Trim all trailing whitespace

Author: andrjohns

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,7 +20,7 @@ A description of what you expected to happen.
 Your operating system (e.g. mac os x 10.15, windows 10, etc.)
 
 **CmdStanR version number**
-Your CmdStanR version number (e.g. from `packageVersion("cmdstanr")`). 
+Your CmdStanR version number (e.g. from `packageVersion("cmdstanr")`).
 
 **Additional context**
 Add any other context about the problem here.

.github/pull_request_template.md

@@ -5,17 +5,17 @@
 
 #### Summary
 
-Please describe the purpose of the pull request. 
+Please describe the purpose of the pull request.
 
 #### Copyright and Licensing
 
-Please list the copyright holder for the work you are submitting 
-(this will be you or your assignee, such as a university or company): 
+Please list the copyright holder for the work you are submitting
+(this will be you or your assignee, such as a university or company):
 **INSERT COPYRIGHT HOLDER HERE**
 
 
-By submitting this pull request, the copyright holder is agreeing to 
+By submitting this pull request, the copyright holder is agreeing to
 license the submitted work under the following licenses:
 
-- Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)    
+- Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
 - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

DESCRIPTION

@@ -2,24 +2,24 @@ Package: cmdstanr
 Title: R Interface to 'CmdStan'
 Version: 0.5.2.1
 Date: 2022-04-24
-Authors@R: 
+Authors@R:
     c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
            email = "[email protected]"),
-      person(given = "Rok", family = "Češnovar", role = "aut", 
-           email = "[email protected]"),     
-      person(given = "Ben", family = "Bales", role = "ctb"),     
-      person(given = "Mitzi", family = "Morris", role = "ctb"), 
-      person(given = "Mikhail", family = "Popov", role = "ctb"), 
-      person(given = "Mike", family = "Lawrence", role = "ctb"), 
+      person(given = "Rok", family = "Češnovar", role = "aut",
+           email = "[email protected]"),
+      person(given = "Ben", family = "Bales", role = "ctb"),
+      person(given = "Mitzi", family = "Morris", role = "ctb"),
+      person(given = "Mikhail", family = "Popov", role = "ctb"),
+      person(given = "Mike", family = "Lawrence", role = "ctb"),
       person(given = c("William", "Michael"), family = "Landau", role = "ctb",
-           email = "[email protected]", comment = c(ORCID = "0000-0003-1878-3253")), 
+           email = "[email protected]", comment = c(ORCID = "0000-0003-1878-3253")),
       person(given = "Jacob", family = "Socolar", role = "ctb"))
 Description: A lightweight interface to 'Stan' <https://mc-stan.org>.
-    The 'CmdStanR' interface is an alternative to 'RStan' that calls the command 
-    line interface for compilation and running algorithms instead of interfacing 
-    with C++ via 'Rcpp'. This has many benefits including always being compatible 
-    with the latest version of Stan, fewer installation errors, fewer unexpected 
-    crashes in RStudio, and a more permissive license. 
+    The 'CmdStanR' interface is an alternative to 'RStan' that calls the command
+    line interface for compilation and running algorithms instead of interfacing
+    with C++ via 'Rcpp'. This has many benefits including always being compatible
+    with the latest version of Stan, fewer installation errors, fewer unexpected
+    crashes in RStudio, and a more permissive license.
 License: BSD_3_clause + file LICENSE
 URL: https://mc-stan.org/cmdstanr/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/cmdstanr/issues
@@ -38,7 +38,7 @@ Imports:
     processx (>= 3.5.0),
     R6 (>= 2.4.0),
     withr (>= 2.5.0)
-Suggests: 
+Suggests:
     bayesplot,
     knitr (>= 1.37),
     loo (>= 2.0.0),

LICENSE.md

@@ -1,7 +1,7 @@
 BSD 3-Clause License
 =====================
 
-Copyright (c) 2019, Stan Developers and their Assignees    
+Copyright (c) 2019, Stan Developers and their Assignees
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

NEWS.md

@@ -2,15 +2,15 @@
 
 ### Bug fixes
 
-* In `cmdstan_default_path()` we now ignore directories inside `.cmdstan` that don't start 
+* In `cmdstan_default_path()` we now ignore directories inside `.cmdstan` that don't start
 with `"cmdstan-"`. (#651)
 
 * Fixed Windows issue related to not locating `grep.exe` or when it is located in a path
 with spaces. (@weshinsley, #661, #663)
 
 * Fixed a bug with diagnostic checks when ebfmi is NaN.
 
-* Fixed a bug that caused issues when using `~` or `.` in paths supplied to the 
+* Fixed a bug that caused issues when using `~` or `.` in paths supplied to the
 `cmdstanr_write_stan_file_dir` global option.
 
 # cmdstanr 0.5.2
@@ -19,7 +19,7 @@ with spaces. (@weshinsley, #661, #663)
 for Rtools42. (#645)
 
 * Expanded the use of `CMDSTAN` environment variable to point to CmdStan installation
-_or_ directory containing CmdStan installations. (#643) 
+_or_ directory containing CmdStan installations. (#643)
 
 * New vignette on how to handle deprecations using the `$format()` method. (#644)
 

R/model.R

@@ -581,7 +581,7 @@ compile <- function(quiet = TRUE,
           )
         }
         if (os_is_macos()) {
-          if (R.version$arch == "aarch64" 
+          if (R.version$arch == "aarch64"
               && grepl("but the current translation unit is being compiled for target", x)) {
             warning(
               "The C++ compiler has errored due to incompatibility between the x86 and ",

README.md

@@ -6,7 +6,7 @@
 [![Codecov test coverage](https://codecov.io/gh/stan-dev/cmdstanr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/stan-dev/cmdstanr?branch=master)
 <!-- badges: end -->
 
-### Overview 
+### Overview
 
 CmdStanR is a lightweight interface to [Stan](https://mc-stan.org) for R users
 (see [CmdStanPy](https://github.com/stan-dev/cmdstanpy) for Python).
@@ -23,7 +23,7 @@ If you are new to CmdStanR we recommend starting with these vignettes:
 releases.
 
 * R code that doesn't interface directly with C++, only calls compiled executables.
-      
+
 * Modularity: CmdStanR runs Stan's algorithms and lets downstream modules do the
 analysis.
 
@@ -34,7 +34,7 @@ analysis.
 
 #### Installing the R package
 
-You can install the latest beta release of the **cmdstanr** R package with 
+You can install the latest beta release of the **cmdstanr** R package with
 
 ```r
 # we recommend running this is a fresh R session or restarting your current session
@@ -53,22 +53,22 @@ remotes::install_github("stan-dev/cmdstanr")
 #### Installing CmdStan
 
 If you don't already have CmdStan installed then, in addition to installing the
-R package, it is also necessary to install CmdStan using CmdStanR's 
-`install_cmdstan()` function. A suitable C++ toolchain is also required. 
+R package, it is also necessary to install CmdStan using CmdStanR's
+`install_cmdstan()` function. A suitable C++ toolchain is also required.
 Instructions are provided in the [_Getting started with
-CmdStanR_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html) vignette. 
+CmdStanR_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html) vignette.
 
 
-### Contributing 
+### Contributing
 
-There is a lot of work still to be done and contributions are very welcome! 
+There is a lot of work still to be done and contributions are very welcome!
 If you are interested in contributing please comment on an open issue
-or open a new one if none are applicable.  
+or open a new one if none are applicable.
 
 ### License
 
-CmdStanR, like CmdStan and the core Stan C++ code, is licensed under the 
-following licenses: 
+CmdStanR, like CmdStan and the core Stan C++ code, is licensed under the
+following licenses:
 
 - Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
 - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

tests/testthat/resources/data/logistic.data.R

@@ -1,11 +1,11 @@
 N <- 100
 K <- 3
-y <- 
+y <-
 c(1, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0,
 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0,
 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1,
 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1)
-X <- 
+X <-
 structure(c(-0.326036490515386, 0.552461855419139, -0.67494384395583,
 0.214359459043425, 0.310769217313602, 1.1739662875627, 0.618789855625968,
 -0.112734314754215, 0.917028289512712, -0.223259364627263, 0.526448098873642,

tests/testthat/resources/metric/bernoulli.inv_metric.dense_e.data.R

@@ -1,3 +1,3 @@
-inv_metric <- 
+inv_metric <-
 structure(c(1),
 .Dim = c(1, 1))

tests/testthat/test-model-compile.R

@@ -581,7 +581,7 @@ test_that("cmdstan_model errors with no args ", {
 })
 
 test_that("cmdstan_model works with user_header", {
-  skip_if(os_is_macos() | os_is_windows()) 
+  skip_if(os_is_macos() | os_is_windows())
   tmpfile <- tempfile(fileext = ".hpp")
   hpp <-
   "

vignettes/children/comparison-with-rstan.md

@@ -14,7 +14,7 @@ but currently they are only available to R users via RStan:
   - `rstan::log_prob()`
   - `rstan::grad_log_prob()`
   - `rstan::expose_stan_functions()`
-  
+
 * Allows other developers to distribute R packages with
 _pre-compiled_ Stan programs (like **rstanarm**) on CRAN.
 
@@ -26,12 +26,12 @@ package and new CRAN releases of both **rstan** and **StanHeaders**. With
 CmdStanR the latest improvements in Stan will be available from R immediately
 after updating CmdStan using `cmdstanr::install_cmdstan()`.
 
-* Fewer installation issues (e.g., no need to mess with Makevars files). 
+* Fewer installation issues (e.g., no need to mess with Makevars files).
 
 * Running Stan via external processes results in fewer unexpected crashes,
 especially in RStudio.
 
-* Less memory overhead. 
+* Less memory overhead.
 
 * More permissive license. RStan uses the GPL-3 license while the license for
 CmdStanR is BSD-3, which is a bit more permissive and is the same license used