Merge branch 'master' into feature/logical-vector-from-bool

Conflicts:
	ChangeLog

Author: kevinushey

.Rinstignore

@@ -1,3 +1,4 @@
 inst/doc/Makefile
 inst/doc/jss.bst
 inst/doc/RJournal.sty
+inst/unitTests/src

.travis.yml

@@ -11,6 +11,7 @@ env:
     - R_BUILD_ARGS="--no-build-vignettes --no-manual"
     - R_CHECK_ARGS="--no-build-vignettes --no-manual --as-cran"
     - RunAllRcppTests="yes"
+    - CRAN="http://cran.us.r-project.org"
 
 before_install:
   - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh

ChangeLog

@@ -1,3 +1,92 @@
+2014-11-19  Dirk Eddelbuettel  <edd@debian.org>
+
+        * .travis.yml: Temporary stop-gap measure of setting CRAN to something
+        other than the RStudio CDN which currently has DNS issue
+
+        * inst/include/Rcpp/internal/NAComparator.h: Support sorting of complex
+        numbers, thanks to patch by Yixuan Qiu (in PR #202)
+
+2014-11-08  Kevin Ushey  <kevinushey@gmail.com>
+
+        * R/Attributes.R: Fix regular expression used to find source files for
+        compileAttributes
+
+2014-11-02  Dirk Eddelbuettel  <edd@debian.org>
+
+        * inst/unitTests/RcppTestA: Rename to inst/unitTests/testRcppPackage
+        * inst/unitTests/testRcppPackage: Updated throughout
+
+        * inst/include/Rcpp/Rmath.h: As suggested by Kevin, test for R_VERSION
+        via #define to conditon on R >= 3.1.2 -- this does not require a hard
+        constraint in DESCRIPTION yet on newer R will get R::[dpq]nbinom_mu()
+
+2014-11-01  Dirk Eddelbuettel  <edd@debian.org>
+
+        * src/api.cpp: Do not include execinfo.h on AIX, per r-devel discussion
+        with Mike Beddo, and http://sf.net/p/predef/wiki/OperatingSystems/
+
+2014-10-29  Dirk Eddelbuettel  <edd@debian.org>
+
+        * inst/include/Rcpp/Rmath.h: Comment out R::[dpqr]nbinom_mu functions as
+        not declared by R with Rf_* name-mapping prefixes
+
+2014-10-17  Chenliang Xu <luckyrand@gmail.com>
+
+        * R/Attributes: Enable scanning of header files
+
+2014-10-03  JJ Allaire  <jj@rstudio.org>
+
+        * R/Attributes.R: Only look for plugins in the package's namespace
+        (rather than entire search path)
+
+2014-10-01  Kevin Ushey  <kevinushey@gmail.com>
+
+        * inst/include/Rcpp/vector/ListOf.h ListOf<T> inherits relevant proxies
+        * inst/unitTests/cpp/ListOf.cpp: Idem
+        * inst/unitTests/runit.ListOf.R: Idem
+
+2014-09-29  Dirk Eddelbuettel  <edd@debian.org>
+
+        * debian/*: Changes for Debian release of 0.11.3
+
+        * inst/NEWS.Rd: Removed a double entry
+
+2014-09-27  Dirk Eddelbuettel  <edd@debian.org>
+
+        * DESCRIPTION: Release 0.11.3
+        * inst/NEWS.Rd: Release 0.11.3
+        * inst/include/Rcpp/config.h: Release 0.11.3
+
+        * ChangeLog: Added a few more entries based on commit log
+        * inst/NEWS.Rd: Idem
+
+2014-09-26  JJ Allaire <jj@rstudio.org>
+
+        * DESCRIPTION: Bump version to enable checking for dryRun.
+
+2014-09-23  JJ Allaire <jj@rstudio.org>
+
+        * R/Attributes.R: Add dryRun parameter to sourceCpp.
+
+2014-09-21  Dirk Eddelbuettel  <edd@debian.org>
+
+        * DESCRIPTION: Shorten Description: to single paragraph
+
+2014-09-21  Kevin Ushey  <kevinushey@gmail.com>
+
+        * inst/unitTests/runit.environments.R: Use 'checkIdentical' as it's a
+        more appropriate expression of intent
+
+2014-09-15  Dirk Eddelbuettel  <edd@debian.org>
+
+        * R/Rcpp.package.skeleton.R: Use more neutral default name, email settings
+        * man/Rcpp.package.skeleton.Rd: Document these
+
+2014-09-14  Dirk Eddelbuettel  <edd@debian.org>
+
+        * inst/unitTests/testRcppClass/man/Rcpp_class_examples.Rd: Similar
+        update to yesterday's update for testRcppModule
+
 2014-09-14  Kevin Ushey  <kevinushey@gmail.com>
 
         * inst/include/Rcpp/vector/Vector.h: Alternate strategy using SFINAE
@@ -17,6 +106,11 @@
 
         * inst/unitTests/testRcppModule/NAMESPACE: Updated for current Modules use
         * inst/unitTests/testRcppModule/R/zzz.R: Updated for current Modules use
+        * inst/unitTests/testRcppModule/man/Rcpp_modules_examples.Rd: Also added here
+
+2014-09-10  Dirk Eddelbuettel  <edd@debian.org>
+
+        * R/R/Rcpp.package.skeleton.R: If available, pkgKitten used for skeleton pkg
 
 2014-09-09  Dirk Eddelbuettel  <edd@debian.org>
 
@@ -43,6 +137,10 @@
         * R/Attributes.R: Include LinkingTo in DESCRIPTION fields scanned
         to confirm that C++ dependencies are referenced by package.
 
+2014-09-01  Yixuan Qiu <yixuan.qiu@cos.name>
+
+        * inst/include/Rcpp/vector/Vector.h: fix return value of range eraser
+
 2014-09-01  Kevin Ushey  <kevinushey@gmail.com>
 
         * inst/include/Rcpp/vector/ListOf.h: `size()` member function should
@@ -55,7 +153,7 @@
 2014-08-30  Dirk Eddelbuettel  <edd@debian.org>
 
         * inst/include/Rcpp/vector/Vector.h: Mark two 'from string' ctors as
-        deprecated following a suggestion by Yixuan Qiu
+        deprecated following a suggestion by Yixuan Qiu [reversed on 2014-09-02]
 
 2014-08-18  Dirk Eddelbuettel  <edd@debian.org>
 
@@ -74,6 +172,13 @@
         * inst/include/Rcpp/proxy/TagProxy.h: Idem
         * inst/include/Rcpp/proxy/proxy.h: Idem
 
+2014-08-08  Christian Authmann <authmanc@Mathematik.Uni-Marburg.de>
+
+        * inst/unitTests/cpp/InternalFunction.cpp: New unit test support
+        * inst/unitTests/cpp/InternalFunctionCPP11.cpp: Idem
+        * inst/unitTests/runit.InternalFunction.R: Idem
+        * inst/unitTests/runit.InternalFunctionCPP11.R: Idem
+
 2014-08-06  Christian Authmann <authmanc@Mathematik.Uni-Marburg.de>
 
         * inst/include/Rcpp/InternalFunctionWithStdFunction.h: Extend the
@@ -101,7 +206,7 @@
 2014-07-29  Dirk Eddelbuettel  <edd@debian.org>
 
         * inst/include/Rcpp/vector/proxy.h: Removed operator bool() cast as
-        discusses by Christian Authmann on rcpp-devel
+        discussed by Christian Authmann on rcpp-devel
 
 2014-07-28  Dirk Eddelbuettel  <edd@debian.org>
 

DESCRIPTION

@@ -1,54 +1,18 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.11.2.4
-Date: 2014-09-10
+Version: 0.11.3.1
+Date: 2014-10-29
 Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, 
  Douglas Bates, and John Chambers
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
-Description: The Rcpp package provides R functions as well as a C++ library
- which facilitate the integration of R and C++.
- .
- R data types (SEXP) are matched to C++ objects in a class hierarchy.  All R
- types are supported (vectors, functions, environment, etc ...)  and each
- type is mapped to a dedicated class. For example, numeric vectors are
- represented as instances of the Rcpp::NumericVector class, environments are
- represented as instances of Rcpp::Environment, functions are represented as
- Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good
- entry point to Rcpp.
- .
- Conversion from C++ to R and back is driven by the templates Rcpp::wrap
- and Rcpp::as which are highly flexible and extensible, as documented
- in the "Rcpp-extending" vignette.
- .
- Rcpp also provides Rcpp modules, a framework that allows exposing
- C++ functions and classes to the R level. The "Rcpp-modules" vignette
- details the current set of features of Rcpp-modules.
- .
- Rcpp includes a concept called Rcpp sugar that brings many R functions
- into C++. Sugar takes advantage of lazy evaluation and expression templates
- to achieve great performance while exposing a syntax that is much nicer
- to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette
- gives an overview of the feature.
- .
- Rcpp attributes provide a high-level syntax for declaring C++
- functions as callable from R and automatically generating the code
- required to invoke them.  Attributes are intended to facilitate both
- interactive use of C++ within R sessions as well as to support R
- package development. Attributes are built on top of Rcpp modules and
- their implementation is based on previous work in the inline package.
- .
- Many examples are included, and around 900 unit tests in 446 unit
- test functions provide additional usage examples.
- .
- An earlier version of Rcpp, containing what we now call the 'classic Rcpp
- API' was written during 2005 and 2006 by Dominick Samperi.  This code has
- been factored out of Rcpp into the package RcppClassic, and it is still
- available for code relying on the older interface. New development should
- always use this Rcpp package instead.
- .
- Additional documentation is available via the paper by Eddelbuettel and
- Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer);
- see 'citation("Rcpp")' for details.
+Description: The Rcpp package provides R functions as well as C++ classes which
+ offer a seamless integration of R and C++. Many R data types and objects can be
+ mapped back and forth to C++ equivalents which facilitates both writing of new
+ code as well as easier integration of third-party libraries. Documentation 
+ about Rcpp is provided by several vignettes included in this package, via the 
+ Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and 
+ Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 
+ 'citation("Rcpp")' for details on these last two.
 Depends: R (>= 3.0.0)
 Imports: methods
 Suggests: RUnit, inline, rbenchmark, highlight, pkgKitten (>= 0.1.2)

R/Attributes.R

@@ -23,7 +23,8 @@ sourceCpp <- function(file = "",
                       embeddedR = TRUE,
                       rebuild = FALSE,
                       showOutput = verbose,
-                      verbose = getOption("verbose")) {
+                      verbose = getOption("verbose"),
+                      dryRun = FALSE) {
 
     # resolve code into a file if necessary. also track the working
     # directory to source the R embedded code chunk within
@@ -112,6 +113,7 @@ sourceCpp <- function(file = "",
                      "CMD SHLIB ",
                      "-o ", shQuote(context$dynlibFilename), " ",
                      ifelse(rebuild, "--preclean ", ""),
+                     ifelse(dryRun, "--dry-run ", ""),
                      shQuote(context$cppSourceFilename), sep="")
         if (showOutput)
             cat(cmd, "\n")
@@ -152,6 +154,10 @@ sourceCpp <- function(file = "",
                 "force a rebuild)\n\n", sep="")
     }
 
+    # return immediately if this was a dry run
+    if (dryRun)
+        return(invisible(NULL))
+
     # load the module if we have exported symbols
     if (length(context$exportedFunctions) > 0 || length(context$modules) > 0) {
 
@@ -360,7 +366,7 @@ compileAttributes <- function(pkgdir = ".", verbose = getOption("verbose")) {
         dir.create(rDir)
 
     # get a list of all source files
-    cppFiles <- list.files(srcDir, pattern="\\.c(c|pp)$")
+    cppFiles <- list.files(srcDir, pattern = "\\.((c(c|pp))|(h(pp)?))$")
 
     # derive base names (will be used for modules)
     cppFileBasenames <- tools::file_path_sans_ext(cppFiles)
@@ -519,7 +525,7 @@ sourceCppFunction <- function(func, isVoid, dll, symbol) {
 
 # Get the inline plugin for the specified package (return NULL if none found)
 .getInlinePlugin <- function(package) {
-    tryCatch(get("inlineCxxPlugin", asNamespace(package)),
+    tryCatch(get("inlineCxxPlugin", asNamespace(package), inherits = FALSE),
              error = function(e) NULL)
 }
 

R/Rcpp.package.skeleton.R

@@ -22,10 +22,10 @@ Rcpp.package.skeleton <- function(name = "anRpackage", list = character(),
                                   path = ".", force = FALSE,
                                   code_files = character(), cpp_files = character(),
                                   example_code = TRUE, attributes = TRUE, module = FALSE,
-                                  author = "Who wrote it",
-                                  maintainer = if (missing(author)) "Who to complain to"
+                                  author = "Your Name",
+                                  maintainer = if (missing(author)) "Your Name"
                                                else author,
-                                  email = "yourfault@somewhere.net",
+                                  email = "your@email.com",
                                   license = "GPL (>= 2)") {
 
     havePkgKitten <- require("pkgKitten", quietly=TRUE, character.only=TRUE)
@@ -209,4 +209,3 @@ Rcpp.package.skeleton <- function(name = "anRpackage", list = character(),
 
 	invisible(NULL)
 }
-

debian/changelog

@@ -1,3 +1,14 @@
+rcpp (0.11.3-1) unstable; urgency=low
+
+  * New upstream release
+
+  * debian/control: New (Build-)Depends: on r-cran-pkgkitten
+
+  * debian/control: Set Build-Depends: to current R version 
+  * debian/control: Set Standards-Version: to current version
+  
+ -- Dirk Eddelbuettel <edd@debian.org>  Mon, 29 Sep 2014 19:54:50 -0500
+
 rcpp (0.11.2-1) unstable; urgency=low
 
   * New release

debian/control

@@ -2,57 +2,21 @@ Source: rcpp
 Section: gnu-r
 Priority: optional
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
-Build-Depends: debhelper (>= 7.0.0), r-base-dev (>= 3.1.0), cdbs, r-cran-codetools
-Standards-Version: 3.9.5
+Build-Depends: debhelper (>= 7.0.0), r-base-dev (>= 3.1.1), cdbs, r-cran-codetools, r-cran-pkgkitten
+Standards-Version: 3.9.6
 Homepage: http://dirk.eddelbuettel.com/code/rcpp.html
 
 Package: r-cran-rcpp
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends}, littler
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends}, littler, r-cran-pkgkitten
 Suggests: r-cran-inline
 Description: GNU R package for Seamless R and C++ Integration
- The Rcpp package provides a C++ library which facilitates the
- integration of R and C++.
- .
- R data types (SEXP) are matched to C++ objects in a class hierarchy.  All R
- types are supported (vectors, functions, environment, etc ...)  and each
- type is mapped to a dedicated class. For example, numeric vectors are
- represented as instances of the Rcpp::NumericVector class, environments are
- represented as instances of Rcpp::Environment, functions are represented as
- Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good
- entry point to Rcpp. 
- .
- Conversion from C++ to R and back is driven by the templates Rcpp::wrap 
- and Rcpp::as which are highly flexible and extensible, as documented
- in the "Rcpp-extending" vignette.
- .
- Rcpp also provides Rcpp modules, a framework that allows exposing 
- C++ functions and classes to the R level. The "Rcpp-modules" vignette
- details the current set of features of Rcpp-modules. 
- .
- Rcpp includes a concept called Rcpp sugar that brings many R functions
- into C++. Sugar takes advantage of lazy evaluation and expression templates
- to achieve great performance while exposing a syntax that is much nicer
- to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette
- gives an overview of the feature.
- .
- Rcpp attributes provide a high-level syntax for declaring C++
- functions as callable from R and automatically generating the code
- required to invoke them.  Attributes are intended to facilitate both
- interactive use of C++ within R sessions as well as to support R
- package development. Attributes are built on top of Rcpp modules and
- their implementation is based on previous work in the inline package.
- .
- Many examples are included, and around 900 unit tests in 446 unit
- test functions provide additional usage examples.
- .
- An earlier version of Rcpp, containing what we now call the 'classic Rcpp
- API' was written during 2005 and 2006 by Dominick Samperi.  This code has
- been factored out of Rcpp into the package RcppClassic and it is still
- available for code relying on this interface. New development should use 
- this package instead.
- .
- Additional documentation is available via the paper by Eddelbuettel and
- Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer); 
- see 'citation("Rcpp")' for details.
+ The Rcpp package provides R functions as well as C++ classes which
+ offer a seamless integration of R and C++. Many R data types and objects can be
+ mapped back and forth to C++ equivalents which facilitates both writing of new
+ code as well as easier integration of third-party libraries. Documentation 
+ about Rcpp is provided by several vignettes included in this package, via the 
+ Rcpp Gallery site at http://gallery.rcpp.org, the paper by Eddelbuettel and 
+ Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 
+ 'citation("Rcpp")' for details on these last two.
 

debian/r-cran-rcpp.lintian-overrides

@@ -78,3 +78,5 @@ r-cran-rcpp: script-not-executable usr/lib/R/site-library/Rcpp/unitTests/runit.n
 r-cran-rcpp: script-not-executable usr/lib/R/site-library/Rcpp/unitTests/runit.subset.R
 r-cran-rcpp: script-not-executable usr/lib/R/site-library/Rcpp/unitTests/runit.table.R
 r-cran-rcpp: script-not-executable usr/lib/R/site-library/Rcpp/unitTests/runit.attributes.R
+r-cran-rcpp: script-not-executable usr/lib/R/site-library/Rcpp/unitTests/runit.InternalFunction.R
+r-cran-rcpp: script-not-executable usr/lib/R/site-library/Rcpp/unitTests/runit.InternalFunctionCPP11.R