

diff --git a/README.md b/README.md
@@ -3,12 +3,13 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-[![Build
+[![Travis Build
 Status](https://travis-ci.org/USCbiostats/xrnet.svg?branch=development)](https://travis-ci.org/USCbiostats/xrnet)
-[![Build
+[![Appveyor Build
 status](https://ci.appveyor.com/api/projects/status/6pr8hlc4wg9vjcxd?svg=true)](https://ci.appveyor.com/project/gmweaver/xrnet)
-[![codecov](https://codecov.io/gh/USCbiostats/xrnet/branch/development/graph/badge.svg)](https://codecov.io/gh/USCbiostats/xrnet)
+[![codecov](https://codecov.io/gh/USCbiostats/xrnet/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/xrnet)
 [![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.01761/status.svg)](https://doi.org/10.21105/joss.01761)
 
 # Introduction
 
@@ -53,7 +54,15 @@ variable-specific generalization and to fit the model described above.
 Currently, we allow for continuous and binary outcomes, but plan to
 extend to other outcomes (i.e. survival) in the next release.
 
-# Setup
+# Installation
+
+#### From CRAN
+
+``` r
+install.packages("xrnet")
+```
+
+#### From Github (most up-to-date)
 
 1.  OS-specific prerequisites
       - *Windows*: Install
@@ -77,21 +86,15 @@ devtools::install_github("USCbiostats/xrnet")
 devtools::install_github("USCbiostats/xrnet", ref = "development")
 ```
 
-4.  Load the package
-
-<!-- end list -->
-
-``` r
-library(xrnet)
-```
-
 # A First Example
 
 As an example of how you might use xrnet, we have provided a small set
 of simulated external data variables (ext), predictors (x), and a
-continuous outcome variable (y). First, load the example data:
+continuous outcome variable (y). First, load the package and the example
+data:
 
 ``` r
+library(xrnet)
 data(GaussianExample)
 ```
 

diff --git a/appveyor.yml b/appveyor.yml
@@ -42,6 +42,12 @@ environment:
     - R_VERSION: devel
       R_ARCH: x64
 
+    - R_VERSION: oldrel
+      R_ARCH: i386
+
+    - R_VERSION: oldrel
+      R_ARCH: x64
+
 artifacts:
   - path: '*.Rcheck\**\*.log'
     name: Logs

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,12 +1,12 @@
-## Resubmission
-This is a resubmission. In this version I have:
+## Submission
 
-* Added reference to paper describing methods in DESCRIPTION
+This is a patch to fix the test errors generated on Solaris OS. 
 
-* Removed the copy of GPL-2 license
+* Checks reran on all other platforms as well
 
-* Added \value to any exported methods that were missing it in .Rd files
+* The test errors were due to incorrect comparison solutions being generated by another R package on Solaris.
+I now pre-generate comparison solutions and have removed the dependency on the other R package previously
+used to generate the comparisons. The changes did not require any modifications to the src code.
 
-* Removed \dontrun from example in plot.tune_xrnet documentation
-
-* Cleaned up error messages from stop("Error: ...") to stop("...")
+* Removed glmnet from 'Suggests' in Description as package is no longer needed for tests. This allowed
+for the minimum R version to be changed from 3.6 back down to 3.5 to accomodate the old release as well.
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