Merge pull request #19 from jamesdunham/v0.2.10-cran

v0.2.10

Author: jamesdunham

NEWS.md

@@ -1,4 +1,13 @@
-# 0.2.9
+## 0.2.10
+
+* Remove Rcpp dependency by rewriting `dichotomize()` in R.
+* Avoid estimating models (using RStan) during tests, with the goal of rendering
+  moot variation in build environments. This addresses a test failure during
+  CRAN's
+  [r-release-osx-x86_64](https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/dgo-00check.html)
+  build.
+
+## 0.2.9
 
 * Switch from compiling Stan models at install time to compiling them at
   runtime, avoiding an Rcpp module issue.
@@ -11,7 +20,7 @@
 * Argument `by` to `get_n()` and `get_item_n()` methods properly accepts a
   vector of variable names when combined with `aggregate` arguments.
 
-# 0.2.8
+## 0.2.8
 
 * Improve Stan models for shorter run times
 * Add `dgmrp()` for fitting single-issue MRP models with hierarchical covariates
@@ -21,7 +30,7 @@
   `dgo_fit` class
 * Bugfixes
 
-# 0.2.7
+## 0.2.7
 
 * Package renamed dgo: Dynamic Estimation of Group-level Opinion
 * Tweaks to pass CRAN checks: clean up examples and docs
@@ -30,12 +39,12 @@
 * Fix Rcpp module issue from 0.2.6 (`Error in .doLoadActions(where, attach)`)
 * Export `expand_rownames()`
 
-# 0.2.6
+## 0.2.6
 
 * Fix error in `dgirt_plot`
 * Fix path in `tools/make_cpp.R`
 
-# 0.2.5
+## 0.2.5
 
 * `group_names` is no longer required. If omitted, the geographic variable given
   by `geo_name` will define groups.

README.Rmd

@@ -351,33 +351,26 @@ dgirt_plot(ps, group_names = NULL, time_name = "year", geo_name = "state")
 Please [report issues](https://github.com/jamesdunham/dgo/issues) that you
 encounter.
 
-OS X only: RStan creates temporary files during estimation in a location given
-by `tempdir`, typically an arbitrary location in `/var/folders`. If a model runs
-for days, these files can be cleaned up while still needed, which induces an
-error. A good solution is to set a safer path for temporary files, using an
-environment variable checked at session startup. As described in `?tempdir`, 
-
-> The environment variables ‘TMPDIR’, ‘TMP’ and ‘TEMP’ are checked in turn and
-> the first found which points to a writable directory is used: if none succeeds
-> ‘/tmp’ is used. The path should not contain spaces.  
-
-For help setting environment variables, see the Stack Overflow question
-[here](https://stackoverflow.com/questions/17107206/change-temporary-directory).
-Confirm the new path before starting your model run by restarting R and checking
-the output from `tempdir()`.
-
-``` r
-# Problematic temporary directories on OS X look like this
-tempdir()   
-#> [1] "/var/folders/2p/_d3c95qd6ljg28j1f5l2jqxm0000gn/T//Rtmp38a10A"
-```
-
-Models fitted before October 2016 (specifically <
-[#8e6a2cf](https://github.com/jamesdunham/dgo/commit/8e6a2cfbe00b2cd4a908b3067241e06124d143cd))
-using dgirtfit are not fully compatible with dgo. Their contents can be
-extracted without using dgo, however, with the `$` indexing operator. For
-example: `as.data.frame(dgirtfit_object$stan.cmb)`.
-
+  * OS X only: RStan creates temporary files during estimation in a location
+    given by `tempdir`, typically an arbitrary location in `/var/folders`. If a
+    model runs for days, these files can be cleaned up while still needed, which
+    induces an error. A good solution is to set a safer path for temporary
+    files, using an environment variable checked at session startup. For help
+    setting environment variables, see the Stack Overflow question
+    [here](https://stackoverflow.com/questions/17107206/change-temporary-directory).
+    Confirm the new path before starting your model run by restarting R and
+    checking the output from `tempdir()`.
+
+  * Models fitted before October 2016 (specifically <
+    [#8e6a2cf](https://github.com/jamesdunham/dgo/commit/8e6a2cfbe00b2cd4a908b3067241e06124d143cd))
+    using dgirtfit are not fully compatible with dgo. Their contents can be
+    extracted without using dgo, however, with the `$` indexing operator. For
+    example: `as.data.frame(dgirtfit_object$stan.cmb)`.
+
+  * Calling `dgirt()` or `dgmrp()` can generate
+    [warnings](http://mc-stan.org/misc/warnings#compiler-warnings) during model
+    compilation. These are safe to ignore, or can be suppressed by following the
+    linked instructions.
 
 ## Contributing and citing
 

README.md

@@ -465,19 +465,11 @@ Troubleshooting
 
 Please [report issues](https://github.com/jamesdunham/dgo/issues) that you encounter.
 
-OS X only: RStan creates temporary files during estimation in a location given by `tempdir`, typically an arbitrary location in `/var/folders`. If a model runs for days, these files can be cleaned up while still needed, which induces an error. A good solution is to set a safer path for temporary files, using an environment variable checked at session startup. As described in `?tempdir`,
+-   OS X only: RStan creates temporary files during estimation in a location given by `tempdir`, typically an arbitrary location in `/var/folders`. If a model runs for days, these files can be cleaned up while still needed, which induces an error. A good solution is to set a safer path for temporary files, using an environment variable checked at session startup. For help setting environment variables, see the Stack Overflow question [here](https://stackoverflow.com/questions/17107206/change-temporary-directory). Confirm the new path before starting your model run by restarting R and checking the output from `tempdir()`.
 
-> The environment variables ‘TMPDIR’, ‘TMP’ and ‘TEMP’ are checked in turn and the first found which points to a writable directory is used: if none succeeds ‘/tmp’ is used. The path should not contain spaces.
+-   Models fitted before October 2016 (specifically < [\#8e6a2cf](https://github.com/jamesdunham/dgo/commit/8e6a2cfbe00b2cd4a908b3067241e06124d143cd)) using dgirtfit are not fully compatible with dgo. Their contents can be extracted without using dgo, however, with the `$` indexing operator. For example: `as.data.frame(dgirtfit_object$stan.cmb)`.
 
-For help setting environment variables, see the Stack Overflow question [here](https://stackoverflow.com/questions/17107206/change-temporary-directory). Confirm the new path before starting your model run by restarting R and checking the output from `tempdir()`.
-
-``` r
-# Problematic temporary directories on OS X look like this
-tempdir()   
-#> [1] "/var/folders/2p/_d3c95qd6ljg28j1f5l2jqxm0000gn/T//Rtmp38a10A"
-```
-
-Models fitted before October 2016 (specifically < [\#8e6a2cf](https://github.com/jamesdunham/dgo/commit/8e6a2cfbe00b2cd4a908b3067241e06124d143cd)) using dgirtfit are not fully compatible with dgo. Their contents can be extracted without using dgo, however, with the `$` indexing operator. For example: `as.data.frame(dgirtfit_object$stan.cmb)`.
+-   Calling `dgirt()` or `dgmrp()` can generate [warnings](http://mc-stan.org/misc/warnings#compiler-warnings) during model compilation. These are safe to ignore, or can be suppressed by following the linked instructions.
 
 Contributing and citing
 -----------------------

cran-comments.md

@@ -1,8 +1,10 @@
 ## Test environments
 
 * local Ubuntu 16.04, R 3.4.0
-* Ubuntu 12.04 (on travis-ci), R 3.4.0 (devel and release)
-* Windows Server 2012 R2 x64 (on appveyor), R 3.4.0 (devel and release)
+* Ubuntu 12.04 (on travis-ci), R 3.4.0 (devel, release) and R 3.3.3
+* OS X 10.11 and 10.12 (on travis-ci), R 3.4.0 (devel, release) and R 3.3.3
+* Windows Server 2012 R2 x64 (on appveyor), R 3.4.0 (devel and release) and R
+  3.3.3
 
 
 ## R CMD check results
@@ -11,5 +13,10 @@ There were no ERRORs or WARNINGs.
 
 There was one NOTE:
 
-* "New submission": This is the first submission with this maintainer email.
-
+* "Days since last update: 6": This submission attempts to resolve a build
+  failure (only) on
+  [r-release-osx-x86_64](https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/dgo-00check.html)
+  resulting from a failing test, which does not occur on travis-ci. This
+  submission avoids using dependency RStan during tests and removes a dependency
+  on Rcpp. The goal of these changes is to render moot variation in build
+  environments.