Merge branch '3.3.0-rc'

Author: jimhester

DESCRIPTION

@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Package: covr
 Title: Test Coverage for Packages
-Version: 2.2.2.9000
+Version: 3.0.0
 Authors@R: c(
     person("Jim", "Hester", email = "[email protected]", role = c("aut", "cre")),
     person("Willem", "Ligtenberg", role = "ctb"),
@@ -26,8 +26,8 @@ Authors@R: c(
     person("David", "Hugh-Jones", role = "ctb"),
     person("Qin", "Wang", role = "ctb"))
 Description: Track and report code coverage for your package and (optionally)
-    upload the results to a coverage service like 'Codecov' (http://codecov.io) or
-    'Coveralls' (http://coveralls.io). Code coverage is a measure of the amount of
+    upload the results to a coverage service like 'Codecov' <http://codecov.io> or
+    'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of
     code being exercised by a set of tests. It is an indirect measure of test
     quality and completeness. This package is compatible with any testing
     methodology or framework and tracks coverage of both R code and compiled

Makefile

@@ -13,7 +13,7 @@ build-docker-checker:
 
 run-rocker: build-docker-checker
 	-docker rm $(RCHECKER)
-	docker run --rm -ti -v $(PWD)/..:/home/docker $(RCHECKER) bash 
+	docker run --rm -ti -v $(PWD)/..:/home/docker $(RCHECKER) bash
 
 test: build-docker-checker fix-permission-tests
 	docker run --rm -ti -v $(PWD)/..:/home/docker $(RCHECKER) Rscript -e 'library(devtools);install("covr");test("covr", "$(FILTER)")'
@@ -24,4 +24,4 @@ check: build-docker-checker fix-permission-tests
 
 
 rox: build-docker-checker
-	docker run --rm -ti -v $(PWD)/..:/home/docker $(RCHECKER) Rscript -e 'devtools::document("covr")'
+	docker run --rm -ti -v $(PWD)/..:/home/docker $(RCHECKER) Rscript -e 'devtools::document("covr")'

NAMESPACE

@@ -31,5 +31,4 @@ importFrom(utils,getSrcFilename)
 importFrom(utils,head)
 importFrom(utils,relist)
 importFrom(utils,str)
-useDynLib(covr,covr_duplicate_)
-useDynLib(covr,covr_reassign_function)
+useDynLib(covr, .registration = TRUE)

NEWS.md

@@ -1,4 +1,6 @@
-## 2.2.2-9000 ##
+## 3.0.0 ##
+* The covr license has been changed to GPL-3.
+* Set environment variable `R_COVR=true` when covr is running (#236, #268).
 * Made the gather-and-merge-results step at the end of package_coverage() more memory efficient (#226, @HenrikBengtsson).
 * Support code coverage with icc (#247, @QinWang).
 

R/covr.R

@@ -236,7 +236,7 @@ package_coverage <- function(path = ".",
       stop("icc is not available")
     }
   }
-    
+
   if (isTRUE(clean)) {
     on.exit({
       clean_objects(pkg$path)
@@ -269,7 +269,8 @@ package_coverage <- function(path = ".",
     c(R_DEFAULT_PACKAGES = "datasets,utils,grDevices,graphics,stats,methods",
       R_LIBS = libs,
       R_LIBS_USER = libs,
-      R_LIBS_SITE = libs), {
+      R_LIBS_SITE = libs,
+      R_COVR = "true"), {
 
 
     withCallingHandlers({
@@ -313,7 +314,7 @@ package_coverage <- function(path = ".",
   } else {
     res <- run_icov(pkg$path, quiet = quiet)
   }
-  
+
   coverage <- structure(c(coverage, res),
       class = "coverage",
       package = pkg,
@@ -364,7 +365,7 @@ merge_coverage <- function(files) {
     }
     y <- NULL
   }
- 
+
   x
 }
 

R/icc.R

@@ -37,7 +37,7 @@ parse_icov <- function(lines, package_path = "") {
         nums <- c(idx1[2L:length(idx1)]-1L, length(r1)) - idx1
         stopifnot(sum(nums) == nrow(m1))
         m1$functions <- unlist(mapply(rep, r1[idx1], nums,
-                                      SIMPLIFY=FALSE, USE.NAMES=FALSE)) 
+                                      SIMPLIFY=FALSE, USE.NAMES=FALSE))
       }
     }
   }
@@ -65,7 +65,7 @@ parse_icov <- function(lines, package_path = "") {
 run_icov <- function(path, quiet = TRUE,
                      icov_path = getOption("covr.icov", ""),
                      icov_args = getOption("covr.icov_args", NULL)) {
-  
+
   src_path <- normalize_path(file.path(path, "src"))
   if (!file.exists(src_path)) {
      return()
@@ -85,7 +85,7 @@ run_icov <- function(path, quiet = TRUE,
   icov_inputs <- list.files(path, pattern = rex::rex(".dyn", end),
                             recursive = TRUE, full.names = TRUE)
   if (length(icov_inputs) == 0L) {
-    warning("no icc .dyn files are generated")  
+    warning("no icc .dyn files are generated")
     return()
   }
 
@@ -97,11 +97,11 @@ run_icov <- function(path, quiet = TRUE,
   system_check(icov_path,
         args = c("-prj", "tmp", "-spi", file.path(src_path, "pgopti.spi"),
                  "-dpi", file.path(src_path, "pgopti.dpi"),
-                 "-include-nonexec", 
+                 "-include-nonexec",
                  "-txtbcvrg", "bcovg.log"),
         quiet = quiet, echo = !quiet)
   })
-  
+
   lines <- readLines(file.path(src_path, "bcovg.log"))
 
   # generate line coverage

R/replace.R

@@ -1,4 +1,4 @@
-#' @useDynLib covr covr_duplicate_
+#' @useDynLib covr, .registration = TRUE
 replacement <- function(name, env = as.environment(-1), target_value = get(name, envir = env)) {
   if (is.function(target_value) && !is.primitive(target_value)) {
     if (is_vectorized(target_value)) {
@@ -26,12 +26,10 @@ replacement <- function(name, env = as.environment(-1), target_value = get(name,
   }
 }
 
-#' @useDynLib covr covr_reassign_function
 replace <- function(replacement) {
   .Call(covr_reassign_function, replacement$name, replacement$env, replacement$target_value, replacement$new_value)
 }
 
-#' @useDynLib covr covr_reassign_function
 reset <- function(replacement) {
   .Call(covr_reassign_function, replacement$name, replacement$env, replacement$target_value, replacement$orig_value)
 }

cran-comments.md

@@ -1,5 +1,5 @@
-This release fixes a test error when run with the soon to be submitted xml2
-1.1.0 release.
+This release changes the package license from MIT to GPL-3. I obtained approval
+from all contributors <https://github.com/jimhester/covr/issues/256> for the license change.
 
 ## Test environments
 * OS X El Capitan, R 3.3.0
@@ -17,7 +17,14 @@ There were no NOTEs, ERRORs or WARNINGs.
 ## Reverse dependencies
 
 Covr is a development tool only so its code is not actually run when building
-any downstream dependencies. Nonetheless I have run R CMD check on the 151
-downstream dependencies. There were no relevant Errors.
+any downstream dependencies. Nonetheless I have run R CMD check on the 262
+downstream dependencies.
+
+The errors in biolink, geofacet, Wmisc are due to `lintr::expect_lint_free()`
+not working properly when it is used while running `devtools::revdep_check()`.
+I opened issue [#251](https://github.com/jimhester/lintr/issues/251) to track
+this bug in lintr.
+
+I did not see any other errors that were relevant to the covr changes.
 
   Summary at: https://github.com/jimhester/covr/tree/master/revdep