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R 3.2 sync #27

Merged
merged 3,931 commits into from
Aug 20, 2015
Merged

R 3.2 sync #27

merged 3,931 commits into from
Aug 20, 2015

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kmillar
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@kmillar kmillar commented Aug 19, 2015

This merges in the changes from CR up until the point where the CR R-3.2 branch diverges from the trunk.

Not all the functionality has been merged in. Things that are known to be missing include:

  • The bytecode compiler and interpreter have not been updated at all.
  • Custom allocators are not supported
  • shallow_duplicate currently does deep duplication
  • Debugger doesn't recognize 'f'
  • Some of the optimizations of S3 method dispatch are missing.
  • Builtin functions don't attempt to reuse the memory allocations used by the inputs.

Unimplemented builtins:

  • do_returnValue
  • do_bcprofcounts
  • do_bcprofstart
  • do_bcprofstop

maechler and others added 30 commits January 27, 2015 16:36
using eigen(*, only.value=TRUE) .. other cosmetic
442e3a6 
git-svn-id: https://svn.r-project.org/R/trunk@67636 00db46b3-68df-0310-9c12-caf00c1e9a41
fix
91fa5f6 
git-svn-id: https://svn.r-project.org/R/trunk@67637 00db46b3-68df-0310-9c12-caf00c1e9a41
Help git lovers tracking R devel; patch proposed by Felipe Balbi at k…
df157bc 
…ernel.org

git-svn-id: https://svn.r-project.org/R/trunk@67638 00db46b3-68df-0310-9c12-caf00c1e9a41
special-case sciencedirect.com
7ad542c 
git-svn-id: https://svn.r-project.org/R/trunk@67639 00db46b3-68df-0310-9c12-caf00c1e9a41
explain when substitute() works; notably extend the examples,
93bfb4c 
also say and show more for the promises in 'e'


git-svn-id: https://svn.r-project.org/R/trunk@67640 00db46b3-68df-0310-9c12-caf00c1e9a41
s/:=/=/ as the former is not portable
7333662 
git-svn-id: https://svn.r-project.org/R/trunk@67641 00db46b3-68df-0310-9c12-caf00c1e9a41
Tweaks.
efe4fbc 
git-svn-id: https://svn.r-project.org/R/trunk@67642 00db46b3-68df-0310-9c12-caf00c1e9a41
Improve .parse_code_file(), and use for spell-checking message strings
4bc10b2 
in R code files.

git-svn-id: https://svn.r-project.org/R/trunk@67643 00db46b3-68df-0310-9c12-caf00c1e9a41
improve speed of logical subsetting
4ca0207 
git-svn-id: https://svn.r-project.org/R/trunk@67645 00db46b3-68df-0310-9c12-caf00c1e9a41
more on whitespace
66f1a23 
git-svn-id: https://svn.r-project.org/R/trunk@67646 00db46b3-68df-0310-9c12-caf00c1e9a41
progress bars can be useful with batch reinstalls
836292a 
git-svn-id: https://svn.r-project.org/R/trunk@67647 00db46b3-68df-0310-9c12-caf00c1e9a41
more on progress bars
b0c0937 
git-svn-id: https://svn.r-project.org/R/trunk@67648 00db46b3-68df-0310-9c12-caf00c1e9a41
Register boxplot.matrix().
d96b354 
git-svn-id: https://svn.r-project.org/R/trunk@67649 00db46b3-68df-0310-9c12-caf00c1e9a41
add new method for download.file() on Windows
df4eb55 
git-svn-id: https://svn.r-project.org/R/trunk@67650 00db46b3-68df-0310-9c12-caf00c1e9a41
cleanup
4d36077 
git-svn-id: https://svn.r-project.org/R/trunk@67651 00db46b3-68df-0310-9c12-caf00c1e9a41
update
68ab0b7 
git-svn-id: https://svn.r-project.org/R/trunk@67652 00db46b3-68df-0310-9c12-caf00c1e9a41
typo
a859bf2 
git-svn-id: https://svn.r-project.org/R/trunk@67653 00db46b3-68df-0310-9c12-caf00c1e9a41
names(<environment>) now gives all (unsorted) object names
2b9dead 
git-svn-id: https://svn.r-project.org/R/trunk@67654 00db46b3-68df-0310-9c12-caf00c1e9a41
add caveat
c469460 
git-svn-id: https://svn.r-project.org/R/trunk@67656 00db46b3-68df-0310-9c12-caf00c1e9a41
Using names(<env>) in our own code {a few are semantical changes, whe…
b553f16 
…re ls() did *not* use "all.names=TRUE"

git-svn-id: https://svn.r-project.org/R/trunk@67658 00db46b3-68df-0310-9c12-caf00c1e9a41
cosmetic (from a while back)
20bec64 
git-svn-id: https://svn.r-project.org/R/trunk@67659 00db46b3-68df-0310-9c12-caf00c1e9a41
Increased R_NGrowIncrFrac and R_VGrowIncrFrac to 0.2 to reduce GC
1571202 
frequency when the heap needs to grow.


git-svn-id: https://svn.r-project.org/R/trunk@67660 00db46b3-68df-0310-9c12-caf00c1e9a41
simplify genericForPrimitive() as suggested by Pete Haverty
8c83b91 
git-svn-id: https://svn.r-project.org/R/trunk@67661 00db46b3-68df-0310-9c12-caf00c1e9a41
callGeneric() now works when called via callNextMethod()
5931951 
git-svn-id: https://svn.r-project.org/R/trunk@67662 00db46b3-68df-0310-9c12-caf00c1e9a41
implicit generics now take their enclosing environment from that of
96f1952 
the corresponding function, instead of the base namespace; other cleanup


git-svn-id: https://svn.r-project.org/R/trunk@67663 00db46b3-68df-0310-9c12-caf00c1e9a41
replace many uses of get0(,inherits=FALSE) with simpler syntax based …
c5454f4 
…on [[ and $

git-svn-id: https://svn.r-project.org/R/trunk@67664 00db46b3-68df-0310-9c12-caf00c1e9a41
Regenerate cmp.R using notangle to bring in missing change.
2c9dd22 
git-svn-id: https://svn.r-project.org/R/trunk@67665 00db46b3-68df-0310-9c12-caf00c1e9a41
Reverted unnecessary cosmetic changes.
599d869 
git-svn-id: https://svn.r-project.org/R/trunk@67666 00db46b3-68df-0310-9c12-caf00c1e9a41
allow reporting overwriting registered S3 methods
7878b48 
git-svn-id: https://svn.r-project.org/R/trunk@67667 00db46b3-68df-0310-9c12-caf00c1e9a41
getPackageName() now falls back to topenv(where) to handle cases like
cae2df7 
nested closures; BiocGenerics should install again


git-svn-id: https://svn.r-project.org/R/trunk@67668 00db46b3-68df-0310-9c12-caf00c1e9a41
ripley and others added 27 commits March 3, 2015 09:27
modernize language
76cd2a1 
git-svn-id: https://svn.r-project.org/R/trunk@67930 00db46b3-68df-0310-9c12-caf00c1e9a41
document the nobs(<arima>) change + example
e92b4c1 
git-svn-id: https://svn.r-project.org/R/trunk@67931 00db46b3-68df-0310-9c12-caf00c1e9a41
print.htest() and print.power.htest() now also have and obey a `digit…
7e90613 
…s` argument properly

git-svn-id: https://svn.r-project.org/R/trunk@67932 00db46b3-68df-0310-9c12-caf00c1e9a41
rm one extraneous "d"
0d02df7 
git-svn-id: https://svn.r-project.org/R/trunk@67933 00db46b3-68df-0310-9c12-caf00c1e9a41
Update for R 3.1.3 release on 2015-03-09.
4442187 
git-svn-id: https://svn.r-project.org/R/trunk@67934 00db46b3-68df-0310-9c12-caf00c1e9a41
Give an error when x is a higher-dimensional array.
38b5bfb 
git-svn-id: https://svn.r-project.org/R/trunk@67937 00db46b3-68df-0310-9c12-caf00c1e9a41
@kmillar
Added API from R 3.2 for creating evaluated promises.
92f1be7
@kmillar
Enable debugging to be globally disabled.
e7cf256
@kmillar
Merge in memory management / reference counting macros from R 3.2
8119337
@kmillar
Add the 'Rf_allocFormalsList' family of functions from R 3.2
455f171
@kmillar
Add some more symbol table shortcuts from R 3.2
eeca2e9
@kmillar
Merge commit '38b5bfb' into r_3_2_sync
b0ff706 
This merges in the changes from CR up until the point where
the CR R-3.2 branch diverges from the trunk.

Not all the functionality has been merged in.
Things that are known to be missing include:
- The bytecode compiler and interpreter have not been updated
  at all.
- Custom allocators are not supported
- shallow_duplicate currently does deep duplication
- Debugger doesn't recognize 'f'
- Some of the optimizations of S3 method dispatch are
  missing.
- Builtin functions don't attempt to reuse the memory
  allocations used by the inputs.

Unimplemented builtins:
- do_returnValue
- do_bcprofcounts
- do_bcprofstart
- do_bcprofstop

In addition there are a number of failing tests that require
investigation.
@kmillar
Fix a number of bugs arising from the R 3.2 merge.
23cda8c
@kmillar
Minor changes to the error and warning messages expected in unit
bb40907 
tests.
@kmillar
Download the recommended packages before configuring on travis.
c42b587 
This is required as they are no longer part of the repo.
@kmillar
Fixup some bad printf format specifications.
495fb0f
@kmillar
Fixed a number of bugs found by running the testr testsuite.
3c7afcc
@kmillar
Treat R_Srcref as global root for GC.
34a2259
@kmillar
Change the way the JIT compiler rethrows unhandled exceptions. Fixes an
99c6461 
infinite loop under some circumstances.
@kmillar
Merge branch 'r_3_2_sync' of github.com:kmillar/cxxr into r_3_2_sync
8ca9b4a
@kmillar
Delete accidentally commited file.
be9e904
@kmillar
Fix some garbage collection bugs.
6aa2f7b 
- A mark/sweep GC would crash if R_SrcRef was nullptr.
- Ensure that R_SrcRef is initialized at process startup.
- Update reference counts for the ByteStack and ProtectStack
  prior to entering a mark/sweep GC.  The sweep phase uses
  the reference counts to immediately delete zero count nodes
  instead of making them moribund, and could incorrectly delete
  objects if the counts don't include those stacks.
@kmillar
Fix an error in a comment.
69be83d
@kmillar
Fixed a bug in the warnings system that caused last.warning() to fail.
ac311f3 
Also updated the warning text for a bunch of cases where the upstream version
had been updated, but not the CXXR version.
@kmillar
Make it a compile-time error to attempt to use a GCEdge or
3bb7192 
GCStackRoot as an array.

This prevents errors of the type:
   GCStackRoot<ListVector> x = ...
   RObject y = x[0];
when the intended statement was:
   RObject y = (*x)[0];
@kmillar
Change the set of transparent builtin functions to match CR's behaviour.
2c13512
@kmillar
Fix the handling of [] with no arguments.
9489688
kmillar added a commit that referenced this pull request Aug 20, 2015
@kmillar
Merge pull request #27 from kmillar/r_3_2_sync
5d10e70 
R 3.2 sync
@kmillar kmillar merged commit 5d10e70 into rho-devel:master Aug 20, 2015
@kmillar kmillar deleted the r_3_2_sync branch August 20, 2015 01:06
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