Merge branch 'development'

.Rbuildignore

@@ -1,9 +1,10 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-.travis.yml
-cran-comments.md
+^\.lintr$
+^\.travis\.yml$
+^appveyor\.yml$
+^cran-comments\.md$
 ^docs$
-LICENSE
+^LICENSE$
 ^_pkgdown\.yml$
 ^revdep$
-

.lintr

@@ -0,0 +1 @@
+linters: with_defaults(line_length_linter(100), object_name_linter("lowerCamelCase"), default = default_linters[-which(names(default_linters) == "object_usage_linter")])

.travis.yml

@@ -5,46 +5,44 @@ matrix:
   include:
   - os: linux
     dist: trusty
-    r: 3.1.3
+    r: 3.1.0
     cran: http://cran.rstudio.com/
-    before_install:
-    - echo "options(repos = c(CRAN='http://cran.rstudio.com'))" >> ~/.Rprofile
   - os: linux
     dist: trusty
-    r: 3.2.5
+    r: 3.2.0
+    cran: http://cran.rstudio.com/
+  - os: linux
+    dist: trusty
+    r: 3.3.0
+    cran: http://cran.rstudio.com/
+  - os: linux
+    dist: trusty
+    r: 3.4.0
     cran: http://cran.rstudio.com/
-    before_install:
-    - echo "options(repos = c(CRAN='http://cran.rstudio.com'))" >> ~/.Rprofile
   - os: linux
     dist: trusty
     r: oldrel
-    before_install:
-    - echo "options(repos = c(CRAN='https://cran.rstudio.com'))" >> ~/.Rprofile
   - os: linux
     dist: trusty
     r: release
-    before_install:
-    - echo "options(repos = c(CRAN='https://cran.rstudio.com'))" >> ~/.Rprofile
     r_github_packages:
     - jimhester/covr
+    - jimhester/lintr
     after_success:
     - Rscript -e 'covr::coveralls(type = "all", quiet = FALSE)'
+    - Rscript -e 'lintr::lint_package()'
   - os: linux
     dist: trusty
     r: devel
-    before_install:
-    - echo "options(repos = c(CRAN='https://cran.rstudio.com'))" >> ~/.Rprofile
     r_packages:
     - devtools
   - os: osx
-    osx_image: xcode8
+    osx_image: xcode9.2
     latex: false
     r_build_args: '--no-build-vignettes'
     r_check_args: '--as-cran --ignore-vignettes --no-examples'
-    before_install:
-    - echo "options(repos = c(CRAN='https://cran.rstudio.com'))" >> ~/.Rprofile
-r_build_args: '--compact-vignettes="gs+qpdf"'
-r_check_args: '--as-cran'
+r_build_args: " "
+r_check_args: "--as-cran"
 warnings_are_errors: true
 notifications:
   email:

DESCRIPTION

@@ -2,10 +2,10 @@ Package: fpCompare
 Type: Package
 Title: Reliable Comparison of Floating Point Numbers
 URL: https://github.com/PredictiveEcology/fpCompare
-Version: 0.2.1
-Date: 2015-09-01
+Version: 0.2.2
+Date: 2018-06-07
 Authors@R: c(
-    person(c("Alex", "M"), "Chubaty", email="alexander.chubaty@canada.ca",
+    person(c("Alex", "M"), "Chubaty", email="alex.chubaty@gmail.com",
     role=c("aut", "cre")),
     person("Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada",
     role="cph")
@@ -15,11 +15,11 @@ Description: Comparisons of floating point numbers are problematic due to errors
     Despite being aware of these problems, people still use numerical methods
     that fail to account for these and other rounding errors (this pitfall is
     the first to be highlighted in Circle 1 of Burns (2012)
-    [The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
+    'The R Inferno' <http://www.burns-stat.com/pages/Tutor/R_inferno.pdf>).
     This package provides new relational operators useful for performing
     floating point number comparisons with a set tolerance.
 Depends:
-    R (>= 3.1.2)
+    R (>= 3.1.0)
 Suggests:
     knitr,
     rmarkdown,

NEWS → NEWS.md

@@ -1,5 +1,9 @@
 Known issues: https://github.com/PredictiveEcology/fpCompare/issues
 
+version 0.2.2
+=============
+* update maintainer's email address
+
 version 0.2.1
 =============
 * update maintainer's email address

R/fpCompare.R

@@ -1,7 +1,3 @@
-### \code{fpCompare.tolerance} is set in \code{options} during package load
-### and is unset on unload.
-
-################################################################################
 #' Relational operators with tolerance
 #'
 #' Binary operators which allow the comparison of values in numeric vectors.
@@ -66,11 +62,11 @@
 #' @export
 #' @rdname relational-operators
 `%==%` <- function(x, y) {
-  (abs(x-y) < getOption("fpCompare.tolerance"))
+  (abs(x - y) < getOption("fpCompare.tolerance"))
 }
 
 #' @export
 #' @rdname relational-operators
 `%!=%` <- function(x, y) {
-  (abs(x-y) > getOption("fpCompare.tolerance"))
+  (abs(x - y) > getOption("fpCompare.tolerance"))
 }

R/zzz.R

@@ -1,5 +1,5 @@
 .onLoad <- function(libname, pkgname) {
-  options(fpCompare.tolerance = .Machine$double.eps^0.5)
+  options(fpCompare.tolerance = .Machine$double.eps ^ 0.5)
 }
 
 .onUnload <- function(libname, pkgname) {

README.md

@@ -2,13 +2,13 @@
 
 [![Build Status](https://travis-ci.org/PredictiveEcology/fpCompare.svg?branch=master)](https://travis-ci.org/PredictiveEcology/fpCompare)
 [![Coverage Status](https://coveralls.io/repos/PredictiveEcology/fpCompare/badge.svg?branch=master)](https://coveralls.io/r/PredictiveEcology/fpCompare?branch=master)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/fpCompare)](https://cran.rstudio.com/package=fpCompare)
-[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/fpCompare)](https://cran.rstudio.com/package=fpCompare)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/fpCompare)](https://CRAN.R-project.org/package=fpCompare)
+[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/fpCompare)](https://CRAN.R-project.org/package=fpCompare)
 [![DOI](https://zenodo.org/badge/17892/PredictiveEcology/fpCompare.svg)](https://zenodo.org/badge/latestdoi/17892/PredictiveEcology/fpCompare)
 
 ## Reliable comparison of floating point numbers
 
-Comparisons of floating point numbers are problematic due to errors associated with the binary representation of decimal numbers. Computer scientists and programmers are aware of these problems and yet people still use numerical methods which fail to account for floating point errors (this pitfall is the first to be highlighted in Circle 1 of Burns (2012) [The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
+Comparisons of floating point numbers are problematic due to errors associated with the binary representation of decimal numbers. Computer scientists and programmers are aware of these problems and yet people still use numerical methods which fail to account for floating point errors (this pitfall is the first to be highlighted in Circle 1 of Burns (2012) [The R Inferno](https://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
 
 To avoid these and other numerical rounding issues, R's help file for relational operators (*e.g.*, `?'>'`) suggests using `identical` and `all.equal` when making numerical comparisons:
 
@@ -19,7 +19,7 @@ x1 == x2                           # FALSE on most machines
 identical(all.equal(x1, x2), TRUE) # TRUE everywhere
 ```
 
-Inspired by [R FAQ 7.31](http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f) and [this Stack Overflow answer](http://stackoverflow.com/a/2769618/1380598), this package provides new relational operators useful for performing floating point number comparisons with a set tolerance:
+Inspired by [R FAQ 7.31](https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f) and [this Stack Overflow answer](https://stackoverflow.com/a/2769618/1380598), this package provides new relational operators useful for performing floating point number comparisons with a set tolerance:
 
 **`fpCompare`**[^1] | **`base`**
 --------------------|-----------

appveyor.yml

@@ -29,15 +29,18 @@ environment:
   - R_VERSION: release
 
   - R_VERSION: oldrel
-    RTOOLS_VERSION: 33
+    RTOOLS_VERSION: 34
+
+  - R_VERSION: 3.4.0
+    RTOOLS_VERSION: 34
 
   - R_VERSION: 3.3.0
     RTOOLS_VERSION: 33
 
-  - R_VERSION: 3.2.5
+  - R_VERSION: 3.2.0
     RTOOLS_VERSION: 32
 
-  - R_VERSION: 3.1.2
+  - R_VERSION: 3.1.0
     RTOOLS_VERSION: 31
     CRAN: http://cran.rstudio.com
 
@@ -52,7 +55,7 @@ branches:
 clone_depth: 5
 
 build_script:
-  - travis-tool.sh r_binary_install knitr rmarkdown testthat
+  - travis-tool.sh r_binary_install knitr rmarkdown stringi testthat
   - travis-tool.sh install_deps
 
 test_script:

cran-comments.md

@@ -2,46 +2,56 @@
 
 In this version I have:
 
-* updated the maintainer's email address
-* switched to using `rmarkdown::render` for vignettes
+* updated the maintainer's email address, about which I emailed CRAN on March 28, 2018.
 
 ## Test environments
 
 ### Previous R versions
-* Windows 7               (local), R 3.1.2
-* Windows 7               (local), R 3.1.3
-* Windows 7               (local), R 3.2.0
-* Windows 7               (local), R 3.2.1
+* Ubuntu 14.04        (travis-ci), R 3.1.0
+* Ubuntu 14.04        (travis-ci), R 3.2.0
+* Ubuntu 14.04        (travis-ci), R 3.3.0
+* Ubuntu 14.04        (travis-ci), R 3.4.0
+* Windows              (appveyor), R 3.1.0
+* Windows              (appveyor), R 3.2.0
+* Windows              (appveyor), R 3.3.0
+* Windows              (appveyor), R 3.4.0
 
 ### Current R versions
-* OS X Yosemite           (local), R 3.2.2
-* Ubuntu 12.04        (travis-ci), R 3.2.2
-* Windows 7               (local), R 3.2.2
-* Windows           (win-builder), R 3.2.2
+* macOS High Sierra    (local), R 3.5.0
+* OS X El Capitan  (travis-ci), R 3.5.0
+* Ubuntu 14.04     (travis-ci), R 3.5.0
+* Ubuntu 18.04         (local), R 3.5.0
+* Windows           (appveyor), R 3.5.0
+* Windows        (win-builder), R 3.5.0
+* Windows 7            (local), R 3.5.0
 
 ### Development R version
-* Debian:testing (rocker/r-devel), R 3.3.0 (2015-08-26 r69190)
-* Windows           (win-builder), R 3.3.0 (2015-09-01 r69241)
+* Ubuntu 14.04     (travis-ci), R 3.6.0 (2018-06-05 r74851)
+* Ubuntu 18.04         (local), R 3.6.0 (2018-06-05 r74852)
+* Windows           (appveyor), R 3.6.0 (2018-06-05 r74852)
+* Windows        (win-builder), R 3.6.0 (2018-06-05 r74852)
 
 ## R CMD check results
 
 There were no ERRORs or WARNINGs
 
 There was 1 NOTE:
 
-1. Maintainer's email address has changed.
+1. Maintainer's email address has changed (notified CRAN 2018-05-28).
 
     * checking CRAN incoming feasibility ... NOTE
-    Maintainer: 'Alex M Chubaty <alexander.chubaty@canada.ca>'
+    Maintainer: 'Alex M Chubaty <alex.chubaty@gmail.com>'
 
     New maintainer:
-      Alex M Chubaty <alexander.chubaty@canada.ca>
+      Alex M Chubaty <alex.chubaty@gmail.com>
     Old maintainer(s):
-      Alex M Chubaty <[email protected].ca>
+      Alex M Chubaty <alexander.chubaty@canada.ca>
 
 ## Downstream dependencies
 
-I have run R CMD check on downstream dependencies of `fpCompare`, and all have passed.
-Summary at https://github.com/PredictiveEcology/fpCompare/blob/master/revdep/summary.md.
+I have run R CMD check on downstream dependencies of `fpCompare`, and all have passed except those noted below.
+Summary at https://github.com/PredictiveEcology/fpCompare/blob/master/revdep/README.md.
+
+* `SpaDES.core` produces an error due to a non-CRAN package in Suggests, but passes once that dependency is installed.
+* `SpaDES.tools` produces an error due to an unrelated error in that package. I am a developer of `SpaDES.tools` and am preparing a fixed version for CRAN which will be submitted soon.
 
-* NOTE: `SpaDES` produces an error due to a non-CRAN package in Suggests, but passes once that dependency is installed.