Fix for recent Fedora and ASAN errors

.travis.yml

@@ -10,10 +10,10 @@ env:
   - _R_CHECK_FORCE_SUGGESTS_=false
   - MAKEFLAGS="-j 2"
 
-include:
-- r: release
-- r: oldrel
-- r: devel
+r:
+- release
+- oldrel
+- devel
 
 before_script:
 - mkdir -p ~/.R; echo 'PKG_CXXFLAGS := ${PKG_CXXFLAGS} -Wall -Wextra -pedantic -Werror' > ~/.R/Makevars

DESCRIPTION

@@ -1,6 +1,6 @@
 Type: Package
 Package: dplyr
-Version: 0.7.3.9000
+Version: 0.7.4
 Title: A Grammar of Data Manipulation
 Description: A fast, consistent tool for working with data frame like objects,
     both in memory and out of memory.

NEWS.md

@@ -1,3 +1,9 @@
+# dplyr 0.7.4
+
+* Fix recent Fedora and ASAN check errors (#3098).
+
+* Avoid dependency on Rcpp 0.12.10 (#3106).
+
 # dplyr 0.7.3
 
 * Fixed protection error that occurred when creating a character column using grouped `mutate()` (#2971).

README.Rmd

@@ -20,7 +20,7 @@ options(tibble.print_min = 5, tibble.print_max = 5)
 [![Build Status](https://travis-ci.org/tidyverse/dplyr.svg?branch=master)](https://travis-ci.org/tidyverse/dplyr)
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/tidyverse/dplyr?branch=master&svg=true)](https://ci.appveyor.com/project/tidyverse/dplyr)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/dplyr)](http://cran.r-project.org/package=dplyr)
-[![Coverage Status](https://img.shields.io/codecov/c/github/tidyverse/dplyr/master.svg)](https://codecov.io/github/tidyverse/dplyr?branch=master)
+[![Coverage Status](https://codecov.io/gh/tidyverse/dplyr/branch/master/graph/badge.svg)](https://codecov.io/gh/tidyverse/dplyr?branch=master)
 
 ## Overview
 

README.md

@@ -3,7 +3,7 @@
 dplyr <img src="man/figures/logo.png" align="right" />
 ======================================================
 
-[![Build Status](https://travis-ci.org/tidyverse/dplyr.svg?branch=master)](https://travis-ci.org/tidyverse/dplyr) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/tidyverse/dplyr?branch=master&svg=true)](https://ci.appveyor.com/project/tidyverse/dplyr) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/dplyr)](http://cran.r-project.org/package=dplyr) [![Coverage Status](https://img.shields.io/codecov/c/github/tidyverse/dplyr/master.svg)](https://codecov.io/github/tidyverse/dplyr?branch=master)
+[![Build Status](https://travis-ci.org/tidyverse/dplyr.svg?branch=master)](https://travis-ci.org/tidyverse/dplyr) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/tidyverse/dplyr?branch=master&svg=true)](https://ci.appveyor.com/project/tidyverse/dplyr) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/dplyr)](http://cran.r-project.org/package=dplyr) [![Coverage Status](https://codecov.io/gh/tidyverse/dplyr/branch/master/graph/badge.svg)](https://codecov.io/gh/tidyverse/dplyr?branch=master)
 
 Overview
 --------
@@ -32,7 +32,7 @@ install.packages("tidyverse")
 # Alternatively, install just dplyr:
 install.packages("dplyr")
 
-# Or the the development version from GitHub:
+# Or the development version from GitHub:
 # install.packages("devtools")
 devtools::install_github("tidyverse/dplyr")
 ```
@@ -48,54 +48,51 @@ library(dplyr)
 starwars %>% 
   filter(species == "Droid")
 #> # A tibble: 5 x 13
-#>    name height  mass hair_color  skin_color eye_color birth_year gender
-#>   <chr>  <int> <dbl>      <chr>       <chr>     <chr>      <dbl>  <chr>
-#> 1 C-3PO    167    75       <NA>        gold    yellow        112   <NA>
-#> 2 R2-D2     96    32       <NA> white, blue       red         33   <NA>
-#> 3 R5-D4     97    32       <NA>  white, red       red         NA   <NA>
-#> 4 IG-88    200   140       none       metal       red         15   none
-#> 5   BB8     NA    NA       none        none     black         NA   none
-#> # ... with 5 more variables: homeworld <chr>, species <chr>, films <list>,
-#> #   vehicles <list>, starships <list>
+#>   name  height  mass hair… skin… eye_… birt… gend… home… spec… films vehi…
+#>   <chr>  <int> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <lis> <lis>
+#> 1 C-3PO    167  75.0 <NA>  gold  yell… 112   <NA>  Tato… Droid <chr… <chr…
+#> 2 R2-D2     96  32.0 <NA>  "whi… red    33.0 <NA>  Naboo Droid <chr… <chr…
+#> 3 R5-D4     97  32.0 <NA>  "whi… red    NA   <NA>  Tato… Droid <chr… <chr…
+#> 4 IG-88    200 140   none  metal red    15.0 none  <NA>  Droid <chr… <chr…
+#> 5 BB8       NA  NA   none  none  black  NA   none  <NA>  Droid <chr… <chr…
+#> # ... with 1 more variable: starships <list>
 
 starwars %>% 
   select(name, ends_with("color"))
 #> # A tibble: 87 x 4
-#>             name hair_color  skin_color eye_color
-#>            <chr>      <chr>       <chr>     <chr>
-#> 1 Luke Skywalker      blond        fair      blue
-#> 2          C-3PO       <NA>        gold    yellow
-#> 3          R2-D2       <NA> white, blue       red
-#> 4    Darth Vader       none       white    yellow
-#> 5    Leia Organa      brown       light     brown
+#>   name             hair_color skin_color    eye_color
+#>   <chr>            <chr>      <chr>         <chr>    
+#> 1 "Luke Skywalker" blond      fair          blue     
+#> 2 C-3PO            <NA>       gold          yellow   
+#> 3 R2-D2            <NA>       "white, blue" red      
+#> 4 "Darth Vader"    none       white         yellow   
+#> 5 "Leia Organa"    brown      light         brown    
 #> # ... with 82 more rows
 
 starwars %>% 
   mutate(name, bmi = mass / ((height / 100)  ^ 2)) %>%
   select(name:mass, bmi)
 #> # A tibble: 87 x 4
-#>             name height  mass      bmi
-#>            <chr>  <int> <dbl>    <dbl>
-#> 1 Luke Skywalker    172    77 26.02758
-#> 2          C-3PO    167    75 26.89232
-#> 3          R2-D2     96    32 34.72222
-#> 4    Darth Vader    202   136 33.33007
-#> 5    Leia Organa    150    49 21.77778
+#>   name             height  mass   bmi
+#>   <chr>             <int> <dbl> <dbl>
+#> 1 "Luke Skywalker"    172  77.0  26.0
+#> 2 C-3PO               167  75.0  26.9
+#> 3 R2-D2                96  32.0  34.7
+#> 4 "Darth Vader"       202 136    33.3
+#> 5 "Leia Organa"       150  49.0  21.8
 #> # ... with 82 more rows
 
 starwars %>% 
   arrange(desc(mass))
 #> # A tibble: 87 x 13
-#>                    name height  mass hair_color       skin_color
-#>                   <chr>  <int> <dbl>      <chr>            <chr>
-#> 1 Jabba Desilijic Tiure    175  1358       <NA> green-tan, brown
-#> 2              Grievous    216   159       none     brown, white
-#> 3                 IG-88    200   140       none            metal
-#> 4           Darth Vader    202   136       none            white
-#> 5               Tarfful    234   136      brown            brown
-#> # ... with 82 more rows, and 8 more variables: eye_color <chr>,
-#> #   birth_year <dbl>, gender <chr>, homeworld <chr>, species <chr>,
-#> #   films <list>, vehicles <list>, starships <list>
+#>   name   heig…  mass hair… skin… eye_… birt… gend… home… spec… films vehi…
+#>   <chr>  <int> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <lis> <lis>
+#> 1 "Jabb…   175  1358 <NA>  "gre… oran… 600   herm… "Nal… Hutt  <chr… <chr…
+#> 2 Griev…   216   159 none  "bro… "gre…  NA   male  Kalee Kale… <chr… <chr…
+#> 3 IG-88    200   140 none  metal red    15.0 none  <NA>  Droid <chr… <chr…
+#> 4 "Dart…   202   136 none  white yell…  41.9 male  Tato… Human <chr… <chr…
+#> 5 Tarff…   234   136 brown brown blue   NA   male  Kash… Wook… <chr… <chr…
+#> # ... with 82 more rows, and 1 more variable: starships <list>
 
 starwars %>%
   group_by(species) %>%
@@ -105,12 +102,12 @@ starwars %>%
   ) %>%
   filter(n > 1)
 #> # A tibble: 9 x 3
-#>    species     n     mass
-#>      <chr> <int>    <dbl>
-#> 1    Droid     5 69.75000
-#> 2   Gungan     3 74.00000
-#> 3    Human    35 82.78182
-#> 4 Kaminoan     2 88.00000
-#> 5 Mirialan     2 53.10000
+#>   species      n  mass
+#>   <chr>    <int> <dbl>
+#> 1 Droid        5  69.8
+#> 2 Gungan       3  74.0
+#> 3 Human       35  82.8
+#> 4 Kaminoan     2  88.0
+#> 5 Mirialan     2  53.1
 #> # ... with 4 more rows
 ```

cran-comments.md

@@ -1,6 +1,6 @@
 ## Release summary
 
-This is a minor bugfix release in response to CRAN's request. This is the third release attempt (with the same version), following up test failures with reverse dependencies from CRAN's incoming checks.
+This is a minor bugfix release in response to errors with ASAN, UBSAN, and Fedora+clang builds on CRAN.  We now were able to finally replicate the problems we were seeing on CRAN in a Docker container, our minimal fix resolves these problems.
 
 ## Test environments
 
@@ -10,31 +10,30 @@ This is a minor bugfix release in response to CRAN's request. This is the third
 
 ## R CMD check results
 
-0 ERRORs | 0 WARNINGs | 1 NOTEs
+0 ERRORs | 0 WARNINGs | 2 NOTEs
 
-* checking installed package size ... NOTE
+* 6 days since last update
 
-  This is all compiled code in the libs/ directory.
+  The UB errors seem important to fix now.
 
-## ASAN errors on CRAN
+* checking installed package size ... NOTE
 
-We could not replicate the ASAN errors on Fedora with clang.  We changed code that we believe may be responsible for the problem, and we'll watch the check results once the package is released.
+  This is all compiled code in the libs/ directory.
 
 ## Reverse dependencies
 
-We checked 795 reverse dependencies (721 from CRAN + 74 from BioConductor) by running R CMD check twice, once with the CRAN version installed, and once with this version installed. We saw 3 new problems. We failed to check 4 packages. Issues are summarised below.
+We checked 804 reverse dependencies (730 from CRAN + 74 from BioConductor) by running R CMD check twice, once with the CRAN version installed, and once with this version installed. We saw 2 new problems. We failed to check 4 packages. Issues are summarised below.
 
 ### New problems
 
 Most likely web API problems:
 
-* censusr
-* hansard
-* roadoi
+* banR
+* FedData
 
 ### Failed to check
 
-* flowWorkspace (failed to install)
-* loon          (failed to install)
-* naniar        (check timed out)
-* visdat        (check timed out)
+* eyetrackingR (check timed out)
+* hypothesisr  (check timed out)
+* loon         (failed to install)
+* MonetDBLite  (check timed out)

inst/include/dplyr/Result/Rank.h

@@ -186,7 +186,7 @@ class Rank_Impl : public Result, public Increment {
 
   void process_slice(OutputVector& out, const SlicingIndex& index) {
     map.clear();
-    Slice slice(data, index);
+    Slice slice(&data, index);
     int m = index.size();
     for (int j = 0; j < m; j++) {
       map[ slice[j] ].push_back(j);
@@ -256,10 +256,10 @@ class RowNumber : public Result {
       int m = index.size();
       for (int j = 0; j < m; j++) tmp[j] = j;
 
-      Slice slice(data, index);
+      Slice slice(&data, index);
       // order( gdf.group(i) )
       Visitor visitor(slice);
-      Comparer comparer = Comparer(visitor);
+      Comparer comparer(visitor);
       std::sort(tmp.begin(), tmp.begin() + m, comparer);
       int j = m - 1;
       for (; j >= 0; j--) {
@@ -290,7 +290,7 @@ class RowNumber : public Result {
     int nrows = index.size();
     if (nrows == 0) return IntegerVector(0);
     IntegerVector x = seq(0, nrows - 1);
-    Slice slice(data, index);
+    Slice slice(&data, index);
     Visitor visitor(slice);
     std::sort(x.begin(), x.end(), Comparer(visitor));
     IntegerVector out = no_init(nrows);
@@ -309,7 +309,7 @@ class RowNumber : public Result {
   }
 
 private:
-  SEXP data;
+  Vector<RTYPE> data;
 };
 
 template <int RTYPE, bool ascending = true>
@@ -337,11 +337,11 @@ class Ntile : public Result {
       // tmp <- 0:(m-1)
       int m = index.size();
       for (int j = 0; j < m; j++) tmp[j] = j;
-      Slice slice(data, index);
+      Slice slice(&data, index);
 
       // order( gdf.group(i) )
       Visitor visitor(slice);
-      Comparer comparer = Comparer(visitor);
+      Comparer comparer(visitor);
       std::sort(tmp.begin(), tmp.begin() + m, comparer);
       int j = m - 1;
       for (; j >= 0; j--) {
@@ -372,7 +372,7 @@ class Ntile : public Result {
     int nrows = index.size();
     if (nrows == 0) return IntegerVector(0);
     IntegerVector x = seq(0, nrows - 1);
-    Slice slice(data, index);
+    Slice slice(&data, index);
     Visitor visitor(slice);
     std::sort(x.begin(), x.end(), Comparer(visitor));
     IntegerVector out = no_init(nrows);
@@ -393,7 +393,7 @@ class Ntile : public Result {
   }
 
 private:
-  SEXP data;
+  Vector<RTYPE> data;
   double ntiles;
 };
 

inst/include/dplyr/Result/VectorSliceVisitor.h

@@ -10,8 +10,8 @@ class VectorSliceVisitor {
 public:
   typedef typename Rcpp::traits::storage_type<RTYPE>::type STORAGE;
 
-  VectorSliceVisitor(const Vector<RTYPE>& data_, const SlicingIndex& index_) :
-    data(data_),
+  VectorSliceVisitor(const Vector<RTYPE>* data_, const SlicingIndex& index_) :
+    data(*data_),
     n(index_.size()),
     index(index_)
   {}