[r-cran-rprotobuf] 01/01: New upstream version 0.4.7

Andreas Tille tille at debian.org
Thu Nov 17 11:36:34 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to annotated tag upstream/0.4.7
in repository r-cran-rprotobuf.

commit 7962996e6c460c880929f3ee7c8a4f535b8b21a9
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 17 12:06:35 2016 +0100

    New upstream version 0.4.7
---
 ChangeLog                           |  34 ++++++++++++++++++++++++
 DESCRIPTION                         |  12 ++++-----
 MD5                                 |  30 +++++++++++-----------
 R/rexp_obj.R                        |   9 +++++--
 README.md                           |  50 +++++++++++++++++++++++++++++++-----
 inst/NEWS.Rd                        |  41 ++++++++++++++++++++++++-----
 inst/doc/RProtoBuf-intro.pdf        | Bin 197785 -> 197853 bytes
 inst/doc/RProtoBuf-paper.Rnw        |   2 +-
 inst/doc/RProtoBuf-paper.pdf        | Bin 411781 -> 411788 bytes
 inst/doc/RProtoBuf-quickref.pdf     | Bin 80706 -> 80702 bytes
 inst/doc/RProtoBuf-unitTests.pdf    | Bin 85096 -> 84058 bytes
 inst/unitTests/runit.serialize_pb.R |   6 +++--
 src/lookup.cpp                      |   2 +-
 vignettes/RProtoBuf-paper.Rnw       |   2 +-
 vignettes/RProtoBuf-paper.bib       |   2 +-
 vignettes/figures/fig-SER.pdf       | Bin 8011 -> 8011 bytes
 16 files changed, 149 insertions(+), 41 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index b1dfa25..52694e7 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,37 @@
+2016-10-29  Dirk Eddelbuettel  <edd at debian.org>
+
+	* DESCRIPTION (Version, Date): Release 0.4.7
+
+2016-10-24  Dirk Eddelbuettel  <edd at debian.org>
+
+	* DESCRIPTION (Version): Roll minor version and date
+
+	* src/lookup.cpp: Replace omegahat.org with omagehat.net
+	* vignettes/RProtoBuf-paper.bib: Ditto
+
+2016-09-09  Dirk Eddelbuettel  <edd at debian.org>
+
+	* DESCRIPTION (Version, Date): New release 0.4.6
+	* README.md: Expanded, added three short sections
+
+2016-09-08  Dirk Eddelbuettel  <edd at debian.org>
+
+	* inst/NEWS.Rd: Ditto, also replace \cpkg{} with \CRANpkg{}
+	* README.md: Use https for CRAN URL
+
+2016-09-06  Dirk Eddelbuettel  <edd at debian.org>
+
+	* vignettes/RProtoBuf-paper.Rnw: Comment-out the use of the \DOI
+	macro from (updated) jss.cls: cannot ship jss.cls (or R will warn)
+	and cannot use \DOI as (as R-release and older do not know \DOI)
+
+2016-09-01  Dirk Eddelbuettel  <edd at debian.org>
+
+	[ Entry for anonymous PR #18 by 'oliverbock' ]
+	* R/rexp_obj.R (unrexp_string): Ensure zero-length strings can be
+	serialized; special case of native encoding for S4 objects
+	* inst/unitTests/runit.serialize_pb.R: New tests
+
 2016-08-29  Dirk Eddelbuettel  <edd at debian.org>
 
 	* DESCRIPTION (Version, Date): New release 0.4.5
diff --git a/DESCRIPTION b/DESCRIPTION
index 981c854..bec7b95 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: RProtoBuf
-Version: 0.4.5
-Date: 2016-08-29
+Version: 0.4.7
+Date: 2016-10-29
 Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
 Maintainer: Dirk Eddelbuettel <edd at debian.org>
-Title: R Interface to the Protocol Buffers API (v2 or v3)
+Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
 Description: Protocol Buffers are a way of encoding structured data in an
  efficient yet extensible format. Google uses Protocol Buffers for almost all
  of its internal 'RPC' protocols and file formats.  Additional documentation
  is available in two included vignettes one of which corresponds to our paper
  in the Journal of Statistical Software (2016, v71i02). Either version 2 or 3
- of the Protocol Buffers API is supported.
+ of the 'Protocol Buffers' 'API' is supported.
 Depends: R (>= 3.0.0), methods
 Imports: utils, stats, tools, Rcpp, RCurl
 LinkingTo: Rcpp
@@ -24,6 +24,6 @@ License: GPL (>= 2)
 URL: https://github.com/eddelbuettel/rprotobuf
 BugReports: https://github.com/eddelbuettel/rprotobuf/issues
 NeedsCompilation: yes
-Packaged: 2016-08-29 14:05:09.24442 UTC; edd
+Packaged: 2016-10-29 14:23:10.96509 UTC; edd
 Repository: CRAN
-Date/Publication: 2016-08-29 17:44:20
+Date/Publication: 2016-10-29 22:23:58
diff --git a/MD5 b/MD5
index 0d27d18..0d7521d 100644
--- a/MD5
+++ b/MD5
@@ -1,5 +1,5 @@
-837029b9c0809ffd6fbf298d38e789ce *ChangeLog
-f0d16c59ba00fc5ad8c6c5451d34a174 *DESCRIPTION
+8c13554836eea09d0fd32be9add5f622 *ChangeLog
+0f62150c340d4b3dd07e7512162c1177 *DESCRIPTION
 9b76f6d15e53a5bddf140ca9df8b7d0c *NAMESPACE
 9d4fc4eca08934288aa92ace963c6ad1 *R/00classes.R
 ad31e4eeef1cfcb9e6052da2884bf818 *R/add.R
@@ -20,7 +20,7 @@ f33da7b20a11bb814500bdd21243b79f *R/internals.R
 0176cbff7f11d23ae2d6de6c57a407af *R/lookup.R
 61478bd1ddd8757ed20fd64adcfe0af9 *R/merge.R
 1ae2bff7191f6a042a82d13d8cfa638a *R/read.R
-7f2c640282f95beb1f608e4ef1f86fe5 *R/rexp_obj.R
+76a5c3dce10560a07821a9268d3aaa4e *R/rexp_obj.R
 c5136c115d0c052aa3baf378c9d488ca *R/rpc.R
 d3a77f8815c1665cb7809823c2aade5c *R/serialize.R
 1e07553fc771bd00c48378440481ccb4 *R/serialize_pb.R
@@ -39,7 +39,7 @@ eaeb7ee0e7ea168d4fdc60de5211de30 *R/wrapper_EnumDescriptor.R
 15200614add0962256aba49748578e0d *R/wrapper_ZeroCopyInputStream.R
 64270847c9aea97babc5dd667ffa4543 *R/zzz.R
 0a7dddaf1478bf6737351c05852168f1 *README
-a897df994f150cc0a9dcc21fd586dfc3 *README.md
+80d4842f38bb9b9c3b3435f6ead159e7 *README.md
 9c2e29fe733b28fbd0058fe8f82a4c86 *TODO
 b3111723e5f05332e08e602c8c63c261 *build/vignette.rds
 07b085e1ed844651495ee3a385765bab *cleanup
@@ -49,20 +49,20 @@ d41d8cd98f00b204e9800998ecf8427e *configure.win
 6275f697db7b64510f10f6bbc95c0498 *demo/addressbook.R
 81d0dda686db1c07b625f49ea321a0af *demo/io.R
 9ed50fca39d7442e4baaf9d24a1b1663 *inst/CITATION
-613b8fad6fd011925f2a778ca6832152 *inst/NEWS.Rd
+ad4f077fa9afefefdf5eb09d9d0b6b15 *inst/NEWS.Rd
 5485d1d9d1bfb19216aaef28bd8fcc89 *inst/THANKS
 58059a5ec15b9adbbc851b4d8879c61f *inst/doc/RProtoBuf-intro.R
 703e882a07b63a5cf58b9e25ccede221 *inst/doc/RProtoBuf-intro.Rnw
-11a4cac31a1e3f4a955b834e0ac1256a *inst/doc/RProtoBuf-intro.pdf
+98a2f84fd3038e8841b4ed45631264b2 *inst/doc/RProtoBuf-intro.pdf
 b83a107abeb06164684bb49afe5cc130 *inst/doc/RProtoBuf-paper.R
-5e509194dca9ecb06b8b66508dafc0a3 *inst/doc/RProtoBuf-paper.Rnw
-f17ef44ad5b7a69900c125a21441538a *inst/doc/RProtoBuf-paper.pdf
+126dcc5fc93ad8be2af332fff046f28c *inst/doc/RProtoBuf-paper.Rnw
+76d3c2e0cc6635fb679733c3b09a0c9e *inst/doc/RProtoBuf-paper.pdf
 bc0070aed4b2950e0ef0449fd9575e43 *inst/doc/RProtoBuf-quickref.R
 63798bdf3a689979494eabf6cf80021b *inst/doc/RProtoBuf-quickref.Rnw
-32be33912f2604f4014762aaa8cd72d0 *inst/doc/RProtoBuf-quickref.pdf
+e4815370e634a1c942554bf39ce09f21 *inst/doc/RProtoBuf-quickref.pdf
 d58f8a01ff830e711be53df88d59d337 *inst/doc/RProtoBuf-unitTests.R
 31ab1ab2350cdc2a0a8df9949484302c *inst/doc/RProtoBuf-unitTests.Rnw
-4bdcf7c7e23bfc9ca6167b55ffceecfb *inst/doc/RProtoBuf-unitTests.pdf
+ee05c25f5c9679b0238b7783ff22022c *inst/doc/RProtoBuf-unitTests.pdf
 8513688afa8b8be605c63815fe85dead *inst/examples/addressbook.pb
 7f6e97dd4d48fcec1cfd7f9998dc0a62 *inst/opencpu/ocpu-getdata.R
 f16a4dde30d41003822a89fc99c7be66 *inst/opencpu/ocpu-getdata.py
@@ -98,7 +98,7 @@ aed1c3a5c9c0c5506d738418cbeec03c *inst/unitTests/runit.import.R
 a09caadfa8de6700fa169f934e182c4b *inst/unitTests/runit.messages.R
 59b793897716193b6a66b437a1c0e332 *inst/unitTests/runit.nested.R
 16fc6613c0ebdf33c65cf44ecb272de2 *inst/unitTests/runit.serialize.R
-04a3b1e24c81bb9871f61b60997b6bfb *inst/unitTests/runit.serialize_pb.R
+1c0bd7e404461bcb0a95e789607f49f2 *inst/unitTests/runit.serialize_pb.R
 c15537a7222614c37c34b745e6c41b0d *man/ArrayInputStream-class.Rd
 40890fed5d4ed64cafc7095aa9a0b46e *man/ArrayInputStream-methods.Rd
 acb73c235784572d89ea3ca53da8a9a0 *man/ArrayOutputStream-class.Rd
@@ -191,7 +191,7 @@ c9da30f2ded23d5631d1cc1515c6858b *src/ZeroCopyInputStreamWrapper.cpp
 a169b617724adce6ee0a43fd78e02b78 *src/extensions.cpp
 52afd56eaa8013202920fc5be4a4dbe6 *src/extractors.cpp
 699307a87cee7adf4a5087b934c27b01 *src/fieldtypes.h
-31dd784f16dd9cf73858618b9c15bc3f *src/lookup.cpp
+a81bea8fd0b5bec76fadf4c63628de2a *src/lookup.cpp
 3406e5f66b1d77ba35ec316cb8608d85 *src/mutators.cpp
 accf81c91861361baced77e04ef97c02 *src/rprotobuf.cpp
 d0741a65fb6fbc342231b171f2ec133e *src/rprotobuf.h
@@ -210,13 +210,13 @@ b67f6ab18ec9182617f8f3a53670c37a *src/wrapper_Message.cpp
 6c1d5df84213b965ae16778455090663 *tests/runUnitTests.R
 bce73d23dc034a96eb3fb50104089a45 *tools/winlibs.R
 703e882a07b63a5cf58b9e25ccede221 *vignettes/RProtoBuf-intro.Rnw
-5e509194dca9ecb06b8b66508dafc0a3 *vignettes/RProtoBuf-paper.Rnw
-8e0316b9a829396482798bd4562562ec *vignettes/RProtoBuf-paper.bib
+126dcc5fc93ad8be2af332fff046f28c *vignettes/RProtoBuf-paper.Rnw
+f136387c11a22105eee7371818beacd6 *vignettes/RProtoBuf-paper.bib
 63798bdf3a689979494eabf6cf80021b *vignettes/RProtoBuf-quickref.Rnw
 31ab1ab2350cdc2a0a8df9949484302c *vignettes/RProtoBuf-unitTests.Rnw
 9d5a9174a82963f2f51863b2dda63257 *vignettes/figures/HistogramTools.pdf
 c727d40ae2834f8a34ba8f541ca87544 *vignettes/figures/fig-021.pdf
-28fbded1eb22362a200046f8b55afbae *vignettes/figures/fig-SER.pdf
+82fc5ad95a972d434cdcd6347b0ef6c9 *vignettes/figures/fig-SER.pdf
 107256baabac9d3c621424b2eeec97c6 *vignettes/figures/histogram-mapreduce-diag1.pdf
 b7c0c609a09de939ce648dd0bb9b3d0e *vignettes/figures/protobuf-distributed-system-crop.pdf
 9ad30eeb7c977dc76b6788f8c54ecf12 *vignettes/inactive/Makefile.in
diff --git a/R/rexp_obj.R b/R/rexp_obj.R
index 91013cd..84c4701 100644
--- a/R/rexp_obj.R
+++ b/R/rexp_obj.R
@@ -5,6 +5,11 @@
 # Modified 2014 by Murray Stokely to support language and environment types
 
 rexp_obj <- function(obj){
+  if(isS4(obj)) {
+    # Some S4 objects do not return "S4" from typeof.  e.g. lubridate interval
+    # These must be natively encoded or we will lose the S4 flag.
+    return(rexp_native(obj))
+  }
   sm <- typeof(obj);
   msg <- switch(sm,
     "character" = rexp_string(obj),
@@ -103,7 +108,7 @@ unrexp_string <- function(myrexp){
   mystring <- unlist(lapply(myrexp$stringValue, "[[", "strval"))
   isNA <- unlist(lapply(myrexp$stringValue, "[[", "isNA"))
   mystring[isNA] <- NA
-  mystring
+  as.character(mystring)
 }
 
 unrexp_raw <- function(myrexp){
@@ -118,7 +123,7 @@ unrexp_complex <- function(myrexp){
   xvalue <- lapply(myrexp$complexValue, function(x){
     complex(real=x$real, imaginary=x$imag)
   })
-  unlist(xvalue)
+  as.complex(unlist(xvalue))
 }
 
 unrexp_integer <- function(myrexp){
diff --git a/README.md b/README.md
index c83f084..ec3a6af 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,56 @@
-## RProtoBuf [![Build Status](https://travis-ci.org/eddelbuettel/rprotobuf.svg)](https://travis-ci.org/eddelbuettel/rprotobuf) [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) [![CRAN](http://www.r-pkg.org/badges/version/RProtoBuf)](http://cran.r-project.org/package=RProtoBuf) [![Downloads](http://cranlogs.r-pkg.org/badges/RProtoBuf?color=brightgreen)](http://www.r-pkg.org/pkg/RProtoBuf)
+## RProtoBuf [![Build Status](https://travis-ci.org/eddelbuettel/rprotobuf.svg)](https://travis-ci.org/eddelbuettel/rprotobuf) [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) [![CRAN](http://www.r-pkg.org/badges/version/RProtoBuf)](https://cran.r-project.org/package=RProtoBuf) [![Downloads](http://cranlogs.r-pkg.org/badges/RProtoBuf?color=brightgreen)](http://www.r-pkg.org/pkg/RProtoBuf)
 
 R Interface to [Google Protocol Buffers](https://developers.google.com/protocol-buffers/)
 
-## Installation
+### What are Protocol Buffers?
+
+A serialization format developed by [Google](https://www.google.com) and used
+widely within Google, and by numerous other projects.  Quoting from the
+[official website](https://developers.google.com/protocol-buffers/):
+
+> Protocol buffers are Google's language-neutral, platform-neutral,
+extensible mechanism for serializing structured data – think XML, but
+smaller, faster, and simpler. You define how you want your data to be
+structured once, then you can use special generated source code to easily
+write and read your structured data to and from a variety of data streams and
+using a variety of languages.
+
+[Protocol Buffers](https://developers.google.com/protocol-buffers/) natively
+support C++, C#, Go, Java and Python. Many other languages are supported via
+contributed extensions. This package adds support for
+[R](https://www.r-project.org).
+
+### Installation
 
 You can either install from source via this repo, or install
-[the CRAN package](http://cran.r-project.org/package=RProtoBuf)
-the usual way from [R](http://www.r-project.org).
+[the CRAN package](https://cran.r-project.org/package=RProtoBuf)
+the usual way from [R](https://www.r-project.org) via
+
+```r
+install.packages("RProtoBuf")
+```
+
+but do make sure you have the system requirements covered when building from
+source.
+
+Under Debian/Ubuntu you may need
+
+```bash
+sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev 
+```
+
+with similar commands on other operating systems or distributions.
+
+### Documentation
+
+The package contains two pdf vignettes; the second one corresponds to 
+[our JSS paper](https://www.jstatsoft.org/article/view/v071i02).
 
-## Authors
+### Authors
 
 Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
 
-## License
+### License
 
 GPL (>= 2)
 
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 7ba9d1e..54a6f95 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,9 +1,38 @@
 \name{NEWS}
 \title{News for Package \pkg{RProtoBuf}}
-\newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\newcommand{\ghpr}{\href{https://github.com/eddelbuettel/rprotobuf/pull/#1}{##1}}
+\newcommand{\ghit}{\href{https://github.com/eddelbuettel/rprotobuf/issues/#1}{##1}}
 
-\section{Changes in RProtoBuf version 0.4.4 (2016-07-10)}{
+\section{Changes in RProtoBuf version 0.4.7 (2016-10-27)}{
   \itemize{
+    \item At the request of CRAN, two documentation instances referring
+    to the Omegehat repository were updated to \url{http://omegahat.net}
+  }
+}
+
+\section{Changes in RProtoBuf version 0.4.6 (2016-09-08)}{
+  \itemize{
+    \item Support for serializing zero-length objects was added (PR
+    \ghpr{18} addressing \ghit{13})
+    \item S4 objects are natively encoded (also PR \ghpr{18})
+    \item The vignette based on the JSS paper no longer uses a macro available
+    only with the R-devel version of jss.cls, and hence builds on all R versions
+  }
+}
+
+\section{Changes in RProtoBuf version 0.4.5 (2016-08-29)}{
+  \itemize{
+    \item Support for version 3 of the Protcol Buffers API
+    \item Added 'syntax = "proto2";' to all proto files (PR \ghpr{17})
+    \item Updated Travis CI script to test against both versions 2 and 3
+    using custom-built .deb packages of version 3 (PR \ghpr{16})
+    \item Improved build system with support for custom CXXFLAGS (Craig
+    Radcliffe in PR \ghpr{15}) 
+  }
+}
+
+\section{Changes in RProtoBuf version 0.4.4 (2016-07-10)}{
+   \itemize{
     \item New vignette based on JSS publication (v71 i02)
     \item Some documentation enhancements were made, as well as other
     minor cleanups to file modes and operations
@@ -41,7 +70,7 @@
     return a proper list instead of a named vector.
     \item Update the default print methods to use
     \code{cat()} with \code{fill=TRUE} instead of \code{show()} to eliminate the confusing
-    \code{[1]} since the classes in \cpkg{RProtoBuf} are not vectorized.
+    \code{[1]} since the classes in \pkg{RProtoBuf} are not vectorized.
     \item Add support for serializing function, language, and
       environment objects by falling back to R's native serialization
       with \code{serialize_pb} and \code{unserialize_pb} to make it
@@ -124,7 +153,7 @@
     been submitted to R-Forge with details about the coding standards
     and how they are enforced with Emacs and clang-format.
     \item Applied changes suggested by Kevin Ushey to the \code{S4}
-    class handling to support both the currently released \cpkg{Rcpp} as
+    class handling to support both the currently released \CRANpkg{Rcpp} as
     well as the currently pending next version.
   }
 }
@@ -137,12 +166,12 @@
     a message of the wrong type instead of causing a C++ check failure
     that terminates the Rsession.
     \item Change object table lookup slightly to allow users to use the
-    \code{<<-} operator in code using \cpkg{RProtoBuf} without hitting a
+    \code{<<-} operator in code using \pkg{RProtoBuf} without hitting a
     \code{stop()} error in the lookup routine.
     \item Add missing \code{enum_type} method and improve show method for
     EnumValueDescriptors.
     \item Improve documentation and tests for all of the above.
-    \item Rewrote \code{tests/} script calling \cpkg{RUnit} tests
+    \item Rewrote \code{tests/} script calling \CRANpkg{RUnit} tests
   }
 }
 
diff --git a/inst/doc/RProtoBuf-intro.pdf b/inst/doc/RProtoBuf-intro.pdf
index 7617cfd..3eb14e1 100644
Binary files a/inst/doc/RProtoBuf-intro.pdf and b/inst/doc/RProtoBuf-intro.pdf differ
diff --git a/inst/doc/RProtoBuf-paper.Rnw b/inst/doc/RProtoBuf-paper.Rnw
index 070cdf5..c61805e 100644
--- a/inst/doc/RProtoBuf-paper.Rnw
+++ b/inst/doc/RProtoBuf-paper.Rnw
@@ -60,7 +60,7 @@
 \Year{2016}
 \Submitdate{2014-02-05}
 \Acceptdate{2015-04-13}
-\DOI{10.18637/jss.v071.i02}
+%\DOI{10.18637/jss.v071.i02}
 
 %% The address of (at least) one author should be given
 %% in the following format:
diff --git a/inst/doc/RProtoBuf-paper.pdf b/inst/doc/RProtoBuf-paper.pdf
index 52b601e..2e97053 100644
Binary files a/inst/doc/RProtoBuf-paper.pdf and b/inst/doc/RProtoBuf-paper.pdf differ
diff --git a/inst/doc/RProtoBuf-quickref.pdf b/inst/doc/RProtoBuf-quickref.pdf
index 6b257f3..e4e433f 100644
Binary files a/inst/doc/RProtoBuf-quickref.pdf and b/inst/doc/RProtoBuf-quickref.pdf differ
diff --git a/inst/doc/RProtoBuf-unitTests.pdf b/inst/doc/RProtoBuf-unitTests.pdf
index 7c9e5ed..8a86675 100644
Binary files a/inst/doc/RProtoBuf-unitTests.pdf and b/inst/doc/RProtoBuf-unitTests.pdf differ
diff --git a/inst/unitTests/runit.serialize_pb.R b/inst/unitTests/runit.serialize_pb.R
index 998a4dd..3157a52 100644
--- a/inst/unitTests/runit.serialize_pb.R
+++ b/inst/unitTests/runit.serialize_pb.R
@@ -19,8 +19,10 @@ test.serialize_pb <- function() {
     mylist = list(foo='bar', 123, NA, NULL, list('test')),
     mylogical = c(TRUE,FALSE,NA),
     mychar = c('foo', NA, 'bar'),
+    myemptychar = character(0),
     somemissings = c(1,2,NA,NaN,5, Inf, 7 -Inf, 9, NA),
-    myrawvec = charToRaw('This is a test')
+    myrawvec = charToRaw('This is a test'),
+    myS4 = asS4("test")
   );
 
   checkEquals(unserialize_pb(serialize_pb(myobject, NULL)), myobject)
@@ -38,4 +40,4 @@ test.serialize_pb.alldatasets <- function() {
   checkTrue(all(sapply(names(unserialized.datasets),
                        function(name) identical(get(name),
 		       unserialized.datasets[[name]]))))
-}
\ No newline at end of file
+}
diff --git a/src/lookup.cpp b/src/lookup.cpp
index f2ca2f3..60959c5 100644
--- a/src/lookup.cpp
+++ b/src/lookup.cpp
@@ -3,7 +3,7 @@
 #include "DescriptorPoolLookup.h"
 
 /* This uses the mechanism of the RObjectTables package
-   see: http://www.omegahat.org/RObjectTables/ */
+   see: http://www.omegahat.net/RObjectTables/ */
 
 namespace rprotobuf {
 
diff --git a/vignettes/RProtoBuf-paper.Rnw b/vignettes/RProtoBuf-paper.Rnw
index 070cdf5..c61805e 100644
--- a/vignettes/RProtoBuf-paper.Rnw
+++ b/vignettes/RProtoBuf-paper.Rnw
@@ -60,7 +60,7 @@
 \Year{2016}
 \Submitdate{2014-02-05}
 \Acceptdate{2015-04-13}
-\DOI{10.18637/jss.v071.i02}
+%\DOI{10.18637/jss.v071.i02}
 
 %% The address of (at least) one author should be given
 %% in the following format:
diff --git a/vignettes/RProtoBuf-paper.bib b/vignettes/RProtoBuf-paper.bib
index 1af2eee..f25d952 100644
--- a/vignettes/RProtoBuf-paper.bib
+++ b/vignettes/RProtoBuf-paper.bib
@@ -37,7 +37,7 @@
   author =	 {Duncan {Temple Lang}},
   year =	 2012,
   url =
-                  {http://www.omegahat.org/RObjectTables/RObjectTables.pdf},
+                  {http://www.omegahat.net/RObjectTables/RObjectTables.pdf},
 }
 
 @InProceedings{sumaray:2012:cds:2184751.2184810,
diff --git a/vignettes/figures/fig-SER.pdf b/vignettes/figures/fig-SER.pdf
index 15d3261..82aa406 100644
Binary files a/vignettes/figures/fig-SER.pdf and b/vignettes/figures/fig-SER.pdf differ

-- 
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