Merge pull request #156 from weecology/cran_patch

v0.2.7
weecology · Mar 18, 2020 · 9c09c0f · 9c09c0f
2 parents 6db257a + 29c489f
commit 9c09c0f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: LDATS
 Title: Latent Dirichlet Allocation Coupled with Time Series Analyses
-Version: 0.2.6
+Version: 0.2.7
 Authors@R: c(
     person(c("Juniper", "L."), "Simonis",
       email = "juniper.simonis@weecology.org", role = c("aut", "cre"),
@@ -51,17 +51,11 @@ Imports:
     topicmodels,
     viridis
 Suggests:
-    dplyr,
-    here,
     knitr,
     pkgdown,
     rmarkdown,
     testthat, 
-    vdiffr, 
-    clue, 
-    reshape,
-    RCurl, 
-    tidyr
+    vdiffr
 VignetteBuilder:
     knitr
 RoxygenNote: 6.1.1
diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,15 @@
 
 Version numbers follow [Semantic Versioning](https://semver.org/).
 
+
+# LDATS 0.2.7(https://github.com/weecology/ldats/releases/tag/v0.2.7)
+*2020-03-18* 
+
+## Patching CRAN issues with vignette building
+* Dependencies are being managed different now
+* For the paper comparison vignette, all of the code is pre-run and saved in the LDATS-replications repository
+* Allows removal of otherwise unused packages from this package's dependency list
+
 # LDATS 0.2.6(https://github.com/weecology/ldats/releases/tag/v0.2.6)
 *2020-03-02* 
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -11,9 +11,9 @@ navbar:
       text: "Vignettes"
       menu: 
         - text: "Rodents example"
-          href: rodents-example.html
+          href: articles/rodents-example.html
         - text: "Comparison to Christensen et al."
-          href: paper-comparison.html
+          href: articles/paper-comparison.html
         - text: "LDATS codebase"
           href: articles/LDATS_codebase.html
     reference: 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,15 +1,17 @@
-This resubmission addresses problems associated with the stringsAsFactors update in R-devel
+This resubmission addresses problems associated with vignette dependencies
 
 ## Test environments
 * local Windows 10 home install, R 3.6.1 64-bit and 32-bit 
-* local Windows 10 home install, R-devel (2020-03-01 r77881) 64-bit and 32-bit 
-* ubuntu 16.04.6 LTS (on travis-ci), R 3.6.2 and R-devel (2019-03-02 r77888) 
+* local Windows 10 home install, R-devel (2020-03-12 r77936) 64-bit and 32-bit 
+* ubuntu 16.04.6 LTS (on travis-ci), R 3.6.2 and R-devel (2020-03-13 r77948) 
+* win builder, R 3.5.3
 * win builder, R 3.6.3
-* win builder, R-devel (2020-01-28 r77738) 
-* R-hub builder, Debian Linux, R-devel, GCC
-* R-hub builder, macOS 10.11 El Capitan, R-release (experimental)
-* R-hub builder, Fedora Linux, R-devel, GCC
+* win builder, R-devel (2020-03-11 r77925) 
+* R-hub builder, Ubuntu Linux 16.04 LTS, R-release, GCC
+* R-hub builder, Windows Server 2008 R2 SP1, R-devel, 32/64 bit
 * R-hub builder, Fedora Linux, R-devel, clang, gfortran
+* R-hub builder, macOS 10.11 El Capitan, R-release (experimental)
+* R-hub builder, Oracle Solaris 10, x86, 32 bit, R-patched (experimental)
 
 ## R CMD check results:
 There were no ERRORs, WARNINGs, or NOTEs

diff --git a/doc/LDATS_codebase.R b/doc/LDATS_codebase.R
@@ -1,15 +1,15 @@
-## ----setup, include=FALSE------------------------------------------------
+## ----setup, include=FALSE-----------------------------------------------------
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
 
-## ---- include=FALSE------------------------------------------------------
+## ---- include=FALSE-----------------------------------------------------------
 library(LDATS)
 vers <- packageVersion("LDATS")
 today <- Sys.Date()
 
-## ---- eval=FALSE---------------------------------------------------------
+## ---- eval=FALSE--------------------------------------------------------------
 #  install.packages("devtools")
 #  devtools::install_github("weecology/LDATS")
 
diff --git a/doc/LDATS_codebase.html b/doc/LDATS_codebase.html
@@ -1,15 +1,14 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
 
 <head>
 
 <meta charset="utf-8" />
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
-<meta name="viewport" content="width=device-width, initial-scale=1">
+<meta name="viewport" content="width=device-width, initial-scale=1" />
 
 <meta name="author" content="Juniper L. Simonis" />
 
@@ -120,9 +119,6 @@
 font-size: 14px;
 line-height: 1.35;
 }
-#header {
-text-align: center;
-}
 #TOC {
 clear: both;
 margin: 0 0 10px 10px;
@@ -290,7 +286,8 @@
 code > span.co { color: #888888; font-style: italic; } 
 code > span.ot { color: #007020; } 
 code > span.al { color: #ff0000; font-weight: bold; } 
-code > span.fu { color: #900; font-weight: bold; }  code > span.er { color: #a61717; background-color: #e3d2d2; } 
+code > span.fu { color: #900; font-weight: bold; } 
+code > span.er { color: #a61717; background-color: #e3d2d2; } 
 </style>
 
 
@@ -310,7 +307,7 @@ <h4 class="author">Juniper L. Simonis</h4>
 
 <div id="overview" class="section level2">
 <h2>Overview</h2>
-<p>This vignette outlines the code base for the <strong>LDATS</strong> package. It was constructed using <strong>LDATS</strong> version 0.3.0 on 2019-10-12.</p>
+<p>This vignette outlines the code base for the <strong>LDATS</strong> package. It was constructed using <strong>LDATS</strong> version 0.2.7 on 2020-03-18.</p>
 </div>
 <div id="installation" class="section level2">
 <h2>Installation</h2>