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authorDaniel Baumann <daniel.baumann@progress-linux.org>2017-12-02 06:29:33 +0000
committerDaniel Baumann <daniel.baumann@progress-linux.org>2017-12-02 06:29:46 +0000
commitce4f5cda62afed5168cb63e57479e7ff2f6954eb (patch)
treef02fd953acf7fed069f7395db237bd20cebc710d
parentReleasing progress-linux version 3.4.2-2~dschinn1. (diff)
downloadr-base-ce4f5cda62afed5168cb63e57479e7ff2f6954eb.zip
r-base-ce4f5cda62afed5168cb63e57479e7ff2f6954eb.tar.xz
Merging upstream version 3.4.3.
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
-rw-r--r--SVN-REVISION4
-rw-r--r--VERSION2
-rw-r--r--VERSION-NICK2
-rwxr-xr-xconfigure34
-rw-r--r--configure.ac11
-rw-r--r--doc/FAQ12
-rw-r--r--doc/NEWS39
-rw-r--r--doc/NEWS.Rd49
-rw-r--r--doc/NEWS.pdfbin497464 -> 499141 bytes
-rw-r--r--doc/html/NEWS.html63
-rw-r--r--doc/html/R-admin.html130
-rw-r--r--doc/manual/R-FAQ.texi13
-rw-r--r--doc/manual/R-admin.texi53
-rw-r--r--doc/manual/R-exts.texi64
-rw-r--r--doc/manual/R-ints.texi8
-rw-r--r--doc/manual/rw-FAQ.texi6
-rw-r--r--share/texmf/bibtex/bib/RJournal.bib206
-rw-r--r--src/extra/tzone/Make.zi2
-rw-r--r--src/extra/tzone/Notes4
-rw-r--r--src/extra/tzone/zoneinfo.zipbin415184 -> 414625 bytes
-rw-r--r--src/gnuwin32/CHANGES.Rd3
-rw-r--r--src/gnuwin32/README.packages5
-rw-r--r--src/gnuwin32/cran/index.in2
-rw-r--r--src/gnuwin32/cran/rdevel.in2
-rw-r--r--src/gnuwin32/cran/rpatched.in2
-rw-r--r--src/gnuwin32/cran/rtest.in2
-rw-r--r--src/gnuwin32/front-ends/Rfe.c4
-rw-r--r--src/gnuwin32/front-ends/rcmdfn.c35
-rw-r--r--src/gnuwin32/front-ends/rpwd.c1
-rw-r--r--src/gnuwin32/rhome.c1
-rw-r--r--src/gnuwin32/run.c9
-rw-r--r--src/include/config.h.in3
l---------src/library/Recommended/Matrix.tgz2
-rw-r--r--src/library/Recommended/Matrix_1.2-11.tar.gzbin1819315 -> 0 bytes
-rw-r--r--src/library/Recommended/Matrix_1.2-12.tar.gzbin0 -> 1821424 bytes
l---------src/library/Recommended/mgcv.tgz2
-rw-r--r--src/library/Recommended/mgcv_1.8-20.tar.gzbin870394 -> 0 bytes
-rw-r--r--src/library/Recommended/mgcv_1.8-22.tar.gzbin0 -> 859949 bytes
-rw-r--r--src/library/base/R/Defunct.R4
-rw-r--r--src/library/base/R/datetime.R16
-rw-r--r--src/library/base/R/namespace.R25
-rw-r--r--src/library/base/R/range.R8
-rw-r--r--src/library/base/R/zdatetime.R8
-rw-r--r--src/library/base/man/append.Rd2
-rw-r--r--src/library/base/man/connections.Rd13
-rw-r--r--src/library/base/man/grep.Rd34
-rw-r--r--src/library/base/man/libcurlVersion.Rd20
-rw-r--r--src/library/base/man/memCompress.Rd7
-rw-r--r--src/library/base/man/pcre_config.Rd9
-rw-r--r--src/library/base/man/seq.Rd2
-rw-r--r--src/library/base/man/timezones.Rd6
-rw-r--r--src/library/base/man/utf8Conversion.Rd41
-rw-r--r--src/library/grDevices/tests/ps-tests.Rout.save4
-rw-r--r--src/library/grDevices/tests/xfig-tests.Rout.save4
-rw-r--r--src/library/grid/inst/doc/displaylist.pdfbin157773 -> 157837 bytes
-rw-r--r--src/library/grid/inst/doc/frame.pdfbin156380 -> 156425 bytes
-rw-r--r--src/library/grid/inst/doc/grid.pdfbin252267 -> 251989 bytes
-rw-r--r--src/library/grid/inst/doc/grobs.pdfbin107549 -> 107598 bytes
-rw-r--r--src/library/grid/inst/doc/interactive.pdfbin91249 -> 91310 bytes
-rw-r--r--src/library/grid/inst/doc/locndimn.pdfbin89901 -> 89964 bytes
-rw-r--r--src/library/grid/inst/doc/moveline.pdfbin87646 -> 87707 bytes
-rw-r--r--src/library/grid/inst/doc/nonfinite.pdfbin79887 -> 79944 bytes
-rw-r--r--src/library/grid/inst/doc/plotexample.pdfbin223798 -> 224240 bytes
-rw-r--r--src/library/grid/inst/doc/rotated.pdfbin122279 -> 122343 bytes
-rw-r--r--src/library/grid/inst/doc/saveload.pdfbin134254 -> 134320 bytes
-rw-r--r--src/library/grid/inst/doc/sharing.pdfbin71213 -> 71278 bytes
-rw-r--r--src/library/grid/inst/doc/viewports.pdfbin163455 -> 163484 bytes
-rw-r--r--src/library/grid/tests/testls.Rout.save4
-rw-r--r--src/library/methods/R/RMethodUtils.R2
-rw-r--r--src/library/parallel/R/unix/mclapply.R5
-rw-r--r--src/library/parallel/inst/doc/parallel.pdfbin291213 -> 291155 bytes
-rw-r--r--src/library/parallel/tests/multicore2.Rout.save4
-rw-r--r--src/library/parallel/tests/snow2.Rout.save4
-rw-r--r--src/library/splines/src/splines.c8
-rw-r--r--src/library/stats/R/zzModels.R7
-rw-r--r--src/library/stats/man/SSlogis.Rd12
-rw-r--r--src/library/stats/src/cov.c14
-rw-r--r--src/library/stats/tests/bandwidth.Rout.save4
-rw-r--r--src/library/stats/tests/glm.Rout.save4
-rw-r--r--src/library/stats/tests/ks-test.Rout.save4
-rw-r--r--src/library/stats/tests/nls.Rout.save4
-rw-r--r--src/library/stats/tests/simulate.Rout.save4
-rw-r--r--src/library/tools/R/utils.R2
-rw-r--r--src/library/utils/R/tar.R30
-rw-r--r--src/library/utils/inst/doc/Sweave.pdfbin322587 -> 322552 bytes
-rw-r--r--src/library/utils/man/download.packages.Rd5
-rw-r--r--src/library/utils/man/setRepositories.Rd8
-rw-r--r--src/main/Rdynload.c4
-rw-r--r--src/main/logic.c41
-rw-r--r--src/main/platform.c6
-rw-r--r--src/main/printvector.c9
-rw-r--r--src/main/raw.c28
-rw-r--r--src/main/seq.c8
-rw-r--r--src/main/subassign.c12
-rw-r--r--src/main/subscript.c2
-rw-r--r--src/main/util.c35
-rw-r--r--src/modules/internet/Rsock.c7
-rw-r--r--src/scripts/javareconf.in6
-rw-r--r--src/unix/sys-std.c6
-rw-r--r--src/unix/system.c2
-rw-r--r--tests/Examples/datasets-Ex.Rout.save4
-rw-r--r--tests/Examples/grDevices-Ex.Rout.save4
-rw-r--r--tests/Examples/graphics-Ex.Rout.save8
-rw-r--r--tests/Examples/grid-Ex.Rout.save4
-rw-r--r--tests/Examples/splines-Ex.Rout.save4
-rw-r--r--tests/Examples/stats-Ex.Rout.save29
-rw-r--r--tests/Examples/stats4-Ex.Rout.save4
-rw-r--r--tests/Examples/tools-Ex.Rout.save6
-rw-r--r--tests/R-intro.Rout.save2
-rw-r--r--tests/any-all.Rout.save2
-rw-r--r--tests/arith-true.Rout.save4
-rw-r--r--tests/arith.Rout.save2
-rw-r--r--tests/complex.Rout.save2
-rw-r--r--tests/d-p-q-r-tests.Rout.save4
-rw-r--r--tests/datasets.Rout.save2
-rw-r--r--tests/datetime.Rout.save2
-rw-r--r--tests/datetime2.Rout.save2
-rw-r--r--tests/demos.Rout.save4
-rw-r--r--tests/eval-etc.Rout.save2
-rw-r--r--tests/iec60559.Rout.save2
-rw-r--r--tests/internet.Rout.save4
-rw-r--r--tests/isas-tests.Rout.save4
-rw-r--r--tests/lapack.Rout.save2
-rw-r--r--tests/lm-tests.Rout.save2
-rw-r--r--tests/method-dispatch.Rout.save2
-rw-r--r--tests/ok-errors.Rout.save2
-rw-r--r--tests/p-r-random-tests.Rout.save4
-rw-r--r--tests/print-tests.Rout.save2
-rw-r--r--tests/reg-IO.Rout.save2
-rw-r--r--tests/reg-IO2.Rout.save2
-rw-r--r--tests/reg-S4.R4
-rw-r--r--tests/reg-S4.Rout.save9
-rw-r--r--tests/reg-examples3.Rout.save2
-rw-r--r--tests/reg-packages.R2
-rw-r--r--tests/reg-tests-2.Rout.save14
-rw-r--r--tests/reg-tests-3.Rout.save2
-rw-r--r--tests/simple-true.Rout.save2
137 files changed, 982 insertions, 441 deletions
diff --git a/SVN-REVISION b/SVN-REVISION
index 96886ea..2937f4c 100644
--- a/SVN-REVISION
+++ b/SVN-REVISION
@@ -1,2 +1,2 @@
-Revision: 73368
-Last Changed Date: 2017-09-28
+Revision: 73796
+Last Changed Date: 2017-11-30
diff --git a/VERSION b/VERSION
index 4d9d11c..6cb9d3d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.4.2
+3.4.3
diff --git a/VERSION-NICK b/VERSION-NICK
index 57cb621..214bdec 100644
--- a/VERSION-NICK
+++ b/VERSION-NICK
@@ -1 +1 @@
-Short Summer
+Kite-Eating Tree
diff --git a/configure b/configure
index 2d9f8e8..caa8cc3 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for R 3.4.2.
+# Generated by GNU Autoconf 2.69 for R 3.4.3.
#
# Report bugs to <https://bugs.r-project.org>.
#
@@ -590,8 +590,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='R'
PACKAGE_TARNAME='R'
-PACKAGE_VERSION='3.4.2'
-PACKAGE_STRING='R 3.4.2'
+PACKAGE_VERSION='3.4.3'
+PACKAGE_STRING='R 3.4.3'
PACKAGE_BUGREPORT='https://bugs.r-project.org'
PACKAGE_URL='https://www.r-project.org'
@@ -753,6 +753,7 @@ LIBOBJS
RMATH_HAVE_LOG1P
RMATH_HAVE_HYPOT
RMATH_HAVE_EXPM1
+MACOS_SIERRA
ALLOCA
R_OPENMP_FFLAGS
R_OPENMP_CFLAGS
@@ -1702,7 +1703,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures R 3.4.2 to adapt to many kinds of systems.
+\`configure' configures R 3.4.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1777,7 +1778,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of R 3.4.2:";;
+ short | recursive ) echo "Configuration of R 3.4.3:";;
esac
cat <<\_ACEOF
@@ -2064,7 +2065,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-R configure 3.4.2
+R configure 3.4.3
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -3216,7 +3217,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by R $as_me 3.4.2, which was
+It was created by R $as_me 3.4.3, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3728,7 +3729,7 @@ _ACEOF
## exclude some unsupported OSes
case "${host_os}" in
## Darwin 1.3.1 was macOS 10.0, 1.4.1 was 10.1, 5 is 10.2 etc
- ## with 13 being 10.9. We no longer support < 10.6 (Snow Leopard)
+ ## with 13 being 10.9. We no longer support < 10.6 (Snow Leopard, Darwin 10)
## https://en.wikipedia.org/wiki/Darwin_OS
darwin1.*)
as_fn_error $? "The earliest supported macOS is 10.6.
@@ -25211,7 +25212,7 @@ _ACEOF
# flags.
r_save_CFLAGS=$CFLAGS
CFLAGS="$CFLAGS $r_verb"
-(eval echo $as_me:25214: \"$ac_link\") >&5
+(eval echo $as_me:25215: \"$ac_link\") >&5
r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
echo "$r_c_v_output" >&5
CFLAGS=$r_save_CFLAGS
@@ -25286,7 +25287,7 @@ _ACEOF
# flags.
r_save_CFLAGS=$CFLAGS
CFLAGS="$CFLAGS $r_cv_prog_c_v"
-(eval echo $as_me:25289: \"$ac_link\") >&5
+(eval echo $as_me:25290: \"$ac_link\") >&5
r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
echo "$r_c_v_output" >&5
CFLAGS=$r_save_CFLAGS
@@ -34881,6 +34882,15 @@ _ACEOF
fi
done
+## Used to avoid a problem with some Xcode 9 updates on macOS 10.12 (Darwin 16)
+case "${host_os}" in
+ darwin1[0123456].*)
+
+$as_echo "#define MACOS_SIERRA 1" >>confdefs.h
+
+ ;;
+esac
+
## clock_gettime is POSIX 1993, but not on macOS prior to 10.12 (Sierra)
## Some OSes need -lrt: Linux (for glibc versions before 2.17), Solaris,
## not FreeBSD.
@@ -51352,7 +51362,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by R $as_me 3.4.2, which was
+This file was extended by R $as_me 3.4.3, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -51419,7 +51429,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-R config.status 3.4.2
+R config.status 3.4.3
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index a73f4ea..f34744d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -79,7 +79,7 @@ AC_DEFINE_UNQUOTED(R_OS, "${host_os}",
## exclude some unsupported OSes
case "${host_os}" in
## Darwin 1.3.1 was macOS 10.0, 1.4.1 was 10.1, 5 is 10.2 etc
- ## with 13 being 10.9. We no longer support < 10.6 (Snow Leopard)
+ ## with 13 being 10.9. We no longer support < 10.6 (Snow Leopard, Darwin 10)
## https://en.wikipedia.org/wiki/Darwin_OS
darwin1.*)
AC_MSG_ERROR([The earliest supported macOS is 10.6.]
@@ -87,7 +87,7 @@ case "${host_os}" in
darwin[[56789]]*)
AC_MSG_ERROR([The earliest supported macOS is 10.6.]
;;
- aix[123]*|aix4.[01]*)
+ aix[[123]]*|aix4.[[01]]*)
## These need a form of linking we no longer support
AC_MSG_ERROR([AIX prior to 4.2 is not supported])
;;
@@ -1872,6 +1872,13 @@ R_CHECK_FUNCS([sched_setaffinity sched_getaffinity], [#include <sched.h>])
R_CHECK_FUNCS([utime], [#include <utime.h>])
## POSIX.1-2008 preferred form
R_CHECK_FUNCS([utimensat], [#include <sys/stat.h>])
+## Used to avoid a problem with some Xcode 9 updates on macOS 10.12 (Darwin 16)
+case "${host_os}" in
+ darwin1[[0123456]].*)
+ AC_DEFINE(MACOS_SIERRA, 1, [macOS 10.12 (Sierra) or earlier])
+ ;;
+esac
+AC_SUBST(MACOS_SIERRA)
## clock_gettime is POSIX 1993, but not on macOS prior to 10.12 (Sierra)
## Some OSes need -lrt: Linux (for glibc versions before 2.17), Solaris,
## not FreeBSD.
diff --git a/doc/FAQ b/doc/FAQ
index 373c2b1..6e564c2 100644
--- a/doc/FAQ
+++ b/doc/FAQ
@@ -227,9 +227,9 @@ code and bug reports.
Since mid-1997 there has been a core group (the "R Core Team") who
can modify the R source code archive. The group currently consists of
-Doug Bates, John Chambers, Peter Dalgaard, Seth Falcon, Robert
-Gentleman, Kurt Hornik, Stefano Iacus, Ross Ihaka, Friedrich Leisch, Uwe
-Ligges, Thomas Lumley, Martin Maechler, Duncan Murdoch, Paul Murrell,
+Doug Bates, John Chambers, Peter Dalgaard, Robert Gentleman, Kurt
+Hornik, Ross Ihaka, Tomas Kalibera, Michael Lawrence, Friedrich Leisch,
+Uwe Ligges, Thomas Lumley, Martin Maechler, Martin Morgan, Paul Murrell,
Martyn Plummer, Brian Ripley, Deepayan Sarkar, Duncan Temple Lang, Luke
Tierney, and Simon Urbanek.
@@ -360,9 +360,9 @@ The 'bin/windows' directory of a CRAN site contains binaries for a base
distribution and add-on packages from CRAN to run on Windows 7 and later
(including 64-bit versions of Windows) on ix86 and x86_64 chips. The
Windows version of R was created by Robert Gentleman and Guido
-Masarotto, Brian D. Ripley made substantial contributions and it is now
-being maintained by Duncan Murdoch <murdoch@stats.uwo.ca> and other
-members of the R Core team.
+Masarotto, Brian D. Ripley and Duncan Murdoch made substantial
+contributions and it is now being maintained by other members of the R
+Core team.
The same directory has links to snapshots of the r-patched and
r-devel versions of R.
diff --git a/doc/NEWS b/doc/NEWS
index 829fda0..199cb20 100644
--- a/doc/NEWS
+++ b/doc/NEWS
@@ -1,5 +1,44 @@
R News
+CHANGES IN R 3.4.3:
+
+ INSTALLATION on a UNIX-ALIKE:
+
+ * A workaround has been added for the changes in location of
+ time-zone files in macOS 10.13 'High Sierra' and again in
+ 10.13.1, so the default time zone is deduced correctly from the
+ system setting when R is configured with --with-internal-tzcode
+ (the default on macOS).
+
+ * R CMD javareconf has been updated to recognize the use of a Java
+ 9 SDK on macOS.
+
+ BUG FIXES:
+
+ * raw(0) & raw(0) and raw(0) | raw(0) again return raw(0) (rather
+ than logical(0)).
+
+ * intToUtf8() converts integers corresponding to surrogate code
+ points to NA rather than invalid UTF-8, as well as values larger
+ than the current Unicode maximum of 0x10FFFF. (This aligns with
+ the current RFC3629.)
+
+ * Fix calling of methods on S4 generics that dispatch on ... when
+ the call contains ....
+
+ * Following Unicode 'Corrigendum 9', the UTF-8 representations of
+ U+FFFE and U+FFFF are now regarded as valid by utf8ToInt().
+
+ * range(c(TRUE, NA), finite = TRUE) and similar no longer return
+ NA. (Reported by Lukas Stadler.)
+
+ * The self starting function attr(SSlogis, "initial") now also
+ works when the y values have exact minimum zero and is slightly
+ changed in general, behaving symmetrically in the y range.
+
+ * The printing of named raw vectors is now formatted nicely as for
+ other such atomic vectors, thanks to Lukas Stadler.
+
CHANGES IN R 3.4.2:
NEW FEATURES:
diff --git a/doc/NEWS.Rd b/doc/NEWS.Rd
index 39ff97c..e703475 100644
--- a/doc/NEWS.Rd
+++ b/doc/NEWS.Rd
@@ -5,6 +5,51 @@
\title{R News}
\encoding{UTF-8}
+\section{\Rlogo CHANGES IN R 3.4.3}{
+
+ \subsection{INSTALLATION on a UNIX-ALIKE}{
+ \itemize{
+ \item A workaround has been added for the changes in location of
+ time-zone files in macOS 10.13 \sQuote{High Sierra} and
+ again in 10.13.1, so the default time zone is deduced
+ correctly from the system setting when \R is configured with
+ \option{--with-internal-tzcode} (the default on macOS).
+
+ \item \command{R CMD javareconf} has been updated to recognize the
+ use of a Java 9 SDK on macOS.
+ }
+ }
+
+ \subsection{BUG FIXES}{
+ \itemize{
+ \item \code{raw(0) & raw(0)} and \code{raw(0) | raw(0)}
+ again return \code{raw(0)} (rather than \code{logical(0)}).
+
+ \item \code{intToUtf8()} converts integers corresponding to
+ surrogate code points to \code{NA} rather than invalid UTF-8, as
+ well as values larger than the current Unicode maximum of
+ \code{0x10FFFF}. (This aligns with the current RFC3629.)
+
+ \item Fix calling of methods on S4 generics that dispatch on
+ \code{\dots} when the call contains \code{\dots}.
+
+ \item Following Unicode \sQuote{Corrigendum 9}, the UTF-8
+ representations of U+FFFE and U+FFFF are now regarded as valid by
+ \code{utf8ToInt()}.
+
+ \item \code{range(c(TRUE, NA), finite = TRUE)} and similar no longer
+ return \code{NA}. (Reported by Lukas Stadler.)
+
+ \item The self starting function \code{attr(SSlogis, "initial")}
+ now also works when the y values have exact minimum zero and is
+ slightly changed in general, behaving symmetrically in the y range.
+
+ \item The printing of named raw vectors is now formatted nicely as
+ for other such atomic vectors, thanks to Lukas Stadler.
+ }
+ }
+}
+
\section{\Rlogo CHANGES IN R 3.4.2}{
\subsection{NEW FEATURES}{
@@ -107,7 +152,7 @@
\item It is again possible to use \command{configure
--enable-maintainer-mode} without having installed
\command{notangle} (it was required in \R 3.4.[01]).
-
+
\item S4 method dispatch on \code{\dots} calls the method by name
instead of \code{.Method} (for consistency with default dispatch),
and only attempts to pass non-missing arguments from the generic.
@@ -365,7 +410,7 @@
\code{tol} in the result, and optionally parts of the internal
matrix computations.
- \item \code{addNA()} is faster now, e.g.{} when applied twice.
+ \item \code{addNA()} is faster now, e.g.\sspace{}when applied twice.
(Part of \PR{16895}.)
\item New option \code{rstandard(<lm>, type = "predicted")}
diff --git a/doc/NEWS.pdf b/doc/NEWS.pdf
index f8ed685..25e1196 100644
--- a/doc/NEWS.pdf
+++ b/doc/NEWS.pdf
Binary files differ
diff --git a/doc/html/NEWS.html b/doc/html/NEWS.html
index 39909a4..0a6872b 100644
--- a/doc/html/NEWS.html
+++ b/doc/html/NEWS.html
@@ -7,6 +7,69 @@
<h2>R News</h2>
+<h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.3</h3>
+
+
+
+<h4>INSTALLATION on a UNIX-ALIKE</h4>
+
+
+<ul>
+<li><p> A workaround has been added for the changes in location of
+time-zone files in macOS 10.13 &lsquo;High Sierra&rsquo; and
+again in 10.13.1, so the default time zone is deduced
+correctly from the system setting when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is configured with
+<span class="option">--with-internal-tzcode</span> (the default on macOS).
+</p>
+</li>
+<li> <p><code>R CMD javareconf</code> has been updated to recognize the
+use of a Java 9 SDK on macOS.
+</p>
+</li></ul>
+
+
+
+
+<h4>BUG FIXES</h4>
+
+
+<ul>
+<li> <p><code>raw(0) &amp; raw(0)</code> and <code>raw(0) | raw(0)</code>
+again return <code>raw(0)</code> (rather than <code>logical(0)</code>).
+</p>
+</li>
+<li> <p><code>intToUtf8()</code> converts integers corresponding to
+surrogate code points to <code>NA</code> rather than invalid UTF-8, as
+well as values larger than the current Unicode maximum of
+<code>0x10FFFF</code>. (This aligns with the current RFC3629.)
+</p>
+</li>
+<li><p> Fix calling of methods on S4 generics that dispatch on
+<code>...</code> when the call contains <code>...</code>.
+</p>
+</li>
+<li><p> Following Unicode &lsquo;Corrigendum 9&rsquo;, the UTF-8
+representations of U+FFFE and U+FFFF are now regarded as valid by
+<code>utf8ToInt()</code>.
+</p>
+</li>
+<li> <p><code>range(c(TRUE, NA), finite = TRUE)</code> and similar no longer
+return <code>NA</code>. (Reported by Lukas Stadler.)
+</p>
+</li>
+<li><p> The self starting function <code>attr(SSlogis, "initial")</code>
+now also works when the y values have exact minimum zero and is
+slightly changed in general, behaving symmetrically in the y range.
+</p>
+</li>
+<li><p> The printing of named raw vectors is now formatted nicely as
+for other such atomic vectors, thanks to Lukas Stadler.
+</p>
+</li></ul>
+
+
+
+
<h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.2</h3>
diff --git a/doc/html/R-admin.html b/doc/html/R-admin.html
index 6cfc720..abbbdb5 100644
--- a/doc/html/R-admin.html
+++ b/doc/html/R-admin.html
@@ -1,6 +1,6 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
-<!-- This manual is for R, version 3.4.2 (2017-09-28).
+<!-- This manual is for R, version 3.4.3 (2017-11-30).
Copyright (C) 2001-2016 R Core Team
@@ -296,11 +296,10 @@ p {
</ul></li>
<li><a name="toc-macOS-2" href="#macOS">C.3 macOS</a>
<ul class="no-bullet">
- <li><a name="toc-High-Sierra-1" href="#High-Sierra">C.3.1 High Sierra</a></li>
- <li><a name="toc-Tcl_002fTk-headers-and-libraries-1" href="#Tcl_002fTk-headers-and-libraries">C.3.2 Tcl/Tk headers and libraries</a></li>
- <li><a name="toc-Java" href="#Java-_0028macOS_0029">C.3.3 Java</a></li>
- <li><a name="toc-Frameworks-1" href="#Frameworks">C.3.4 Frameworks</a></li>
- <li><a name="toc-Building-R_002eapp-1" href="#Building-R_002eapp">C.3.5 Building R.app</a></li>
+ <li><a name="toc-Tcl_002fTk-headers-and-libraries-1" href="#Tcl_002fTk-headers-and-libraries">C.3.1 Tcl/Tk headers and libraries</a></li>
+ <li><a name="toc-Java" href="#Java-_0028macOS_0029">C.3.2 Java</a></li>
+ <li><a name="toc-Frameworks-1" href="#Frameworks">C.3.3 Frameworks</a></li>
+ <li><a name="toc-Building-R_002eapp-1" href="#Building-R_002eapp">C.3.4 Building R.app</a></li>
</ul></li>
<li><a name="toc-Solaris-1" href="#Solaris">C.4 Solaris</a>
<ul class="no-bullet">
@@ -334,7 +333,7 @@ p {
<p>This is a guide to installation and administration for R.
</p>
-<p>This manual is for R, version 3.4.2 (2017-09-28).
+<p>This manual is for R, version 3.4.3 (2017-11-30).
</p>
<p>Copyright &copy; 2001&ndash;2016 R Core Team
</p>
@@ -928,13 +927,13 @@ specified on the <code>make install</code> command line (at least for
<code>libdir</code>. The C header files can be installed to the value of
<code>rincludedir</code>: note that as the headers are not installed into a
subdirectory you probably want something like
-<code>rincludedir=/usr/local/include/R-3.4.2</code>.
+<code>rincludedir=/usr/local/include/R-3.4.3</code>.
</p>
<p>If you want the R home to be something other than
<samp><var>libdir</var>/R</samp>, use <samp>rhome</samp>: for example
</p>
<div class="example">
-<pre class="example">make install rhome=/usr/local/lib64/R-3.4.2
+<pre class="example">make install rhome=/usr/local/lib64/R-3.4.3
</pre></div>
<p>will use a version-specific R home on a non-Debian Linux 64-bit
@@ -1408,7 +1407,7 @@ conversion to short name equivalents (a.k.a. DOS 8.3 names), then R
<em>must</em> be installed in a path that does not contain spaces.
</p>
<p>Installation is <em>via</em> the installer
-<samp>R-3.4.2-win.exe</samp>. Just double-click on the icon and
+<samp>R-3.4.3-win.exe</samp>. Just double-click on the icon and
follow the instructions. When installing on a 64-bit version of Windows
the options will include 32- or 64-bit versions of R (and the default is
to install both). You can uninstall R from the Control Panel.
@@ -1475,12 +1474,12 @@ will call this directory <samp><var>R_HOME</var></samp> below.
<p>You need to collect the following sets of files:
</p><ul>
-<li> Get the R source code tarball <samp>R-3.4.2.tar.gz</samp> from
+<li> Get the R source code tarball <samp>R-3.4.3.tar.gz</samp> from
<acronym>CRAN</acronym>. Open a command window (or another shell) at directory
<var>R_HOME</var>, and run
<div class="example">
-<pre class="example">tar -xf R-3.4.2.tar.gz
+<pre class="example">tar -xf R-3.4.3.tar.gz
</pre></div>
<p>to create the source tree in <var>R_HOME</var>. <strong>Beware</strong>: do use
@@ -1489,7 +1488,7 @@ If you are using an account with administrative privileges you may get a
lot of messages which can be suppressed by
</p>
<div class="example">
-<pre class="example">tar --no-same-owner -xf R-3.4.2.tar.gz
+<pre class="example">tar --no-same-owner -xf R-3.4.3.tar.gz
</pre></div>
<a name="index-TAR_005fOPTIONS-1"></a>
@@ -1804,7 +1803,7 @@ source tree) in <samp>src/gnuwin32/installer</samp> run
installation (in double quotes if it contains spaces or backslashes).
</p>
<p>Both methods create an executable with a standard name such as
-<samp>R-3.4.2-win.exe</samp>, so please rename it to indicate that
+<samp>R-3.4.3-win.exe</samp>, so please rename it to indicate that
it is customized. If you intend to <em>distribute</em> a customized
installer please do check that license requirements are met &ndash; note that
the installer will state that the contents are distributed under GPL
@@ -1863,21 +1862,21 @@ make msi
</pre></div>
<p>which will result in a file with a name like
-<samp>R-3.4.2-win32.msi</samp>. This can be double-clicked to be
+<samp>R-3.4.3-win32.msi</samp>. This can be double-clicked to be
installed, but those who need it will know what to do with it (usually
by running <code>msiexec /i</code> with additional options). Properties
that users might want to set from the <code>msiexec</code> command line
include &lsquo;<samp>ALLUSERS</samp>&rsquo;, &lsquo;<samp>INSTALLDIR</samp>&rsquo; (something like
-<samp>c:\Program Files\R\R-3.4.2</samp>) and &lsquo;<samp>RMENU</samp>&rsquo; (the path
+<samp>c:\Program Files\R\R-3.4.3</samp>) and &lsquo;<samp>RMENU</samp>&rsquo; (the path
to the &lsquo;<samp>R</samp>&rsquo; folder on the start menu) and &lsquo;<samp>STARTDIR</samp>&rsquo; (the
starting directory for R shortcuts, defaulting to something like
<samp>c:\Users\name\Documents\R</samp>).
</p>
<p>The MSI installer can be built both from a 32-bit build of R
-(<samp>R-3.4.2-win32.msi</samp>) and from a 64-bit build of R
-(<samp>R-3.4.2-win64.msi</samp>, optionally including 32-bit files
+(<samp>R-3.4.3-win32.msi</samp>) and from a 64-bit build of R
+(<samp>R-3.4.3-win64.msi</samp>, optionally including 32-bit files
by setting the macro <code>HOME32</code>, when the name is
-<samp>R-3.4.2-win.msi</samp>). Unlike the main installer, a 64-bit
+<samp>R-3.4.3-win.msi</samp>). Unlike the main installer, a 64-bit
MSI installer can only be run on 64-bit Windows.
</p>
<p>Thanks to David del Campo (Dept of Statistics, University of Oxford)
@@ -1947,7 +1946,7 @@ Windows&rsquo; CRLF line endings.
<p>(&lsquo;macOS&rsquo; was known as &lsquo;OS X&rsquo; from 2012&ndash;2016 and as &lsquo;Mac OS X&rsquo; before that.)
</p>
<p>The front page of a <acronym>CRAN</acronym> site has a link &lsquo;Download R for OS
-X&rsquo;. Click on that, then download the file <samp>R-3.4.2.pkg</samp>
+X&rsquo;. Click on that, then download the file <samp>R-3.4.3.pkg</samp>
and install it. This runs on macOS 10.11 and later (El Capitan, Sierra,
High Sierra, &hellip;).
</p>
@@ -1989,10 +1988,6 @@ are not often used on macOS) such as <code>png(type = &quot;cairo&quot;)</code>.
perhaps XQuartz): the installer may tailor the installation to the
current version of the OS.
</p>
-<p>When running under High Sierra (10.13), R may not be able to deduce
-the system timezone, in which case you will need to set the environment
-variable <code>TZ</code>: see <code>?Sys.timezone</code>.
-</p>
<p>For building R from source, see <a href="#macOS">macOS</a>.
</p>
@@ -2997,7 +2992,7 @@ in most of the Chinese-speaking world.
<p>macOS supports locales in its own particular way, but the R GUI tries to
make this easier for users. See
-<a href="https://developer.apple.com/documentation/MacOSX/Conceptual/BPInternational/">https://developer.apple.com/documentation/MacOSX/Conceptual/BPInternational/</a>
+<a href="https://developer.apple.com/library/content/documentation/MacOSX/Conceptual/BPInternational/">https://developer.apple.com/library/content/documentation/MacOSX/Conceptual/BPInternational/</a>
for how users can set their locales. As with Windows, end users will
generally only see lists of languages/territories. Users of R in a
terminal may need to set the locale to something like &lsquo;<samp>en_GB.UTF-8</samp>&rsquo;
@@ -4937,8 +4932,8 @@ reinstalled when macOS is upgraded, as upgrading partially removes them.)
binary components are available from
<a href="https://r.research.att.com/libs">https://r.research.att.com/libs</a>: you will need <code>pcre</code> and
<code>xz</code> (for <code>libzma</code>) as recent macOS versions provide libraries
-but not headers for these (and the system <code>pcre</code> is too old at
-version 8.02).
+but not headers for these (and the system <code>pcre</code> is too old at 8.02
+for versions up to Sierra, although High Sierra has 8.40).
</p>
<p>An X sub-system is required unless configuring using
<samp>--without-x</samp>: see <a href="https://xquartz.macosforge.org/">https://xquartz.macosforge.org/</a>. R&rsquo;s
@@ -5005,7 +5000,7 @@ FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
</p>
<p>More recent and complete distributions of <code>clang</code> are often
available from <a href="http://llvm.org/releases/">http://llvm.org/releases/</a>: for example at the time
-of writing for 4.0.1, built for Sierra or later. In particular, these
+of writing of 5.0.0 built for Sierra or later. In particular, these
should include support for OpenMP. Another build of clang 4.0.0 is
available at
<a href="https://r.research.att.com/libs/clang-4.0.0-darwin15.6-Release.tar.gz">https://r.research.att.com/libs/clang-4.0.0-darwin15.6-Release.tar.gz</a>.
@@ -5100,24 +5095,10 @@ some upgrades but not others).
</p>
-
-<hr>
-<a name="High-Sierra"></a>
-<a name="High-Sierra-1"></a>
-<h4 class="subsection">C.3.1 High Sierra</h4>
-
-<p>Default builds<a name="DOCF73" href="#FOOT73"><sup>73</sup></a> of R on High Sierra fail
-to detect the system time zone, as it gets reported something like
-</p><div class="example">
-<pre class="example"> unknown timezone 'default/Europe/London'
-</pre></div>
-<p>which is not a standard form. This can be circumvented by setting the
-environment variable <code>TZ</code> (in the example, to &lsquo;<samp>Europe/London</samp>&rsquo;.
-</p>
<hr>
<a name="Tcl_002fTk-headers-and-libraries"></a>
<a name="Tcl_002fTk-headers-and-libraries-1"></a>
-<h4 class="subsection">C.3.2 Tcl/Tk headers and libraries</h4>
+<h4 class="subsection">C.3.1 Tcl/Tk headers and libraries</h4>
<p>If you plan to use the <code>tcltk</code> package for R, you need to
install a distribution of Tcl/Tk. There are two alternatives. If you
@@ -5164,9 +5145,9 @@ tclvalue(.Tcl(&quot;tk windowingsystem&quot;)) # &quot;x11&quot; or &quot;aqua&
<hr>
<a name="Java-_0028macOS_0029"></a>
<a name="Java"></a>
-<h4 class="subsection">C.3.3 Java</h4>
+<h4 class="subsection">C.3.2 Java</h4>
-<p>The situation with Java support on macOS is messy.<a name="DOCF74" href="#FOOT74"><sup>74</sup></a> As from
+<p>The situation with Java support on macOS is messy.<a name="DOCF73" href="#FOOT73"><sup>73</sup></a> As from
R 3.4.0 the <acronym>CRAN</acronym> distribution of <a href="https://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> requires
Java 8 (aka 1.8).
</p>
@@ -5174,13 +5155,13 @@ Java 8 (aka 1.8).
upgrade may remove one if already installed: it is intended to be
installed at first use. Check if a JRE is installed by running
<code>java -version</code> in a <code>Terminal</code> window: if Java is not
-installed<a name="DOCF75" href="#FOOT75"><sup>75</sup></a> this should
-prompt you to install it. You can also install directly the latest Java
-from Oracle (currently from
+installed<a name="DOCF74" href="#FOOT74"><sup>74</sup></a>
+this should prompt you to install it. You can also install directly the
+latest Java from Oracle (currently from
<a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">http://www.oracle.com/technetwork/java/javase/downloads/index.html</a>).
</p>
<p>Binary distributions of R are built against a specific version (e.g.
-1.8.0_131) of Oracle Java so <code>sudo R CMD javareconf</code> may be
+1.8.0_121) of Oracle Java so <code>sudo R CMD javareconf</code> may be
needed before using Java-using packages.
</p>
@@ -5196,14 +5177,21 @@ compiling JNI programs (used by packages <a href="https://CRAN.R-project.org/pac
JRE.
</p>
<p>The build process tries to fathom out what JRE/JDK to use, but it may
-need some help, e.g. by setting <code>JAVA_HOME</code>. The Oracle JDK can
+need some help, e.g. by setting <code>JAVA_HOME</code>. An Oracle JDK can
be specified explicitly by something like
</p><div class="example">
-<pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home
+<pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home
JAVA_CPPFLAGS=&quot;-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin&quot;
JAVA_LD_LIBRARY_PATH=&quot;${JAVA_HOME}/jre/lib/server&quot;
JAVA_LIBS=&quot;-L/${JAVA_HOME}/jre/lib/server -ljvm&quot;
</pre></div>
+<p>or
+</p><div class="example">
+<pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home
+JAVA_CPPFLAGS=&quot;-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin&quot;
+JAVA_LD_LIBRARY_PATH=&quot;${JAVA_HOME}/lib/server&quot;
+JAVA_LIBS=&quot;-L/${JAVA_HOME}/lib/server -ljvm&quot;
+</pre></div>
<p>in <samp>config.site</samp>.
</p>
<p>(An Apple JRE, if available, can be specified explicitly by something
@@ -5223,7 +5211,7 @@ JAVA_LIBS=&quot;-framework JavaVM&quot;
<hr>
<a name="Frameworks"></a>
<a name="Frameworks-1"></a>
-<h4 class="subsection">C.3.4 Frameworks</h4>
+<h4 class="subsection">C.3.3 Frameworks</h4>
<p>The <acronym>CRAN</acronym> build of R is installed as a framework, which is
selected by the option
@@ -5256,7 +5244,7 @@ to <code>pkg-config</code>).
<hr>
<a name="Building-R_002eapp"></a>
<a name="Building-R_002eapp-1"></a>
-<h4 class="subsection">C.3.5 Building R.app</h4>
+<h4 class="subsection">C.3.4 Building R.app</h4>
<p>Note that building the <small>R.APP</small> GUI console is a separate project, using
Xcode. Before compiling <small>R.APP</small> make sure the current version of R
@@ -5290,11 +5278,11 @@ in the <samp>/Applications</samp> folder.
<p>R has been built successfully on Solaris 10 using the (zero cost)
-Oracle Developer Studio<a name="DOCF76" href="#FOOT76"><sup>76</sup></a> compilers: there has been some success with
+Oracle Developer Studio<a name="DOCF75" href="#FOOT75"><sup>75</sup></a> compilers: there has been some success with
<code>gcc</code>/<code>gfortran</code>. (Recent Sun machines are AMD Opterons
or Intel Xeons (&lsquo;<samp>amd64</samp>&rsquo;) rather than &lsquo;<samp>x86</samp>&rsquo;, but 32-bit
&lsquo;<samp>x86</samp>&rsquo; executables are the default.) How these compilers
-identify<a name="DOCF77" href="#FOOT77"><sup>77</sup></a> themselves is slightly
+identify<a name="DOCF76" href="#FOOT76"><sup>76</sup></a> themselves is slightly
confusing: Solaris Studio versions 12.3 and 12.4 report C++ 5.12 and
5.13, and Developer Studio 12.5 reports C++ 5.14. We will only consider
12.5 (May 2016): instructions for 12.3 can be found in versions of this
@@ -5422,7 +5410,7 @@ selected as LAPACK <em>via</em>
</pre></div>
<p>This has often given test failures in the past, in several different
-places.<a name="DOCF78" href="#FOOT78"><sup>78</sup></a>
+places.<a name="DOCF77" href="#FOOT77"><sup>77</sup></a>
</p>
<p>Parsing very complex R expressions needs a lot of stack space when
the Oracle compilers are used: several packages require the stack
@@ -5483,7 +5471,7 @@ version of Solaris in use. (This can be ascertained from <code>gcc
several reports of problems were due to using <code>gcc</code> compiled on
one version of Solaris on a later version. Note that this can even
apply to OS patches: some 2016 patches to Solaris 10 changed its C
-header files in way incompatible<a name="DOCF79" href="#FOOT79"><sup>79</sup></a> with the modified versions included with OpenCSW&rsquo;s
+header files in way incompatible<a name="DOCF78" href="#FOOT78"><sup>78</sup></a> with the modified versions included with OpenCSW&rsquo;s
binary distribution.
</p>
<p>The notes here are for <code>gcc</code> set up to use the Solaris linker:
@@ -5780,7 +5768,7 @@ will not need to build add-on packages from source; see <a href="#Add_002don-pac
</p>
<p>We have found that the build process for R is quite sensitive to
the choice of tools: please follow our instructions <strong>exactly</strong>,
-even to the choice of particular versions of the tools.<a name="DOCF80" href="#FOOT80"><sup>80</sup></a> The build process for add-on packages is somewhat more
+even to the choice of particular versions of the tools.<a name="DOCF79" href="#FOOT79"><sup>79</sup></a> The build process for add-on packages is somewhat more
forgiving, but we recommend using the exact toolset at first, and only
substituting other tools once you are familiar with the process.
</p>
@@ -5833,7 +5821,7 @@ use filepaths containing spaces: you can always use the short forms
<p>It is essential that the directory containing the command line tools
comes first or second in the path: there are typically like-named
-tools<a name="DOCF81" href="#FOOT81"><sup>81</sup></a> in other directories, and they will <strong>not</strong>
+tools<a name="DOCF80" href="#FOOT80"><sup>80</sup></a> in other directories, and they will <strong>not</strong>
work. The ordering of the other directories is less important, but if in
doubt, use the order above.
</p>
@@ -5882,7 +5870,7 @@ install LaTeX packages on first use.
<a name="The-Inno-Setup-installer-1"></a>
<h3 class="section">D.2 The Inno Setup installer</h3>
-<p>To make the installer package (<samp>R-3.4.2-win.exe</samp>) we
+<p>To make the installer package (<samp>R-3.4.3-win.exe</samp>) we
currently require the Unicode version of Inno Setup 5.3.7 or later from
<a href="http://jrsoftware.org/">http://jrsoftware.org/</a>. This is <em>not</em> included in
<samp>Rtools*.exe</samp>.
@@ -6533,7 +6521,7 @@ versions 3.4.0 to 3.10.1 are compatible.</p>
<p>as well as its equivalence to the <code>Rcomplex</code>
structure defined in <samp>R_ext/Complex.h</samp>.</p>
<h3><a name="FOOT61" href="#DOCF61">(61)</a></h3>
-<p>at the time of revsion of
+<p>at the time of revision of
this para in 2017, <strong>autoconf-2.69</strong> from 2012 and <strong>automake-1.15</strong>
from 2015.</p>
<h3><a name="FOOT62" href="#DOCF62">(62)</a></h3>
@@ -6577,34 +6565,30 @@ not needed for <code>clang</code> 4.0.0, though.</p>
<p>E.g. <em>via</em> <code>tlmgr install cm-super helvetic
inconsolata texinfo</code> .</p>
<h3><a name="FOOT73" href="#DOCF73">(73)</a></h3>
-<p>This is not the case if the non-default
-<code>configure</code> option <samp>--without-internal-tzcode</samp> was used
-&ndash; but R then does not pass its checks.</p>
-<h3><a name="FOOT74" href="#DOCF74">(74)</a></h3>
<p>For more
details see <a href="http://www.macstrategy.com/article.php?3">http://www.macstrategy.com/article.php?3</a>.</p>
-<h3><a name="FOOT75" href="#DOCF75">(75)</a></h3>
+<h3><a name="FOOT74" href="#DOCF74">(74)</a></h3>
<p>In the unlikely event that the version reported does
-not start with <code>1.8.0</code> you need to update your Java.</p>
-<h3><a name="FOOT76" href="#DOCF76">(76)</a></h3>
+not start with <code>1.8.0</code> or <code>9</code> you need to update your Java.</p>
+<h3><a name="FOOT75" href="#DOCF75">(75)</a></h3>
<p>Oracle Solaris Studio prior to 2016,
and previously Sun Studio.</p>
-<h3><a name="FOOT77" href="#DOCF77">(77)</a></h3>
+<h3><a name="FOOT76" href="#DOCF76">(76)</a></h3>
<p>using the <samp>-V</samp> flag.</p>
-<h3><a name="FOOT78" href="#DOCF78">(78)</a></h3>
+<h3><a name="FOOT77" href="#DOCF77">(77)</a></h3>
<p>When last checked it failed in <samp>tests/reg-BLAS.R</samp>,
and on some builds, including for &lsquo;<samp>amd64</samp>&rsquo;, it failed in
<code>example(eigen)</code>.</p>
-<h3><a name="FOOT79" href="#DOCF79">(79)</a></h3>
+<h3><a name="FOOT78" href="#DOCF78">(78)</a></h3>
<p>In particular, header
<samp>cmath</samp> in C++11 mode includes <samp>math.h</samp> and
<samp>iso/math_c99.h</samp> and <code>gcc</code> had &lsquo;fixed&rsquo; an earlier version
of the latter.</p>
-<h3><a name="FOOT80" href="#DOCF80">(80)</a></h3>
+<h3><a name="FOOT79" href="#DOCF79">(79)</a></h3>
<p>For
example, the Cygwin version of <code>make 3.81</code> fails to work
correctly.</p>
-<h3><a name="FOOT81" href="#DOCF81">(81)</a></h3>
+<h3><a name="FOOT80" href="#DOCF80">(80)</a></h3>
<p>such as <code>sort</code>, <code>find</code> and perhaps
<code>make</code>.</p>
</div>
diff --git a/doc/manual/R-FAQ.texi b/doc/manual/R-FAQ.texi
index 498ec4f..e30ff00 100644
--- a/doc/manual/R-FAQ.texi
+++ b/doc/manual/R-FAQ.texi
@@ -262,9 +262,9 @@ by sending code and bug reports.
Since mid-1997 there has been a core group (the ``R Core Team'') who can
modify the R source code archive. The group currently consists of Doug
-Bates, John Chambers, Peter Dalgaard, Seth Falcon, Robert Gentleman,
-Kurt Hornik, Stefano Iacus, Ross Ihaka, Friedrich Leisch, Uwe Ligges,
-Thomas Lumley, Martin Maechler, Duncan Murdoch, Paul Murrell, Martyn
+Bates, John Chambers, Peter Dalgaard, Robert Gentleman,
+Kurt Hornik, Ross Ihaka, Tomas Kalibera, Michael Lawrence, Friedrich Leisch, Uwe Ligges,
+Thomas Lumley, Martin Maechler, Martin Morgan, Paul Murrell, Martyn
Plummer, Brian Ripley, Deepayan Sarkar, Duncan Temple Lang, Luke
Tierney, and Simon Urbanek.
@@ -461,10 +461,9 @@ The @file{bin/windows} directory of a @CRAN{} site contains binaries for
a base distribution and add-on packages from @CRAN{} to run on Windows
7 and later (including 64-bit versions of Windows) on ix86 and x86_64
chips. The Windows version of R was created by Robert Gentleman and
-Guido Masarotto, Brian D. Ripley made substantial contributions
-and it is now being maintained by
-@email{murdoch@@stats.uwo.ca, Duncan Murdoch} and other members
-of the R Core team.
+Guido Masarotto, Brian D. Ripley and Duncan Murdoch made substantial
+contributions and it is now being maintained by
+other members of the R Core team.
The same directory has links to snapshots of the r-patched and r-devel
versions of R.
diff --git a/doc/manual/R-admin.texi b/doc/manual/R-admin.texi
index 0d5cd8b..8b165d7 100644
--- a/doc/manual/R-admin.texi
+++ b/doc/manual/R-admin.texi
@@ -1788,10 +1788,6 @@ If you update your macOS version, you should re-install @R{} (and
perhaps XQuartz): the installer may tailor the installation to the
current version of the OS.
-When running under High Sierra (10.13), @R{} may not be able to deduce
-the system timezone, in which case you will need to set the environment
-variable @env{TZ}: see @code{?Sys.timezone}.
-
For building @R{} from source, see @ref{macOS}.
@@ -2842,7 +2838,7 @@ in most of the Chinese-speaking world.
macOS supports locales in its own particular way, but the @R{} GUI tries to
make this easier for users. See
-@uref{https://developer.apple.com/@/documentation/@/MacOSX/@/Conceptual/@/BPInternational/}
+@uref{https://developer.apple.com/@/library/@/content/@/documentation/@/MacOSX/@/Conceptual/@/BPInternational/}
for how users can set their locales. As with Windows, end users will
generally only see lists of languages/territories. Users of @R{} in a
terminal may need to set the locale to something like @samp{en_GB.UTF-8}
@@ -4489,7 +4485,7 @@ File @file{configure} is created from @file{configure.ac} and the files
under @file{m4} by @command{autoconf} and @command{aclocal} (part of the
@pkg{automake} package). There is a formal version requirement on
@command{autoconf} of 2.62 or later, but it is unlikely that anything
-other than the most recent versions@footnote{at the time of revsion of
+other than the most recent versions@footnote{at the time of revision of
this para in 2017, @pkg{autoconf-2.69} from 2012 and @pkg{automake-1.15}
from 2015.} have been thoroughly tested.
@@ -4873,8 +4869,8 @@ will make use of it if GNU readline is not found.} That and other
binary components are available from
@uref{https://r.research.att.com/libs}: you will need @code{pcre} and
@code{xz} (for @code{libzma}) as recent macOS versions provide libraries
-but not headers for these (and the system @code{pcre} is too old at
-version 8.02).
+but not headers for these (and the system @code{pcre} is too old at 8.02
+for versions up to Sierra, although High Sierra has 8.40).
An X sub-system is required unless configuring using
@option{--without-x}: see @uref{https://xquartz.macosforge.org/}. @R{}'s
@@ -4947,7 +4943,7 @@ FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
More recent and complete distributions of @command{clang} are often
available from @uref{http://llvm.org/releases/}: for example at the time
-of writing for 4.0.1, built for Sierra or later. In particular, these
+of writing of 5.0.0 built for Sierra or later. In particular, these
should include support for OpenMP. Another build of clang 4.0.0 is
available at
@uref{https://r.research.att.com/@/libs/@/clang-4.0.0-darwin15.6-Release.tar.gz}.
@@ -5051,29 +5047,13 @@ some upgrades but not others).
@menu
-* High Sierra::
* Tcl/Tk headers and libraries::
* Java (macOS)::
* Frameworks::
* Building R.app::
@end menu
-
-@node High Sierra, Tcl/Tk headers and libraries, macOS, macOS
-@subsection High Sierra
-
-Default builds@footnote{This is not the case if the non-default
-@command{configure} option @option{--without-internal-tzcode} was used
--- but @R{} then does not pass its checks.} of @R{} on High Sierra fail
-to detect the system time zone, as it gets reported something like
-@example
- unknown timezone 'default/Europe/London'
-@end example
-@noindent
-which is not a standard form. This can be circumvented by setting the
-environment variable @env{TZ} (in the example, to @samp{Europe/London}.
-
-@node Tcl/Tk headers and libraries, Java (macOS), High Sierra, macOS
+@node Tcl/Tk headers and libraries, Java (macOS), macOS, macOS
@subsection Tcl/Tk headers and libraries
If you plan to use the @code{tcltk} package for @R{}, you need to
@@ -5132,13 +5112,13 @@ upgrade may remove one if already installed: it is intended to be
installed at first use. Check if a JRE is installed by running
@command{java -version} in a @command{Terminal} window: if Java is not
installed@footnote{In the unlikely event that the version reported does
-not start with @code{1.8.0} you need to update your Java.} this should
-prompt you to install it. You can also install directly the latest Java
-from Oracle (currently from
+not start with @code{1.8.0} or @code{9} you need to update your Java.}
+this should prompt you to install it. You can also install directly the
+latest Java from Oracle (currently from
@uref{http://www.oracle.com/@/technetwork/@/java/@/javase/@/downloads/@/index.html}).
Binary distributions of @R{} are built against a specific version (e.g.@:
-1.8.0_131) of Oracle Java so @command{sudo R CMD javareconf} may be
+1.8.0_121) of Oracle Java so @command{sudo R CMD javareconf} may be
needed before using Java-using packages.
@c You may need to install what Apple calls `legacy Java'@footnote{e.g.@:
@@ -5158,14 +5138,23 @@ compiling JNI programs (used by packages @CRANpkg{rJava} and
JRE.
The build process tries to fathom out what JRE/JDK to use, but it may
-need some help, e.g.@: by setting @env{JAVA_HOME}. The Oracle JDK can
+need some help, e.g.@: by setting @env{JAVA_HOME}. An Oracle JDK can
be specified explicitly by something like
@example
-JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home
+JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home
JAVA_CPPFLAGS="-I/$@{JAVA_HOME@}/include -I/$@{JAVA_HOME@}/include/darwin"
JAVA_LD_LIBRARY_PATH="$@{JAVA_HOME@}/jre/lib/server"
JAVA_LIBS="-L/$@{JAVA_HOME@}/jre/lib/server -ljvm"
@end example
+@noindent
+or
+@example
+JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home
+JAVA_CPPFLAGS="-I/$@{JAVA_HOME@}/include -I/$@{JAVA_HOME@}/include/darwin"
+JAVA_LD_LIBRARY_PATH="$@{JAVA_HOME@}/lib/server"
+JAVA_LIBS="-L/$@{JAVA_HOME@}/lib/server -ljvm"
+@end example
+@noindent
in @file{config.site}.
(An Apple JRE, if available, can be specified explicitly by something
diff --git a/doc/manual/R-exts.texi b/doc/manual/R-exts.texi
index 2cdeb68..a77bfb3 100644
--- a/doc/manual/R-exts.texi
+++ b/doc/manual/R-exts.texi
@@ -738,8 +738,10 @@ combined @emph{via} @samp{,} (see below for an example). For versioned
licenses, one can also specify the name followed by the version, or
combine an existing abbreviation and the version with a @samp{-}.
-Abbreviations @code{GPL} and @code{LGPL} are ambiguous and usually taken
-to mean any version of the license: but it is better not to use them.
+Abbreviations @code{GPL} and @code{LGPL} are ambiguous and
+usually@footnote{@acronym{CRAN} expands them to e.g.@: @code{GPL-2
+| GPL-3}.} taken to mean any version of the license: but it is better
+not to use them.
@item
One of the strings @samp{file LICENSE} or @samp{file LICENCE} referring
to a file named @file{LICENSE} or @file{LICENCE} in the package (source
@@ -2478,9 +2480,9 @@ features which are not otherwise implemented in C++, and C++ compilers
commonly accept C99 extensions to C++98. A minor update@footnote{The
changes are linked from
@uref{https://isocpp.org/@/std/@/standing-documents/@/sd-6-sg10-feature-test-recommendations}.}
-to C++11 (C++14) was published in December 2014. The next standard has
-been sent to ISO and is likely to be approved in 2017: it is informally
-known as C++17.
+to C++11 (C++14) was published in December 2014. The next standard
+(C++17) was approved in Sept 2017 and will be published by ISO in due
+course.
What standard a C++ compiler aims to support can be hard to determine:
the value@footnote{Values @code{199711}, @code{201103L} and
@@ -2495,7 +2497,8 @@ native@footnote{Some distributions, notably Debian, have supplied a
build of @command{clang} with @command{g++}'s headers and library.
Conversely, Apple's command named @command{g++} is based on
@command{clang} using @code{libc++}.} @code{libc++} headers and library
-includes many C++11 features, and does not support TR1.
+includes most C++14 features, and does not support TR1. As from version
+6.0.0, @command{clang} is expected to default to C++14.
Since version 3.1.0, @R{} has provided support for C++11 in packages in
addition to C++98. This support is not uniform across platforms as it
@@ -2625,7 +2628,7 @@ SystemRequirements: C++14
@end example
@noindent
in the @file{DESCRIPTION} file. Finally, the C++14 compiler can be
-used systematically by setting the environment variable @env{USE_CXX17}.
+used systematically by setting the environment variable @env{USE_CXX14}.
Note that code written for C++11 that emulates features of C++14 will
not necessarily compile under a C++14 compiler@footnote{As from @R{}
@@ -4380,7 +4383,8 @@ interfaces to @R{}'s RNGs described in @ref{Random numbers}. In
particular, if more than one package initializes the system RNG (e.g.@:
@emph{via} @code{srand}), they will interfere with each other.
-Nor should the C++11 random number library be used.
+Nor should the C++11 random number library be used, nor any other
+third-party random number generators such as those in GSL.
@item
Errors in memory allocation and reading/writing outside arrays are very
@@ -4528,9 +4532,13 @@ suitable test for packages using @CRANpkg{rJava} would be
@example
.jinit()
jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
-jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))
-if(jvn < 1.8) stop("Java 8 is needed for this package but not available")
+if(substr(jv, 1L, 1L) == "1") @{
+ jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))
+ if(jvn < 1.8) stop("Java 8 is needed for this package but not available")
+@}
@end example
+@noindent
+(Java 9 changed the format of this string.)
Some packages have stated a requirement on a particular JDK, but a
package should only be requiring a JRE unless providing its own Java
@@ -8411,6 +8419,17 @@ Recent versions@footnote{including @command{gcc} 7.1 and @command{clang}
added the flag @option{-fsanitize-address-use-after-scope}: see
@uref{https://github.com/@/google/@/sanitizers/@/wiki/@/AddressSanitizerUseAfterScope}.
+One of the checks done by ASAN is that @code{malloc/free} and in C++
+@code{new/delete} and @code{new[]/delete[]} are used consistently
+(rather than say @code{free} being used to dealloc memory allocated by
+@code{new[]}). This matters on some systems but not all: unfortunately
+on some of those where it does not matter, system libraries@footnote{for
+example, X11/GL libraries on Linux, seen when checking package
+@CRANpkg{rgl} and some others using it---a workaround is to set
+environment variable @env{RGL_USE_NULL=true}.} are not consistent. The
+check can be suppressed by including @samp{alloc_dealloc_mismatch=0} in
+@env{ASAN_OPTIONS}.
+
@menu
* Using Leak Sanitizer::
@end menu
@@ -8439,7 +8458,8 @@ and as the parser retains some memory to the end of the process, if @R{}
itself was built against ASan, all runs will have a failure error status
(which may include running @R{} as part of building @R{} itself).
-To disable both this and some strict checking use
+To disable this, allocation-mismatch checking and some strict C++
+checking use
@example
setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_odr_violation=0'
@@ -8515,7 +8535,7 @@ See
Instrumentation Options') for the options supported by GCC: 6 and 7 support
@example
-fsanitize=alignment,bool,bounds,enum,integer-divide-by-zero,
-nonnull-attribute,null,object-size, return,returns-nonnull-attribute,
+nonnull-attribute,null,object-size,return,returns-nonnull-attribute,
shift,signed-integer-overflow,unreachable,vla-bound,vptr
@end example
@noindent
@@ -8531,8 +8551,10 @@ where @code{float-divide-by-zero} is not desirable for @R{} uses and
@c and @code{vptr} checks produced many warnings on GCC's own C++ headers,
@c so should be disabled.
-From GCC 8 @code{signed-integer-overflow} will no longer be a default part
-of @option{-fsanitize=undefined}, but can be specified separately.
+From GCC 8 @code{signed-integer-overflow} will no longer be a default
+part of @option{-fsanitize=undefined}, but can be specified separately.
+It adds options @option{-fsanitize=pointer-overflow} an
+@option{-fsanitize=builtin}.
Other useful flags include
@example
@@ -8561,6 +8583,11 @@ For more details on the topic see
@uref{http://blog.llvm.org/@/2011/@/05/@/what-every-c-programmer-should-know.html}
(which has 3 parts).
+It may or may not be possible to build @R{} itself with
+@option{-fsanitize=undefined}: when last tried it worked with
+@command{clang} but there were problems with OpenMP-using code with
+@command{gcc}.
+
@node Other analyses with `clang', Using `Dr. Memory', Using Undefined Behaviour Sanitizer, Checking memory access
@subsection Other analyses with `clang'
@@ -8777,9 +8804,7 @@ Continue execution of @R{} by typing @kbd{signal 0@key{RET}}.
@end itemize
Under Windows signals may not be able to be used, and if so the procedure is
-more complicated. See the rw-FAQ and
-@uref{http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/gdb.shtml,
-@code{www.stats.uwo.ca/faculty/murdoch/@/software/@/debuggingR/@/gdb.shtml}}.
+more complicated. See the rw-FAQ.
@node Inspecting R objects, , Finding entry points, Debugging compiled code
@@ -10021,9 +10046,8 @@ Under Windows the same commands work, but @file{Makevars.win} will be
used in preference to @file{Makevars}, and only @file{src/Makefile.win}
will be used by @code{R CMD INSTALL} with @file{src/Makefile} being
ignored. For past experiences of building DLLs with a variety of
-compilers, see file @samp{README.packages} and
-@uref{http://www.stats.uwo.ca/@/faculty/@/murdoch/@/software/@/compilingDLLs/}
-. Under Windows you can supply an exports definitions file called
+compilers, see file @samp{README.packages}.
+Under Windows you can supply an exports definitions file called
@file{@var{dllname}-win.def}: otherwise all entry points in objects (but
not libraries) supplied to @code{R CMD SHLIB} will be exported from the
DLL. An example is @file{stats-win.def} for the @pkg{stats} package: a
diff --git a/doc/manual/R-ints.texi b/doc/manual/R-ints.texi
index 1b1557d..262a369 100644
--- a/doc/manual/R-ints.texi
+++ b/doc/manual/R-ints.texi
@@ -225,7 +225,9 @@ solely of a simple type such as an atomic vector or function.
@node Rest of header, The 'data', SEXPTYPEs, SEXPs
@subsection Rest of header
-The @code{sxpinfo} header is defined as a 32-bit C structure by
+Note that the size and structure of the header will change in @R{} 3.5.0.
+
+The @code{sxpinfo} header is currently defined as a 32-bit C structure by
@example
struct sxpinfo_struct @{
@@ -254,8 +256,8 @@ The @code{trace} bit is used for functions for @code{trace()} and for
other objects when tracing duplications (see @code{tracemem}).
@findex spare bit
-The @code{spare} bit is used for closures to mark them for one
-time debugging.
+The @code{spare} bit is used for closures to mark them for one-time
+debugging.
@findex named bit
@findex NAMED
diff --git a/doc/manual/rw-FAQ.texi b/doc/manual/rw-FAQ.texi
index 604142a..d6ea6df 100644
--- a/doc/manual/rw-FAQ.texi
+++ b/doc/manual/rw-FAQ.texi
@@ -1100,7 +1100,7 @@ C/C++/Fortran code which needs compilation can simply be installed by
pkgname} at a Windows command prompt. For packages with code that needs
compilation you will need to collect and install several tools: you can
download them via the portal at
-@uref{http://www.murdoch-sutherland.com/Rtools/}. Once you have done
+@uref{https://cran.r-project.org/bin/windows/Rtools/}. Once you have done
so, just run @command{R CMD INSTALL pkgname} at a Windows command
prompt. To check the package (including running all the examples on its
help pages and in its test suite, if any) use @command{R CMD check
@@ -1778,10 +1778,6 @@ drop control back to the debugger does not work with a MinGW version of
@end itemize
-See
-@uref{http://www.stats.uwo.ca/@/faculty/@/murdoch/@/software/@/debuggingR/@/gdb.shtml}
-for some further details.
-
@node How do I include C++ code?, The output from my C code disappears., How do I debug code that I have compiled and dyn.load-ed?, Building from Source
@section How do I include C++ code?
diff --git a/share/texmf/bibtex/bib/RJournal.bib b/share/texmf/bibtex/bib/RJournal.bib
index 438d6f4..37390eb 100644
--- a/share/texmf/bibtex/bib/RJournal.bib
+++ b/share/texmf/bibtex/bib/RJournal.bib
@@ -100,6 +100,212 @@
}
+
+@article{RJ-2017-042,
+ author = {Aurélie Siberchicot and Alice Julien-Laferrière and Anne-
+ Béatrice Dufour and Jean Thioulouse and Stéphane Dray},
+ title = {{adegraphics: An S4 Lattice-Based Package for the
+ Representation of Multivariate Data}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-042/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-043,
+ author = {Mirta Benšić and Petar Taler and Safet Hamedović and
+ Emmanuel Karlo Nyarko and Kristian Sabo},
+ title = {{LeArEst: Length and Area Estimation from Data Measured with
+ Additive Error}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-043/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-044,
+ author = {Guillermo Basulto-Elias and Alicia Carriquiry and Kris De
+ Brabanter and Daniel J. Nordman},
+ title = {{fourierin: An R package to compute Fourier integrals}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-044/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-045,
+ author = {Rafael Benítez and Vicente J. Bolós and José-Luis Toca-
+ Herrera},
+ title = {{afmToolkit: an R Package for Automated AFM Force-Distance
+ Curves Analysis}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-045/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-046,
+ author = {Patrick Breheny and Woodrow Burchett},
+ title = {{Visualization of Regression Models Using visreg}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-046/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-047,
+ author = {Michael Hahsler},
+ title = {{arulesViz: Interactive Visualization of Association Rules
+ with R}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-047/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-048,
+ author = {Muhammad Imdadullah and Muhammad Aslam and Saima Altaf},
+ title = {{liureg: A Comprehensive R Package for the Liu Estimation of
+ Linear Regression Model with Collinear Regressors}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-048/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-049,
+ author = {Pablo J. Villacorta},
+ title = {{The welchADF Package for Robust Hypothesis Testing in
+ Unbalanced Multivariate Mixed Models with Heteroscedastic
+ and Non-normal Data}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-049/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-050,
+ author = {Clifford Anderson-Bergman},
+ title = {{Bayesian Regression Models for Interval-censored Data in R}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-050/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-051,
+ author = {Pedro Cañadilla Jiménez and Yolanda Román Montoya},
+ title = {{queueing: A Package For Analysis Of Queueing Networks and
+ Models in R}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-051/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-052,
+ author = {Nicholas Syring and Meng Li},
+ title = {{BayesBD: An R Package for Bayesian Inference on Image
+ Boundaries}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-052/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-053,
+ author = {Ruby Sharma and Sajal Kumar and Hua Zhong and Mingzhou Song},
+ title = {{Simulating Noisy, Nonparametric, and Multivariate Discrete
+ Patterns}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-053/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-054,
+ author = {Hideitsu Hino},
+ title = {{ider: Intrinsic Dimension Estimation with R}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-054/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-055,
+ author = {Josmar Mazucheli and André Felipe B. Menezes and Saralees
+ Nadarajah},
+ title = {{mle.tools: An R Package for Maximum Likelihood Bias
+ Correction}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-055/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-056,
+ author = {Andreas Beger and Daniel W. Hill and Jr. and Nils. W.
+ Metternich and Shahryar Minhas and Michael D. Ward},
+ title = {{Splitting It Up: The spduration Split-Population Duration
+ Regression Package for Time-varying Covariates}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-056/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-057,
+ author = {Nathan Medina-Rodríguez and Ángelo Santana},
+ title = {{Allele Imputation and Haplotype Determination from Databases
+ Composed of Nuclear Families}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-057/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
+
+@article{RJ-2017-058,
+ author = {David J. Winter},
+ title = {{rentrez: An R package for the NCBI eUtils API}},
+ year = {2017},
+ journal = {{The R Journal}},
+ url = {https://journal.r-project.org/archive/2017/RJ-2017-058/index.html}
+ note = {Accepted, may change after copy-editing.}
+}
+
+
diff --git a/src/extra/tzone/Make.zi b/src/extra/tzone/Make.zi
index c8c543f..599067b 100644
--- a/src/extra/tzone/Make.zi
+++ b/src/extra/tzone/Make.zi
@@ -1,6 +1,6 @@
## Makefile to be run on a Unix box with zic
-VERSION = 2017b
+VERSION = 2017c
TZDIR = zoneinfo
TZTMP = tz
TARFILE = tzdata$(VERSION).tar.gz
diff --git a/src/extra/tzone/Notes b/src/extra/tzone/Notes
index 1e47fc2..5476f2c 100644
--- a/src/extra/tzone/Notes
+++ b/src/extra/tzone/Notes
@@ -22,11 +22,11 @@ R's implemntation, where time_t is int_fast64_t, hence signed.)
To remake it, download the current version of tzdataXXXXx.tar.gz from
http://www.iana.org/time-zones to this directory and run
-make -f Make.zi VERSION=2017b
+make -f Make.zi VERSION=2017c
for the appropriate version. If zic is not on the path, use something like
-make -f Make.zi VERSION=2017b ZIC=/usr/sbin/zic
+make -f Make.zi VERSION=2017c ZIC=/usr/sbin/zic
NB: it seems that this needs to be done on a system with 64-bit time_t
or the catalogs will be confined to 1902-2038. And even that did not
diff --git a/src/extra/tzone/zoneinfo.zip b/src/extra/tzone/zoneinfo.zip
index e4bc625..fa13253 100644
--- a/src/extra/tzone/zoneinfo.zip
+++ b/src/extra/tzone/zoneinfo.zip
Binary files differ
diff --git a/src/gnuwin32/CHANGES.Rd b/src/gnuwin32/CHANGES.Rd
index 047d045..6594160 100644
--- a/src/gnuwin32/CHANGES.Rd
+++ b/src/gnuwin32/CHANGES.Rd
@@ -589,8 +589,7 @@
\item The recommended 64-bit toolchain has been changed to one
that does not add leading underscores. See
- \url{http://www.murdoch-sutherland.com/Rtools/} or
- \url{http://www.stats.ox.ac.uk/pub/Rtools/}. Any static or import
+ \url{http://cran.r-project.org/bin/windows/Rtools/}. Any static or import
libraries for external software used in installing packages will
need to be re-compiled for this toolchain, but the use of DLLs is
unaffected.
diff --git a/src/gnuwin32/README.packages b/src/gnuwin32/README.packages
index c120b3a..45ab40d 100644
--- a/src/gnuwin32/README.packages
+++ b/src/gnuwin32/README.packages
@@ -131,10 +131,7 @@ even the MinGW g77 Fortran used null-terminated strings. (g77 was in
GCC 3.x.y, superseded by gfortran.)
WARNING: DLLs made with some compilers reset the FPU in their startup
-code (Delphi has been one), and this will cause operations such as
+code and this will cause operations such as
0./0. to crash R. You can re-set the FPU to the correct values by a
call to the C entry point Rwin_fpset().
-For some further details and Delphi examples see
-http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/
-
diff --git a/src/gnuwin32/cran/index.in b/src/gnuwin32/cran/index.in
index 42d878e..7a24c73 100644
--- a/src/gnuwin32/cran/index.in
+++ b/src/gnuwin32/cran/index.in
@@ -74,6 +74,6 @@ current Windows binary release is<br>
<hr>
-<p>Last change: @DATE@, by Duncan Murdoch</p>
+<p>Last change: @DATE@</p>
</body>
</html>
diff --git a/src/gnuwin32/cran/rdevel.in b/src/gnuwin32/cran/rdevel.in
index 7b6e218..05dfa64 100644
--- a/src/gnuwin32/cran/rdevel.in
+++ b/src/gnuwin32/cran/rdevel.in
@@ -87,6 +87,6 @@ FAQ</a> for Windows-specific information.</p>
<hr>
-<p>Last build: @DATE@, by Duncan Murdoch</p>
+<p>Last build: @DATE@</p>
</body>
</html>
diff --git a/src/gnuwin32/cran/rpatched.in b/src/gnuwin32/cran/rpatched.in
index ea352bd..54520e1 100644
--- a/src/gnuwin32/cran/rpatched.in
+++ b/src/gnuwin32/cran/rpatched.in
@@ -75,6 +75,6 @@ the next major release of R) is available in the <a href="../../windows/base/rde
<hr>
-<p>Last build: @DATE@, by Duncan Murdoch</p>
+<p>Last build: @DATE@</p>
</body>
</html>
diff --git a/src/gnuwin32/cran/rtest.in b/src/gnuwin32/cran/rtest.in
index 05ec7ea..6c8e0e7 100644
--- a/src/gnuwin32/cran/rtest.in
+++ b/src/gnuwin32/cran/rtest.in
@@ -75,6 +75,6 @@ a later major release of R) is available in the <a href="rdevel.html">r-devel sn
<hr>
-<p>Last build: @DATE@, by Duncan Murdoch</p>
+<p>Last build: @DATE@</p>
</body>
</html>
diff --git a/src/gnuwin32/front-ends/Rfe.c b/src/gnuwin32/front-ends/Rfe.c
index d9c27dc..3235cb9 100644
--- a/src/gnuwin32/front-ends/Rfe.c
+++ b/src/gnuwin32/front-ends/Rfe.c
@@ -66,9 +66,9 @@ int main (int argc, char **argv)
if (stricmp(argv[0] + strlen(argv[0]) - 11, "Rscript.exe") == 0
|| stricmp(argv[0] + strlen(argv[0]) - 7, "Rscript") == 0)
- snprintf(cmd, CMD_LEN, "%s\\bin\\%s\\Rscript.exe", getRHOME(2), arch);
+ snprintf(cmd, CMD_LEN, "\"%s\\bin\\%s\\Rscript.exe\"", getRHOME(2), arch);
else {
- snprintf(cmd, CMD_LEN, "%s\\bin\\%s\\R.exe", getRHOME(2), arch);
+ snprintf(cmd, CMD_LEN, "\"%s\\bin\\%s\\R.exe\"", getRHOME(2), arch);
interactive = 1;
}
diff --git a/src/gnuwin32/front-ends/rcmdfn.c b/src/gnuwin32/front-ends/rcmdfn.c
index 1d430c3..cba4969 100644
--- a/src/gnuwin32/front-ends/rcmdfn.c
+++ b/src/gnuwin32/front-ends/rcmdfn.c
@@ -1,6 +1,6 @@
/*
* R : A Computer Language for Statistical Data Analysis
- * Copyright (C) 2000-2013 R Core Team
+ * Copyright (C) 2000-2017 R Core Team
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -146,7 +146,7 @@ int rcmdfn (int cmdarg, int argc, char **argv)
return(0);
}
/* R --help */
- snprintf(cmd, CMD_LEN, "%s/%s/Rterm.exe --help", getRHOME(3), BINDIR);
+ snprintf(cmd, CMD_LEN, "\"%s/%s/Rterm.exe\" --help", getRHOME(3), BINDIR);
system(cmd);
fprintf(stderr, "%s", "\n\nOr: R CMD command args\n\n");
rcmdusage(RCMD);
@@ -160,7 +160,7 @@ int rcmdfn (int cmdarg, int argc, char **argv)
fprintf(stdout, "%s", getRHOME(3));
return(0);
}
- snprintf(cmd, CMD_LEN, "%s/%s/Rterm.exe", getRHOME(3), BINDIR);
+ snprintf(cmd, CMD_LEN, "\"%s/%s/Rterm.exe\"", getRHOME(3), BINDIR);
for (i = cmdarg + 1; i < argc; i++){
strcat(cmd, " ");
if (strlen(cmd) + strlen(argv[i]) > 9900) {
@@ -276,7 +276,7 @@ int rcmdfn (int cmdarg, int argc, char **argv)
}
/* Unix has --restore --save --no-readline */
- snprintf(cmd, CMD_LEN, "%s/%s/Rterm.exe -f \"%s\" --restore --save",
+ snprintf(cmd, CMD_LEN, "\"%s/%s/Rterm.exe\" -f \"%s\" --restore --save",
getRHOME(3), BINDIR, infile);
if(strlen(cmd) + strlen(cmd_extra) >= CMD_LEN) {
fprintf(stderr, "command line too long\n");
@@ -381,14 +381,15 @@ int rcmdfn (int cmdarg, int argc, char **argv)
if (!strcmp(argv[cmdarg], "INSTALL")) {
+ fprintf(stderr, "In R CMD INSTALL\n");
/* Unix has --no-restore except for MM's undocumented --use-vanilla */
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.install_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::.install_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "REMOVE")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -f \"%s/share/R/REMOVE.R\" R_DEFAULT_PACKAGES=NULL --no-restore --slave --args",
+ "\"%s/%s/Rterm.exe\" -f \"%s/share/R/REMOVE.R\" R_DEFAULT_PACKAGES=NULL --no-restore --slave --args",
getRHOME(3), BINDIR, getRHOME(3));
for (i = cmdarg + 1; i < argc; i++){
strcat(cmd, " ");
@@ -406,17 +407,17 @@ int rcmdfn (int cmdarg, int argc, char **argv)
return(system(cmd));
} else if (!strcmp(argv[cmdarg], "build")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.build_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::.build_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "check")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.check_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::.check_packages() R_DEFAULT_PACKAGES= LC_COLLATE=C --no-restore --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "Rprof")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.Rprof() R_DEFAULT_PACKAGES=utils LC_COLLATE=C --vanilla --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::.Rprof() R_DEFAULT_PACKAGES=utils LC_COLLATE=C --vanilla --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "texify")) {
@@ -425,41 +426,41 @@ int rcmdfn (int cmdarg, int argc, char **argv)
return(1);
}
snprintf(cmd, CMD_LEN,
- "texify.exe -I %s/share/texmf/tex/latex -I %s/share/texmf/bibtex/bst", getRHOME(3), getRHOME(3));
+ "texify.exe -I \"%s/share/texmf/tex/latex\" -I \"%s/share/texmf/bibtex/bst\"", getRHOME(3), getRHOME(3));
PROCESS_CMD(" ");
} else if (!strcmp(argv[cmdarg], "SHLIB")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.SHLIB() R_DEFAULT_PACKAGES=NULL --no-restore --slave --no-site-file --no-init-file --args",
+ "\"%s/%s/Rterm.exe\" -e tools:::.SHLIB() R_DEFAULT_PACKAGES=NULL --no-restore --slave --no-site-file --no-init-file --args",
getRHOME(3), BINDIR);
PROCESS_CMD(" ");
} else if (!strcmp(argv[cmdarg], "Rdiff")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.Rdiff() R_DEFAULT_PACKAGES=NULL --vanilla --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::.Rdiff() R_DEFAULT_PACKAGES=NULL --vanilla --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "Rdconv")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.Rdconv() R_DEFAULT_PACKAGES= LC_COLLATE=C --vanilla --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::.Rdconv() R_DEFAULT_PACKAGES= LC_COLLATE=C --vanilla --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "Rd2txt")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::.Rdconv() R_DEFAULT_PACKAGES= LC_COLLATE=C --vanilla --slave --args nextArg-tnextArgtxt",
+ "\"%s/%s/Rterm.exe\" -e tools:::.Rdconv() R_DEFAULT_PACKAGES= LC_COLLATE=C --vanilla --slave --args nextArg-tnextArgtxt",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "Rd2pdf")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe -e tools:::..Rd2pdf() R_DEFAULT_PACKAGES= LC_ALL=C --vanilla --slave --args ",
+ "\"%s/%s/Rterm.exe\" -e tools:::..Rd2pdf() R_DEFAULT_PACKAGES= LC_ALL=C --vanilla --slave --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "Sweave")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe --no-restore --slave -e utils:::.Sweave() --args ",
+ "\"%s/%s/Rterm.exe\" --no-restore --slave -e utils:::.Sweave() --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else if (!strcmp(argv[cmdarg], "Stangle")) {
snprintf(cmd, CMD_LEN,
- "%s/%s/Rterm.exe --vanilla --slave -e utils:::.Stangle() --args ",
+ "\"%s/%s/Rterm.exe\" --vanilla --slave -e utils:::.Stangle() --args ",
getRHOME(3), BINDIR);
PROCESS_CMD("nextArg");
} else {
diff --git a/src/gnuwin32/front-ends/rpwd.c b/src/gnuwin32/front-ends/rpwd.c
index ff8a202..0924fd5 100644
--- a/src/gnuwin32/front-ends/rpwd.c
+++ b/src/gnuwin32/front-ends/rpwd.c
@@ -45,6 +45,7 @@ int main (int argc, char **argv)
for (p = buf; *p; p++)
if (isspace(*p)) { hasspace = 1; break; }
if (hasspace)
+ /* NOTE: short names are not always enabled */
GetShortPathName(buf, buf, MAX_PATH);
for (p = buf; *p; p++)
if (*p == '\\') *p = '/';
diff --git a/src/gnuwin32/rhome.c b/src/gnuwin32/rhome.c
index c29b71c..c9a0d27 100644
--- a/src/gnuwin32/rhome.c
+++ b/src/gnuwin32/rhome.c
@@ -66,6 +66,7 @@ char *getRHOME(int m)
for (p = rhomebuf; *p; p++)
if (isspace(*p)) { hasspace = 1; break; }
if (hasspace)
+ /* NOTE: this fails when short names are not enabled */
GetShortPathName(rhomebuf, rhomebuf, MAX_PATH);
return (rhomebuf);
}
diff --git a/src/gnuwin32/run.c b/src/gnuwin32/run.c
index be3058a..5acd023 100644
--- a/src/gnuwin32/run.c
+++ b/src/gnuwin32/run.c
@@ -2,7 +2,7 @@
* R : A Computer Language for Statistical Data Analysis
* file run.c: a simple 'reading' pipe (and a command executor)
* Copyright (C) 1999-2001 Guido Masarotto and Brian Ripley
- * (C) 2007-2014 The R Core Team
+ * (C) 2007-2017 The R Core Team
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -117,6 +117,7 @@ static char *expandcmd(const char *cmd, int whole)
since SearchPath already returns 'short names'. However,
this is not documented so I prefer to be explicit.
*/
+ /* NOTE: short names are not always enabled */
GetShortPathName(fn, s, MAX_PATH);
if (!whole) {
*q = c;
@@ -583,6 +584,12 @@ int rpipeClose(rpipe * r)
if (!r) return NOLAUNCH;
rpipeTerminate(r);
+ /* threadedwait may have obtained the exit code of the pipe process,
+ but also may have been terminated too early; retrieve the exit
+ code again to avoid race condition */
+ DWORD ret;
+ GetExitCodeProcess(r->pi.hProcess, &ret);
+ r->exitcode = ret;
CloseHandle(r->read);
CloseHandle(r->write);
CloseHandle(r->pi.hProcess);
diff --git a/src/include/config.h.in b/src/include/config.h.in
index 36b70f4..5465f21 100644
--- a/src/include/config.h.in
+++ b/src/include/config.h.in
@@ -980,6 +980,9 @@
/* Define to the sub-directory where libtool stores uninstalled libraries. */
#undef LT_OBJDIR
+/* macOS 10.12 (Sierra) or earlier */
+#undef MACOS_SIERRA
+
/* Define if mktime sets errno. */
#undef MKTIME_SETS_ERRNO
diff --git a/src/library/Recommended/Matrix.tgz b/src/library/Recommended/Matrix.tgz
index af0bfa1..309dab3 120000
--- a/src/library/Recommended/Matrix.tgz
+++ b/src/library/Recommended/Matrix.tgz
@@ -1 +1 @@
-Matrix_1.2-11.tar.gz \ No newline at end of file
+Matrix_1.2-12.tar.gz \ No newline at end of file
diff --git a/src/library/Recommended/Matrix_1.2-11.tar.gz b/src/library/Recommended/Matrix_1.2-11.tar.gz
deleted file mode 100644
index da75f6d..0000000
--- a/src/library/Recommended/Matrix_1.2-11.tar.gz
+++ /dev/null
Binary files differ
diff --git a/src/library/Recommended/Matrix_1.2-12.tar.gz b/src/library/Recommended/Matrix_1.2-12.tar.gz
new file mode 100644
index 0000000..f829e4e
--- /dev/null
+++ b/src/library/Recommended/Matrix_1.2-12.tar.gz
Binary files differ
diff --git a/src/library/Recommended/mgcv.tgz b/src/library/Recommended/mgcv.tgz
index 8e7ba20..a88e6e5 120000
--- a/src/library/Recommended/mgcv.tgz
+++ b/src/library/Recommended/mgcv.tgz
@@ -1 +1 @@
-mgcv_1.8-20.tar.gz \ No newline at end of file
+mgcv_1.8-22.tar.gz \ No newline at end of file
diff --git a/src/library/Recommended/mgcv_1.8-20.tar.gz b/src/library/Recommended/mgcv_1.8-20.tar.gz
deleted file mode 100644
index 84fe1f8..0000000
--- a/src/library/Recommended/mgcv_1.8-20.tar.gz
+++ /dev/null
Binary files differ
diff --git a/src/library/Recommended/mgcv_1.8-22.tar.gz b/src/library/Recommended/mgcv_1.8-22.tar.gz
new file mode 100644
index 0000000..1aa80e0
--- /dev/null
+++ b/src/library/Recommended/mgcv_1.8-22.tar.gz
Binary files differ
diff --git a/src/library/base/R/Defunct.R b/src/library/base/R/Defunct.R
index 9208621..c04c668 100644
--- a/src/library/base/R/Defunct.R
+++ b/src/library/base/R/Defunct.R
@@ -18,8 +18,8 @@
.Defunct <- function(new, package=NULL, msg) {
if (missing(msg)) {
- msg <- gettextf("'%s' is defunct.\n",
- as.character(sys.call(sys.parent())[[1L]]))
+ fname <- as.character(sys.call(sys.parent())[[1L]])
+ msg <- gettextf("'%s' is defunct.\n", fname[length(fname)])
if(!missing(new))
msg <- c(msg, gettextf("Use '%s' instead.\n", new))
msg <- c(msg,
diff --git a/src/library/base/R/datetime.R b/src/library/base/R/datetime.R
index 6815478..3055656 100644
--- a/src/library/base/R/datetime.R
+++ b/src/library/base/R/datetime.R
@@ -23,8 +23,10 @@ Sys.timezone <- function(location = TRUE)
{
tz <- Sys.getenv("TZ", names = FALSE)
if(!location || nzchar(tz)) return(Sys.getenv("TZ", unset = NA_character_))
- lt <- normalizePath("/etc/localtime") # Linux, macOS, ...
- if (grepl(pat <- "^/usr/share/zoneinfo/", lt)) sub(pat, "", lt)
+ lt <- normalizePath("/etc/localtime") # most Linux, macOS, ...
+ if (grepl(pat <- "^/usr/share/zoneinfo/", lt) ||
+ grepl(pat <- "^/usr/share/zoneinfo.default/", lt)) sub(pat, "", lt)
+ else if(grepl(pat <- ".*/zoneinfo/(.*)", lt)) sub(pat, "\\1", lt)
else if (lt == "/etc/localtime" && file.exists("/etc/timezone") &&
dir.exists("/usr/share/zoneinfo") &&
{ # Debian etc.
@@ -1064,6 +1066,10 @@ OlsonNames <- function()
if(.Platform$OS.type == "windows")
tzdir <- Sys.getenv("TZDIR", file.path(R.home("share"), "zoneinfo"))
else {
+ ## Try known locations in turn.
+ ## The list is not exhaustive (mac OS 10.13's real location is
+ ## /usr/share/zoneinfo.default) and there is a risk that
+ ## the wrong one is found.
tzdirs <- c(Sys.getenv("TZDIR"),
file.path(R.home("share"), "zoneinfo"),
"/usr/share/zoneinfo", # Linux, macOS, FreeBSD
@@ -1075,9 +1081,11 @@ OlsonNames <- function()
if (!length(tzdirs)) {
warning("no Olson database found")
return(character())
- } else tzdir <- tzdirs[1]
+ } else tzdir <- tzdirs[1L]
}
x <- list.files(tzdir, recursive = TRUE)
- ## all auxiliary files are l/case.
+ ## some databases have VERSION, some +VERSION, some neither
+ x <- setdiff(x, "VERSION")
+ ## all other auxiliary files are l/case.
grep("^[ABCDEFGHIJKLMNOPQRSTUVWXYZ]", x, value = TRUE)
}
diff --git a/src/library/base/R/namespace.R b/src/library/base/R/namespace.R
index 7f4731b..e2d6924 100644
--- a/src/library/base/R/namespace.R
+++ b/src/library/base/R/namespace.R
@@ -999,17 +999,26 @@ namespaceImportMethods <- function(self, ns, vars, from = NULL)
allFuns <- methods:::.getGenerics(ns) # all the methods tables in ns
allPackages <- attr(allFuns, "package")
pkg <- methods::getPackageName(ns)
- if(!all(vars %in% allFuns)) {
- message(gettextf("No methods found in \"%s\" for requests: %s",
- pkg, paste(vars[is.na(match(vars, allFuns))], collapse = ", ")),
+ found <- vars %in% allFuns
+ if(!all(found)) {
+ message(sprintf(ngettext(sum(!found),
+ "No methods found in package %s for request: %s when loading %s",
+ "No methods found in package %s for requests: %s when loading %s"),
+ sQuote(pkg),
+ paste(sQuote(vars[!found]), collapse = ", "),
+ sQuote(getNamespaceName(self))),
domain = NA)
vars <- vars[vars %in% allFuns]
}
- if(any(is.na(match(vars, allFuns))))
- stop(gettextf("requested methods not found in environment/package %s: %s",
- sQuote(pkg),
- paste(vars[is.na(match(vars, allFuns))],
- collapse = ", ")), call. = FALSE, domain = NA)
+ found <- vars %in% allFuns
+ if(!all(found))
+ stop(sprintf(ngettext(sum(!found),
+ "requested method not found in environment/package %s: %s when loading %s",
+ "requested methods not found in environment/package %s: %s when loading %s"),
+ sQuote(pkg),
+ paste(sQuote(vars[!found]), collapse = ", "),
+ sQuote(getNamespaceName(self))),
+ call. = FALSE, domain = NA)
for(i in seq_along(allFuns)) {
## import methods tables if asked for
## or if the corresponding generic was imported
diff --git a/src/library/base/R/range.R b/src/library/base/R/range.R
index 982730b..d450f8b 100644
--- a/src/library/base/R/range.R
+++ b/src/library/base/R/range.R
@@ -1,7 +1,7 @@
# File src/library/base/R/range.R
# Part of the R package, https://www.R-project.org
#
-# Copyright (C) 1995-2012 The R Core Team
+# Copyright (C) 1995-2017 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -22,7 +22,9 @@ range.default <- function(..., na.rm = FALSE, finite = FALSE)
if(is.numeric(x)) {
if(finite) x <- x[is.finite(x)]
else if(na.rm) x <- x[!is.na(x)]
- return (c(min(x), max(x)))
+ c(min(x), max(x))
+ } else {
+ if(finite) na.rm <- TRUE
+ c(min(x, na.rm=na.rm), max(x, na.rm=na.rm))
}
- c(min(x, na.rm=na.rm), max(x, na.rm=na.rm))
}
diff --git a/src/library/base/R/zdatetime.R b/src/library/base/R/zdatetime.R
index a874c8c..f25ee15 100644
--- a/src/library/base/R/zdatetime.R
+++ b/src/library/base/R/zdatetime.R
@@ -1,7 +1,7 @@
# File src/library/base/R/zdatetime.R
# Part of the R package, https://www.R-project.org
#
-# Copyright (C) 1995-2016 The R Core Team
+# Copyright (C) 1995-2017 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -24,9 +24,9 @@
"1979-12-31", "1981-6-30", "1982-6-30", "1983-6-30",
"1985-6-30", "1987-12-31", "1989-12-31", "1990-12-31",
"1992-6-30", "1993-6-30", "1994-6-30","1995-12-31",
- "1997-6-30", "1998-12-31", "2005-12-31", "2008-12-31",
+ "1997-6-30", "1998-12-31", "2005-12-31", "2008-12-31",
"2012-6-30", "2015-6-30", "2016-12-31")
.leap.seconds <- strptime(paste(.leap.seconds , "23:59:60"),
- "%Y-%m-%d %H:%M:%S")
- c(as.POSIXct(.leap.seconds, "GMT")) # lose the timezone
+ "%Y-%m-%d %H:%M:%S", tz = "UTC")
+ c(as.POSIXct(.leap.seconds, "GMT")) # lose the timezone attribute
})
diff --git a/src/library/base/man/append.Rd b/src/library/base/man/append.Rd
index 48a5fc1..892ce36 100644
--- a/src/library/base/man/append.Rd
+++ b/src/library/base/man/append.Rd
@@ -13,7 +13,7 @@
append(x, values, after = length(x))
}
\arguments{
- \item{x}{the vector to be modified.}
+ \item{x}{the vector the values are to be appended to.}
\item{values}{to be included in the modified vector.}
\item{after}{a subscript, after which the values are to be appended.}
}
diff --git a/src/library/base/man/connections.Rd b/src/library/base/man/connections.Rd
index 50a4855..fd7d294 100644
--- a/src/library/base/man/connections.Rd
+++ b/src/library/base/man/connections.Rd
@@ -236,9 +236,8 @@ isIncomplete(con)
Server-side cached data is always accepted.
- Function \code{\link{download.file}} and contributed package
- \CRANpkg{RCurl} provide more comprehensive facilities to download
- from URLs.
+ Function \code{\link{download.file}} and several contributed packages
+ provide more comprehensive facilities to download from URLs.
}
\value{
@@ -539,10 +538,12 @@ isIncomplete(con)
\code{\link{memCompress}} for more ways to (de)compress and references
on data compression.
-#ifdef windows
+
+ \code{\link{extSoftVersion}} for the versions of the \code{zlib} (for
+ \code{gzfile}), \code{bzip2} and \code{xz} libraries in use.
- To flush output to the console, see \code{\link{flush.console}}.
-#endif
+ To flush output to the Windows and maOS consoles, see
+ \code{\link{flush.console}}.
}
\examples{
diff --git a/src/library/base/man/grep.Rd b/src/library/base/man/grep.Rd
index eeedad3..2835dee 100644
--- a/src/library/base/man/grep.Rd
+++ b/src/library/base/man/grep.Rd
@@ -89,7 +89,7 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
\item \code{fixed = TRUE}: use exact matching.
\item \code{perl = TRUE}: use Perl-style regular expressions.
\item \code{fixed = FALSE, perl = FALSE}: use POSIX 1003.2
- extended regular expressions.
+ extended regular expressions (the default).
}
See the help pages on \link{regular expression} for details of the
different types of regular expressions.
@@ -138,7 +138,7 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
\code{grepl} returns a logical vector (match or not for each element of
\code{x}).
- For \code{sub} and \code{gsub} return a character vector of the same
+ \code{sub} and \code{gsub} return a character vector of the same
length and with the same attributes as \code{x} (after possible
coercion to character). Elements of character vectors \code{x} which
are not substituted will be returned unchanged (including any declared
@@ -152,9 +152,12 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
\eqn{-1} if there is none, with attribute \code{"match.length"}, an
integer vector giving the length of the matched text (or \eqn{-1} for
no match). The match positions and lengths are in characters unless
- \code{useBytes = TRUE} is used, when they are in bytes. If named
- capture is used there are further attributes \code{"capture.start"},
- \code{"capture.length"} and \code{"capture.names"}.
+ \code{useBytes = TRUE} is used, when they are in bytes (as they are
+ for an ASCII-only matching: in either case an attribute
+ \code{useBytes} with value \code{TRUE} is set on the result). If
+ named capture is used there are further attributes
+ \code{"capture.start"}, \code{"capture.length"} and
+ \code{"capture.names"}.
\code{gregexpr} returns a list of the same length as \code{text} each
element of which is of the same form as the return value for
@@ -166,14 +169,16 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
sequence of integers with the starting positions of the match and all
substrings corresponding to parenthesized subexpressions of
\code{pattern}, with attribute \code{"match.length"} a vector
- giving the lengths of the matches (or \eqn{-1} for no match).
+ giving the lengths of the matches (or \eqn{-1} for no match). The
+ interpretation of positions and length and the attributes follows
+ \code{regexpr}.
Where matching failed because of resource limits (especially for PCRE)
this is regarded as a non-match, usually with a warning.
}
\section{Warning}{
- POSIX 1003.2 mode of \code{gsub} and \code{gregexpr} does not
+ The POSIX 1003.2 mode of \code{gsub} and \code{gregexpr} does not
work correctly with repeated word-boundaries (e.g., \code{pattern =
"\\b"}). Use \code{perl = TRUE} for such matches (but that may not
work as expected with non-ASCII inputs, as the meaning of
@@ -209,8 +214,9 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
People working with PCRE and very long strings can adjust the maximum
size of the JIT stack by setting environment variable
\env{R_PCRE_JIT_STACK_MAXSIZE} before JIT is used to a value between
- \code{1} and \code{1000} in MB: the default is \code{64}. (Then would
- usually be wise to set the \link{option} \code{PCRE_limit_recursion}.)
+ \code{1} and \code{1000} in MB: the default is \code{64}. (Then it
+ would usually be wise to set the \link{option}
+ \code{PCRE_limit_recursion}.)
}
\source{
@@ -221,7 +227,8 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
handling of invalid regular expressions and the collation of character
ranges, so the results will have changed slightly over the years.
- For Perl-style matching PCRE (\url{http://www.pcre.org}) is used.
+ For Perl-style matching PCRE (\url{http://www.pcre.org}) is used:
+ again the results may depend (slightly) on the version of PCRE in use.
}
\references{
@@ -253,7 +260,12 @@ regexec(pattern, text, ignore.case = FALSE, perl = FALSE,
\code{\link{grepRaw}} for matching raw vectors.
- Options \code{PCRE_study} and \code{PCRE_use_JIT}.
+ Options \code{PCRE_limit_recursion}, \code{PCRE_study} and
+ \code{PCRE_use_JIT}.
+
+ \code{\link{extSoftVersion}} for the versions of regex and PCRE
+ libraries in use, \code{\link{pcre_config}} for more details for
+ PCRE.
}
\examples{
grep("[a-z]", letters)
diff --git a/src/library/base/man/libcurlVersion.Rd b/src/library/base/man/libcurlVersion.Rd
index 2ac6db3..62afec0 100644
--- a/src/library/base/man/libcurlVersion.Rd
+++ b/src/library/base/man/libcurlVersion.Rd
@@ -1,6 +1,6 @@
% File src/library/base/man/curlVersion.Rd
% Part of the R package, https://www.R-project.org
-% Copyright 2015 R Core Team
+% Copyright 2015-2017 R Core Team
% Distributed under GPL 2 or later
\name{libcurlVersion}
@@ -18,7 +18,7 @@ libcurlVersion()
A character string, with value the \code{libcurl} version in use or
\code{""} if none is. If \code{libcurl} is available, has attributes
- \item{ssl_version}{A character string naming the SSL implementation
+ \item{ssl_version}{A character string naming the SSL/TLS implementation
and version, possibly \code{"none"}. It is intended for the version
of OpenSSL used, but not all implementations of \code{libcurl} use
OpenSSL --- for example macOS reports \code{"SecureTranspart"}, its
@@ -32,6 +32,13 @@ libcurlVersion()
\item{protocols}{A character vector of the names of supported
protocols, also known as \sQuote{schemes} when part of a URL.}
}
+\section{Warning}{
+ In late 2017 a \code{libcurl} installation was seen divided into two
+ libraries, \code{libcurl} and \code{libcurl-feature}, and the first
+ had been updated but not the second. As the compiled function
+ recording the version was in the latter, the version reported by
+ \code{libcurlVersion} was misleading.
+}
\seealso{
\code{\link{extSoftVersion}} for versions of other third-party
software.
@@ -41,10 +48,11 @@ libcurlVersion()
\url{http://curl.haxx.se/docs/sslcerts.html} and
\url{http://curl.haxx.se/docs/ssl-compared.html} for more details on
- SSL versions. Normally \code{libcurl} used with \R uses
- SecureTransport on macOS, OpenSSL on Windows and GnuTLS, NSS or OpenSSL
- on Unix-alikes. (At the time of writing Debian-based Linuxen use
- GnuTLS, RedHat-based ones use NSS.)
+ SSL versions (the current standard being known as TLS). Normally
+ \code{libcurl} used with \R uses SecureTransport on macOS, OpenSSL on
+ Windows and GnuTLS, NSS or OpenSSL on Unix-alikes. (At the time of
+ writing Debian-based Linuxen use GnuTLS and RedHat-based ones use NSS,
+ but it has been announced that Fedora 27 will switch to OpenSSL.)
}
\examples{
libcurlVersion()
diff --git a/src/library/base/man/memCompress.Rd b/src/library/base/man/memCompress.Rd
index 68c0bf2..82122e7 100644
--- a/src/library/base/man/memCompress.Rd
+++ b/src/library/base/man/memCompress.Rd
@@ -1,6 +1,6 @@
% File src/library/base/man/memCompress.Rd
% Part of the R package, https://www.R-project.org
-% Copyright 2009-11 R Core Team
+% Copyright 2009-2017 R Core Team
% Distributed under GPL 2 or later
\name{memCompress}
@@ -52,7 +52,7 @@ memDecompress(from,
streams, that are not currently handled.
All the types of compression can expand the input: for \code{"gzip"}
- and \code{"bzip"} the maximum expansion is known and so
+ and \code{"bzip2"} the maximum expansion is known and so
\code{memCompress} can always allocate sufficient space. For
\code{"xz"} it is possible (but extremely unlikely) that compression
will fail if the output would have been too large.
@@ -65,6 +65,9 @@ memDecompress(from,
\seealso{
\link{connections}.
+ \code{\link{extSoftVersion}} for the versions of the \code{zlib},
+ \code{bzip2} and \code{xz} libraries in use.
+
\url{https://en.wikipedia.org/wiki/Data_compression} for background on
data compression, \url{http://zlib.net/},
\url{https://en.wikipedia.org/wiki/Gzip}, \url{http://www.bzip.org/},
diff --git a/src/library/base/man/pcre_config.Rd b/src/library/base/man/pcre_config.Rd
index b113762..c7e4978 100644
--- a/src/library/base/man/pcre_config.Rd
+++ b/src/library/base/man/pcre_config.Rd
@@ -21,18 +21,13 @@ pcre_config()
\item{Unicode properties}{Support for \samp{\p{xx}} and \samp{\P{xx}}
in regular expressions. Desirable and used by some CRAN packages.}
\item{JIT}{Support for just-in-time compilation. Desirable for speed
- (but only available as compile-time option on certain architectures
- as from PCRE 8.20).}
+ (but only available as a compile-time option on certain
+ architectures).}
\item{stack}{Does match recursion use a stack (\code{TRUE}, the PCRE
default) or a heap? See the discussion at
\url{http://www.pcre.org/original/doc/html/pcrestack.html}. (Added
in \R 3.4.0.)}
}
-\details{
- Detection of JIT requires \R to have been compiled against the headers
- of PCRE 8.20 or later: it then checks at runtime the capabilities of
- the running PCRE library (which could conceivably be earlier).
-}
\seealso{
\code{\link{extSoftVersion}} for the PCRE version.
}
diff --git a/src/library/base/man/seq.Rd b/src/library/base/man/seq.Rd
index a5a64e6..2161f44 100644
--- a/src/library/base/man/seq.Rd
+++ b/src/library/base/man/seq.Rd
@@ -50,7 +50,7 @@ seq_len(length.out)
Note that it dispatches on the class of the \strong{first} argument
irrespective of argument names. This can have unintended consequences
if it is called with just one argument intending this to be taken as
- \code{along.with}: it is much better to use \code{seg_along} in that
+ \code{along.with}: it is much better to use \code{seq_along} in that
case.
\code{seq.int} is an \link{internal generic} which dispatches on
diff --git a/src/library/base/man/timezones.Rd b/src/library/base/man/timezones.Rd
index 20abaeb..027fcf2 100644
--- a/src/library/base/man/timezones.Rd
+++ b/src/library/base/man/timezones.Rd
@@ -181,6 +181,12 @@ OlsonNames()
(abbreviated) time-zone names which can be as low as 6 (as required by
POSIX). Some OSes allow the setting of time zones with names which
exceed their limit, and that can crash the \R session.
+
+ \code{OlsonNames} tries to find an Olson database in known locations.
+ It might not succeed (when it returns an empty vector with a warning)
+ and even if it does it might not locate the database used by the
+ date-time code linked into \R. Fortunately names are added rarely
+ and most databases are pretty complete.
}
\note{
diff --git a/src/library/base/man/utf8Conversion.Rd b/src/library/base/man/utf8Conversion.Rd
index 0d67cbb..7a2006d 100644
--- a/src/library/base/man/utf8Conversion.Rd
+++ b/src/library/base/man/utf8Conversion.Rd
@@ -10,7 +10,8 @@
\alias{code point}
\title{Convert Integer Vectors to or from UTF-8-encoded Character Vectors}
\description{
- Conversion of UTF-8 encoded character vectors to and from integer vectors.
+ Conversion of UTF-8 encoded character vectors to and from integer
+ vectors representing a UTF-32 encoding.
}
\usage{
utf8ToInt(x)
@@ -24,24 +25,40 @@ intToUtf8(x, multiple = FALSE)
\details{
These will work in any locale, including on platforms that do not
otherwise support multi-byte character sets.
-}
-\value{
+
Unicode defines a name and a number of all of the glyphs it
- encompasses: the numbers are called \emph{code points}: they run from
- \code{0} to \code{0x10FFFF}.
+ encompasses: the numbers are called \emph{code points}: since RFC3629
+ they run from \code{0} to \code{0x10FFFF} (with about 12\% being
+ assigned by version 10.0 of the Unicode standard).
+ \code{intToUtf8} does not handle surrogate pairs (which should not
+ occur in UTF-32): inputs in the surrogate ranges are mapped to
+ \code{NA}.
+}
+\value{
\code{utf8ToInt} converts a length-one character string encoded in
UTF-8 to an integer vector of Unicode code points. It checks validity
- of the input and returns \code{NA} if it is invalid.
+ of the input. (Currently it accepts UTF-8 encodings of code points
+ greater than \code{0x10FFFF}: these are no longer regarded as valid by
+ the UTF-8 RFC and will in future be mapped to \code{NA}. Following
+ \sQuote{Corrigendum 9} the UTF-8 encodings of the
+ \sQuote{noncharacters} \code{0xFFFE} and \code{0xFFFF} are regarded as
+ valid as from \R 3.4.3.)
\code{intToUtf8} converts a numeric vector of Unicode code points
- either to a single character string or a character vector of single
- characters. (For a single character string \code{0} is silently
- omitted: otherwise \code{0} is mapped to \code{""}. Non-integral
- numeric values are truncated to integers.) The \code{\link{Encoding}}
- is declared as \code{"UTF-8"}.
+ either (default) to a single character string or a character vector of
+ single characters. Non-integral numeric values are truncated to
+ integers: values above the maximum are mapped to \code{NA}. For a
+ single character string \code{0} is silently omitted: otherwise
+ \code{0} is mapped to \code{""}. The \code{\link{Encoding}} of a
+ non-\code{NA} return value is declared as \code{"UTF-8"}.
- \code{NA} inputs are mapped to \code{NA} output.
+ Invalid and \code{NA} inputs are mapped to \code{NA} output.
+}
+\references{
+ \url{https://tools.ietf.org/html/rfc3629}, the current standard for UTF-8.
+
+ \url{http://www.unicode.org/versions/corrigendum9.html} for non-characters.
}
\examples{\donttest{
## will only display in some locales and fonts
diff --git a/src/library/grDevices/tests/ps-tests.Rout.save b/src/library/grDevices/tests/ps-tests.Rout.save
index aea7b6a..24eefa4 100644
--- a/src/library/grDevices/tests/ps-tests.Rout.save
+++ b/src/library/grDevices/tests/ps-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -95,4 +95,4 @@ null device
>
> proc.time()
user system elapsed
- 0.430 0.017 0.437
+ 0.550 0.040 0.572
diff --git a/src/library/grDevices/tests/xfig-tests.Rout.save b/src/library/grDevices/tests/xfig-tests.Rout.save
index 16ac81c..6e436ad 100644
--- a/src/library/grDevices/tests/xfig-tests.Rout.save
+++ b/src/library/grDevices/tests/xfig-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -102,4 +102,4 @@ Type 'q()' to quit R.
>
> proc.time()
user system elapsed
- 0.193 0.013 0.195
+ 0.224 0.036 0.240
diff --git a/src/library/grid/inst/doc/displaylist.pdf b/src/library/grid/inst/doc/displaylist.pdf
index f2c8dcf..989c2c0 100644
--- a/src/library/grid/inst/doc/displaylist.pdf
+++ b/src/library/grid/inst/doc/displaylist.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/frame.pdf b/src/library/grid/inst/doc/frame.pdf
index 6afb489..971680d 100644
--- a/src/library/grid/inst/doc/frame.pdf
+++ b/src/library/grid/inst/doc/frame.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/grid.pdf b/src/library/grid/inst/doc/grid.pdf
index f10adac..8a5d2c6 100644
--- a/src/library/grid/inst/doc/grid.pdf
+++ b/src/library/grid/inst/doc/grid.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/grobs.pdf b/src/library/grid/inst/doc/grobs.pdf
index 6be60ea..a0c033c 100644
--- a/src/library/grid/inst/doc/grobs.pdf
+++ b/src/library/grid/inst/doc/grobs.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/interactive.pdf b/src/library/grid/inst/doc/interactive.pdf
index c931e63..de1efc8 100644
--- a/src/library/grid/inst/doc/interactive.pdf
+++ b/src/library/grid/inst/doc/interactive.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/locndimn.pdf b/src/library/grid/inst/doc/locndimn.pdf
index c83bb3b..e8fcbc7 100644
--- a/src/library/grid/inst/doc/locndimn.pdf
+++ b/src/library/grid/inst/doc/locndimn.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/moveline.pdf b/src/library/grid/inst/doc/moveline.pdf
index 125dac7..da233b0 100644
--- a/src/library/grid/inst/doc/moveline.pdf
+++ b/src/library/grid/inst/doc/moveline.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/nonfinite.pdf b/src/library/grid/inst/doc/nonfinite.pdf
index 97ba097..1087f3b 100644
--- a/src/library/grid/inst/doc/nonfinite.pdf
+++ b/src/library/grid/inst/doc/nonfinite.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/plotexample.pdf b/src/library/grid/inst/doc/plotexample.pdf
index bd3d15e..94c5dc0 100644
--- a/src/library/grid/inst/doc/plotexample.pdf
+++ b/src/library/grid/inst/doc/plotexample.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/rotated.pdf b/src/library/grid/inst/doc/rotated.pdf
index 8185a9c..38aad9d 100644
--- a/src/library/grid/inst/doc/rotated.pdf
+++ b/src/library/grid/inst/doc/rotated.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/saveload.pdf b/src/library/grid/inst/doc/saveload.pdf
index c07f355..ff9c099 100644
--- a/src/library/grid/inst/doc/saveload.pdf
+++ b/src/library/grid/inst/doc/saveload.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/sharing.pdf b/src/library/grid/inst/doc/sharing.pdf
index 8844cd4..a97c8aa 100644
--- a/src/library/grid/inst/doc/sharing.pdf
+++ b/src/library/grid/inst/doc/sharing.pdf
Binary files differ
diff --git a/src/library/grid/inst/doc/viewports.pdf b/src/library/grid/inst/doc/viewports.pdf
index 43a26ee..56cc201 100644
--- a/src/library/grid/inst/doc/viewports.pdf
+++ b/src/library/grid/inst/doc/viewports.pdf
Binary files differ
diff --git a/src/library/grid/tests/testls.Rout.save b/src/library/grid/tests/testls.Rout.save
index 387c3c4..6e991ac 100644
--- a/src/library/grid/tests/testls.Rout.save
+++ b/src/library/grid/tests/testls.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -340,4 +340,4 @@ List of 6
>
> proc.time()
user system elapsed
- 0.207 0.011 0.214
+ 0.317 0.028 0.328
diff --git a/src/library/methods/R/RMethodUtils.R b/src/library/methods/R/RMethodUtils.R
index 9a1a69a..3da488f 100644
--- a/src/library/methods/R/RMethodUtils.R
+++ b/src/library/methods/R/RMethodUtils.R
@@ -1587,7 +1587,7 @@ utils::globalVariables(c(".MTable", ".AllMTable", ".dotsCall"))
stop(gettextf("no method or default matching the \"...\" arguments in %s",
deparse(sys.call(sys.parent()), nlines = 1)), domain = NA)
mc <- match.call(sys.function(sys.parent()), sys.call(sys.parent()),
- expand.dots=FALSE)
+ expand.dots=FALSE, envir=parent.frame(2))
args <- names(mc)[-1L]
mc[args] <- lapply(args, as.name)
names(mc)[names(mc) == "..."] <- ""
diff --git a/src/library/parallel/R/unix/mclapply.R b/src/library/parallel/R/unix/mclapply.R
index b88e5b3..a914e4d 100644
--- a/src/library/parallel/R/unix/mclapply.R
+++ b/src/library/parallel/R/unix/mclapply.R
@@ -166,7 +166,10 @@ mclapply <- function(X, FUN, ..., mc.preschedule = TRUE, mc.set.seed = TRUE,
this <- job.res[[i]]
if (inherits(this, "try-error")) { ## length-1 result
for (j in sindex[[i]]) res[[j]] <- this
- } else res[sindex[[i]]] <- this
+ } else
+ ## we can't just assign it since a NULL
+ ## assignment would remove it from the list
+ if (!is.null(this)) res[sindex[[i]]] <- this
}
if (length(has.errors)) {
if (length(has.errors) == cores)
diff --git a/src/library/parallel/inst/doc/parallel.pdf b/src/library/parallel/inst/doc/parallel.pdf
index 32f6117..fcdac03 100644
--- a/src/library/parallel/inst/doc/parallel.pdf
+++ b/src/library/parallel/inst/doc/parallel.pdf
Binary files differ
diff --git a/src/library/parallel/tests/multicore2.Rout.save b/src/library/parallel/tests/multicore2.Rout.save
index 03a2952..fe816d7 100644
--- a/src/library/parallel/tests/multicore2.Rout.save
+++ b/src/library/parallel/tests/multicore2.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -45,4 +45,4 @@ Calculations on Transformed Scale; Intervals on Original Scale
>
> proc.time()
user system elapsed
- 0.181 0.023 0.311
+ 0.214 0.041 0.416
diff --git a/src/library/parallel/tests/snow2.Rout.save b/src/library/parallel/tests/snow2.Rout.save
index 2be3ba0..0b8e5ba 100644
--- a/src/library/parallel/tests/snow2.Rout.save
+++ b/src/library/parallel/tests/snow2.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -50,4 +50,4 @@ Calculations on Transformed Scale; Intervals on Original Scale
>
> proc.time()
user system elapsed
- 0.177 0.031 0.671
+ 0.218 0.049 0.872
diff --git a/src/library/splines/src/splines.c b/src/library/splines/src/splines.c
index 190c7b7..05dda75 100644
--- a/src/library/splines/src/splines.c
+++ b/src/library/splines/src/splines.c
@@ -216,13 +216,15 @@ spline_basis(SEXP knots, SEXP order, SEXP xvals, SEXP derivs)
valM[i * ord + j] = R_NaN;
}
} else if (der_i > 0) { /* slow method for derivatives */
- if (der_i >= ord)
- if(nd == 1)
+ if (der_i >= ord) {
+ if(nd == 1) {
error(_("derivs = %d >= ord = %d, but should be in {0,..,ord-1}"),
der_i, ord);
- else
+ } else {
error(_("derivs[%d] = %d >= ord = %d, but should be in {0,..,ord-1}"),
i+1, der_i, ord);
+ }
+ }
for(int ii = 0; ii < ord; ii++) {
for(int j = 0; j < ord; j++) sp->a[j] = 0;
sp->a[ii] = 1;
diff --git a/src/library/stats/R/zzModels.R b/src/library/stats/R/zzModels.R
index 538b3e5..22b849d 100644
--- a/src/library/stats/R/zzModels.R
+++ b/src/library/stats/R/zzModels.R
@@ -1,8 +1,8 @@
# File src/library/stats/R/zzModels.R
# Part of the R package, https://www.R-project.org
#
+# Copyright 1999--2017 The R Core Team
# Copyright 1997, 1999 (C) Jose C. Pinheiro and Douglas M. Bates
-# Copyright 1999-2012 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -373,8 +373,9 @@ SSlogis <- # selfStart(~ Asym/(1 + exp((xmid - input)/scal)),
stop("too few distinct input values to fit a logistic model")
}
z <- xy[["y"]]
- if (min(z) <= 0) { z <- z - 1.05 * min(z) } # avoid zeroes
- z <- z/(1.05 * max(z)) # scale to within unit height
+ ## transform to proportion, i.e. in (0,1) :
+ rng <- range(z); dz <- diff(rng)
+ z <- (z - rng[1L] + 0.05 * dz)/(1.1 * dz)
xy[["z"]] <- log(z/(1 - z)) # logit transformation
aux <- coef(lm(x ~ z, xy))
pars <- as.vector(coef(nls(y ~ 1/(1 + exp((xmid - x)/scal)),
diff --git a/src/library/stats/man/SSlogis.Rd b/src/library/stats/man/SSlogis.Rd
index 090969e..0ba2819 100644
--- a/src/library/stats/man/SSlogis.Rd
+++ b/src/library/stats/man/SSlogis.Rd
@@ -1,6 +1,6 @@
% File src/library/stats/man/SSlogis.Rd
% Part of the R package, https://www.R-project.org
-% Copyright 1995-2007 R Core Team
+% Copyright 1995-2017 R Core Team
% Distributed under GPL 2 or later
\name{SSlogis}
@@ -22,7 +22,8 @@ SSlogis(input, Asym, xmid, scal)
This \code{selfStart} model evaluates the logistic
function and its gradient. It has an \code{initial} attribute that
creates initial estimates of the parameters \code{Asym},
- \code{xmid}, and \code{scal}.
+ \code{xmid}, and \code{scal}. In \R 3.4.2 and earlier, that
+ init function failed when \code{min(input)} was exactly zero.
}
\value{
a numeric vector of the same length as \code{input}. It is the value of
@@ -47,6 +48,13 @@ summary(fm1)
\dontshow{
require(graphics)
+dwlg1 <- data.frame(Prop = c(rep(0,5), 2, 5, rep(9, 9)), end = 1:16)
+iPar <- getInitial(Prop ~ SSlogis(end, Asym, xmid, scal), data = dwlg1)
+## failed in R <= 3.4.2 (because of the '0's in 'Prop')
+stopifnot(all.equal(tol = 1e-6,
+ iPar, c(Asym = 9.0678, xmid = 6.79331, scal = 0.499934)))
+
+## Visualize the SSlogis() model parametrization :
xx <- seq(-0.5, 5, len = 101)
yy <- 5 / ( 1 + exp((2-xx)))
par(mar = c(0, 0, 3.5, 0))
diff --git a/src/library/stats/src/cov.c b/src/library/stats/src/cov.c
index d4b392c..8040f24 100644
--- a/src/library/stats/src/cov.c
+++ b/src/library/stats/src/cov.c
@@ -1,6 +1,6 @@
/*
* R : A Computer Language for Statistical Data Analysis
- * Copyright (C) 1995-2015 The R Core Team
+ * Copyright (C) 1995-2017 The R Core Team
* Copyright (C) 2003 The R Foundation
*
* This program is free software; you can redistribute it and/or modify
@@ -268,7 +268,7 @@ cov_complete1(int n, int ncx, double *x, double *xm,
sum = 0.;
for (k = 0 ; k < n ; k++)
if (ind[k] != 0)
- sum += (xx[k] - xxm) * (yy[k] - yym);
+ sum += (LDOUBLE)(xx[k] - xxm) * (yy[k] - yym);
ANS(j,i) = ANS(i,j) = (double)(sum / n1);
}
}
@@ -336,7 +336,7 @@ cov_na_1(int n, int ncx, double *x, double *xm,
yym = xm[j];
sum = 0.;
for (k = 0 ; k < n ; k++)
- sum += (xx[k] - xxm) * (yy[k] - yym);
+ sum += (LDOUBLE)(xx[k] - xxm) * (yy[k] - yym);
ANS(j,i) = ANS(i,j) = (double)(sum / n1);
}
}
@@ -397,7 +397,7 @@ cov_complete2(int n, int ncx, int ncy, double *x, double *y,
sum = 0.;
for (k = 0 ; k < n ; k++)
if (ind[k] != 0)
- sum += (xx[k] - xxm) * (yy[k] - yym);
+ sum += (LDOUBLE)(xx[k] - xxm) * (yy[k] - yym);
ANS(i,j) = (double)(sum / n1);
}
}
@@ -426,7 +426,7 @@ cov_complete2(int n, int ncx, int ncy, double *x, double *y,
xxm = _X_##m [i]; \
for (k = 0 ; k < n ; k++) \
if (ind[k] != 0) \
- sum += (xx[k] - xxm) * (xx[k] - xxm); \
+ sum += (LDOUBLE)(xx[k] - xxm) * (xx[k] - xxm); \
sum /= n1; \
} \
else { /* Kendall's tau */ \
@@ -486,7 +486,7 @@ cov_na_2(int n, int ncx, int ncy, double *x, double *y,
yym = ym[j];
sum = 0.;
for (k = 0 ; k < n ; k++)
- sum += (xx[k] - xxm) * (yy[k] - yym);
+ sum += (LDOUBLE)(xx[k] - xxm) * (yy[k] - yym);
ANS(i,j) = (double)(sum / n1);
}
}
@@ -516,7 +516,7 @@ cov_na_2(int n, int ncx, int ncy, double *x, double *y,
if(!kendall) { \
xxm = _X_##m [i]; \
for (k = 0 ; k < n ; k++) \
- sum += (xx[k] - xxm) * (xx[k] - xxm); \
+ sum += (LDOUBLE)(xx[k] - xxm) * (xx[k] - xxm); \
sum /= n1; \
} \
else { /* Kendall's tau */ \
diff --git a/src/library/stats/tests/bandwidth.Rout.save b/src/library/stats/tests/bandwidth.Rout.save
index 1d71eec..535da67 100644
--- a/src/library/stats/tests/bandwidth.Rout.save
+++ b/src/library/stats/tests/bandwidth.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -46,4 +46,4 @@ In bw.bcv(precip) : minimum occurred at one end of the range
>
> proc.time()
user system elapsed
- 0.205 0.012 0.207
+ 0.226 0.038 0.245
diff --git a/src/library/stats/tests/glm.Rout.save b/src/library/stats/tests/glm.Rout.save
index 8bffaea..fb2cffb 100644
--- a/src/library/stats/tests/glm.Rout.save
+++ b/src/library/stats/tests/glm.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -29,4 +29,4 @@ Warning messages:
>
> proc.time()
user system elapsed
- 0.167 0.014 0.169
+ 0.189 0.034 0.203
diff --git a/src/library/stats/tests/ks-test.Rout.save b/src/library/stats/tests/ks-test.Rout.save
index 87596db..0e7d7d2 100644
--- a/src/library/stats/tests/ks-test.Rout.save
+++ b/src/library/stats/tests/ks-test.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -362,4 +362,4 @@ difference in location 3.741417e-05 3.741417e-05 3.741417e-05
>
> proc.time()
user system elapsed
- 0.320 0.024 0.334
+ 0.397 0.033 0.413
diff --git a/src/library/stats/tests/nls.Rout.save b/src/library/stats/tests/nls.Rout.save
index 2cfb3d4..d9a4740 100644
--- a/src/library/stats/tests/nls.Rout.save
+++ b/src/library/stats/tests/nls.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -703,4 +703,4 @@ Warning in nls(y ~ b0[fac] + b1 * x, start = list(b0 = c(1, 1), b1 = 101), :
>
> proc.time()
user system elapsed
- 1.180 0.024 1.197
+ 1.604 0.049 1.641
diff --git a/src/library/stats/tests/simulate.Rout.save b/src/library/stats/tests/simulate.Rout.save
index c87d624..ac3dfe3 100644
--- a/src/library/stats/tests/simulate.Rout.save
+++ b/src/library/stats/tests/simulate.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -408,4 +408,4 @@ log(u) 0.015569 0.00033659 46.256 5.7704e-10
>
> proc.time()
user system elapsed
- 0.285 0.011 0.286
+ 0.335 0.045 0.362
diff --git a/src/library/tools/R/utils.R b/src/library/tools/R/utils.R
index 9c18915..7c91820 100644
--- a/src/library/tools/R/utils.R
+++ b/src/library/tools/R/utils.R
@@ -497,7 +497,7 @@ function(file, pdf = FALSE, clean = FALSE, quiet = TRUE,
### ** .BioC_version_associated_with_R_version
.BioC_version_associated_with_R_version <-
- function() numeric_version(Sys.getenv("R_BIOC_VERSION", "3.5"))
+ function() numeric_version(Sys.getenv("R_BIOC_VERSION", "3.6"))
## Things are more complicated from R-2.15.x with still two BioC
## releases a year, so we do need to set this manually.
## Wierdly, 3.0 is the second version (after 2.14) for the 3.1.x series.
diff --git a/src/library/utils/R/tar.R b/src/library/utils/R/tar.R
index feb693a..cd4e96b 100644
--- a/src/library/utils/R/tar.R
+++ b/src/library/utils/R/tar.R
@@ -1,7 +1,7 @@
# File src/library/utils/R/tar.R
# Part of the R package, https://www.R-project.org
#
-# Copyright (C) 1995-2016 The R Core Team
+# Copyright (C) 1995-2017 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -329,17 +329,18 @@ tar <- function(tarfile, files = NULL,
compression_level = 6, tar = Sys.getenv("tar"),
extra_flags = "")
{
- files <- ## list the files before 'tarfile' is created!
- if(is.null(files)) ## is fine
- list.files(recursive = TRUE, all.files = TRUE,
- full.names = TRUE, include.dirs = TRUE)
- else ## is *not* ok when 'files' are simple files !
- ## list.files(path, ....) : first argument are *directories*
- list.files(files, recursive = TRUE, all.files = TRUE,
- full.names = TRUE, include.dirs = TRUE)
if(is.character(tarfile)) {
if(nzchar(tar) && tar != "internal") {
- ## FIXME: could pipe through gzip etc: might be safer for xz
+ ## Assume external command will expand directories,
+ ## so keep command-line as simple as possible
+ ## But files = '.' will not work as tarfile would be included.
+ if(is.null(files)) {
+ files <- list.files(all.files = TRUE, full.names = TRUE,
+ include.dirs = TRUE)
+ files <- setdiff(files, c("./.", "./.."))
+ }
+
+ ## Could pipe through gzip etc: might be safer for xz
## as -J was lzma in GNU tar 1.20:21
flags <- switch(match.arg(compression),
"none" = "-cf",
@@ -361,8 +362,15 @@ tar <- function(tarfile, files = NULL,
paste(shQuote(files), collapse=" "))
return(invisible(system(cmd)))
}
+
+### ----- from here on, using internal code -----
+ ## must do this before tarfile is created
+ if(is.null(files)) files <- "."
+ files <- list.files(files, recursive = TRUE, all.files = TRUE,
+ full.names = TRUE, include.dirs = TRUE)
+
con <- switch(match.arg(compression),
- "none" = file(tarfile, "wb"),
+ "none" = file(tarfile, "wb"),
"gzip" = gzfile(tarfile, "wb", compression = compression_level),
"bzip2" = bzfile(tarfile, "wb", compression = compression_level),
"xz" = xzfile(tarfile, "wb", compression = compression_level))
diff --git a/src/library/utils/inst/doc/Sweave.pdf b/src/library/utils/inst/doc/Sweave.pdf
index 7e15f24..1b3ff8b 100644
--- a/src/library/utils/inst/doc/Sweave.pdf
+++ b/src/library/utils/inst/doc/Sweave.pdf
Binary files differ
diff --git a/src/library/utils/man/download.packages.Rd b/src/library/utils/man/download.packages.Rd
index 7fc72d5..fdaecf1 100644
--- a/src/library/utils/man/download.packages.Rd
+++ b/src/library/utils/man/download.packages.Rd
@@ -47,7 +47,7 @@ download.packages(pkgs, destdir, available = NULL,
}
\item{type}{
character string, indicate which type of packages: see
- \code{\link{install.packages}}.
+ \code{\link{install.packages}} and \sQuote{Details}.
}
\item{\dots}{
additional arguments to be passed to
@@ -64,6 +64,9 @@ download.packages(pkgs, destdir, available = NULL,
\code{"file:///"} are allowed as prefixes to a file path. Use the
latter only for URLs: see \code{\link{url}} for their interpretation.
(Other forms of \samp{file://} URLs are not supported.)
+
+ For \code{download.packages}, \code{type = "both"} looks at source
+ packages only.
}
\value{
A two-column matrix of names and destination file names of those
diff --git a/src/library/utils/man/setRepositories.Rd b/src/library/utils/man/setRepositories.Rd
index f6e8bfe..d940c21 100644
--- a/src/library/utils/man/setRepositories.Rd
+++ b/src/library/utils/man/setRepositories.Rd
@@ -1,6 +1,6 @@
% File src/library/utils/man/setRepositories.Rd
% Part of the R package, https://www.R-project.org
-% Copyright 1995-2015 R Core Team
+% Copyright 1995-2017 R Core Team
% Distributed under GPL 2 or later
\name{setRepositories}
@@ -36,6 +36,9 @@ setRepositories(graphics = getOption("menu.graphics"),
\code{\link{options}("BioC_mirror")}, e.g.\sspace{}via
\code{\link{chooseBioCmirror}} --- the default value is
\samp{"https://bioconductor.org"}.
+
+ A repository \sQuote{BioC extra} is offered but only exists up to BioC
+ 3.5, not for the current default BioC 3.6.
The items that are preselected are those that are currently in
\code{options("repos")} plus those marked as default in the
@@ -59,6 +62,9 @@ setRepositories(graphics = getOption("menu.graphics"),
This does \strong{not} set the list of repositories at startup: to do
so set \code{\link{options}(repos =)} in a start up file (see help topic
\link{Startup}).
+
+ The mapping from numbers (e.g., in \code{ind}) to repositories has
+ changed in the past and will change again at \R 3.5.0.
}
\value{
This function is invoked mainly for its side effect of updating
diff --git a/src/main/Rdynload.c b/src/main/Rdynload.c
index b230fbd..5b0b5a7 100644
--- a/src/main/Rdynload.c
+++ b/src/main/Rdynload.c
@@ -195,11 +195,11 @@ static void initLoadedDLL()
R_Suicide(_("R_MAX_NUM_DLLS must be at least 100"));
if (reqlimit > maxlimit) {
if (maxlimit == 1000)
- R_Suicide(_("MAX_NUM_DLLS cannot be bigger than 1000"));
+ R_Suicide(_("R_MAX_NUM_DLLS cannot be bigger than 1000"));
char msg[128];
snprintf(msg, 128,
- _("MAX_NUM_DLLS bigger than %d may exhaust open files limit"),
+ _("R_MAX_NUM_DLLS bigger than %d may exhaust open files limit"),
maxlimit);
R_Suicide(msg);
}
diff --git a/src/main/logic.c b/src/main/logic.c
index 3c62ac2..7c64f63 100644
--- a/src/main/logic.c
+++ b/src/main/logic.c
@@ -1,7 +1,7 @@
/*
* R : A Computer Language for Statistical Data Analysis
+ * Copyright (C) 1999--2017 The R Core Team.
* Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka
- * Copyright (C) 1999--2016 The R Core Team.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -131,28 +131,28 @@ static SEXP lbinary(SEXP call, SEXP op, SEXP args)
PROTECT(klass = getAttrib(y, R_ClassSymbol));
}
}
- if (nx > 0 && ny > 0) {
+ if (nx > 0 && ny > 0) {
if(((nx > ny) ? nx % ny : ny % nx) != 0) // mismatch
- warningcall(call,
- _("longer object length is not a multiple of shorter object length"));
+ warningcall(call,
+ _("longer object length is not a multiple of shorter object length"));
- if (isRaw(x) && isRaw(y)) {
- x = binaryLogic2(PRIMVAL(op), x, y);
- }
- else {
- if(isNull(x))
- x = SETCAR(args, allocVector(LGLSXP, 0));
- else // isNumeric(x)
- x = SETCAR(args, coerceVector(x, LGLSXP));
- if(isNull(y))
- y = SETCAR(args, allocVector(LGLSXP, 0));
- else // isNumeric(y)
- y = SETCADR(args, coerceVector(y, LGLSXP));
- x = binaryLogic(PRIMVAL(op), x, y);
+ if (isRaw(x) && isRaw(y)) {
+ x = binaryLogic2(PRIMVAL(op), x, y);
+ }
+ else {
+ if(isNull(x))
+ x = SETCAR(args, allocVector(LGLSXP, 0));
+ else // isNumeric(x)
+ x = SETCAR(args, coerceVector(x, LGLSXP));
+ if(isNull(y))
+ y = SETCAR(args, allocVector(LGLSXP, 0));
+ else // isNumeric(y)
+ y = SETCADR(args, coerceVector(y, LGLSXP));
+ x = binaryLogic(PRIMVAL(op), x, y);
+ }
+ } else { // nx == 0 || ny == 0
+ x = allocVector((isRaw(x) && isRaw(y)) ? RAWSXP : LGLSXP, 0);
}
- } else { // nx == 0 || ny == 0
- x = allocVector(LGLSXP, 0);
- }
PROTECT(x);
if (dims != R_NilValue) {
@@ -346,6 +346,7 @@ static SEXP binaryLogic(int code, SEXP s1, SEXP s2)
return ans;
}
+// called only when both s1 and s2 are RAWSXP
static SEXP binaryLogic2(int code, SEXP s1, SEXP s2)
{
R_xlen_t i, n, n1, n2, i1, i2;
diff --git a/src/main/platform.c b/src/main/platform.c
index 8b6c20f..24bcfb0 100644
--- a/src/main/platform.c
+++ b/src/main/platform.c
@@ -2442,9 +2442,9 @@ SEXP attribute_hidden do_filecopy(SEXP call, SEXP op, SEXP args, SEXP rho)
#else
-/* Only 10.13 (High Sierra) has this, but the headers in Xcode 9
- declare it, for some people. As it is optional, disable it for now. */
-#ifdef __APPLE__
+/* Only 10.13 (High Sierra) has this, but the headers in Xcode 9 on 10.12
+ declare it, for some people. */
+#if defined(__APPLE__) && defined(MACOS_SIERRA)
# undef HAVE_UTIMENSAT
#endif
diff --git a/src/main/printvector.c b/src/main/printvector.c
index 8e677aa..90fea56 100644
--- a/src/main/printvector.c
+++ b/src/main/printvector.c
@@ -1,7 +1,7 @@
/*
* R : A Computer Language for Statistical Data Analysis
- * Copyright (C) 1995-1997, 1998 Robert Gentleman and Ross Ihaka
- * Copyright (C) 1998-2014 The R Core Team.
+ * Copyright (C) 1998-2017 The R Core Team.
+ * Copyright (C) 1995-1998 Robert Gentleman and Ross Ihaka
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -272,7 +272,7 @@ static void printNamedIntegerVector(int * x, int n, SEXP * names)
static void printNamedRealVector(double * x, int n, SEXP * names)
PRINT_N_VECTOR(INI_F_REAL,
- Rprintf("%s%*s",
+ Rprintf("%s%*s",
EncodeReal0(x[k],w,d,e, OutDec),R_print.gap,""))
#undef INI_F_CPLX
@@ -312,7 +312,8 @@ static void printNamedStringVector(SEXP * x, int n, int quote, SEXP * names)
static void printNamedRawVector(Rbyte * x, int n, SEXP * names)
PRINT_N_VECTOR(formatRaw(x, n, &w),
- Rprintf("%s%*s", EncodeRaw(x[k], ""), R_print.gap,""))
+ Rprintf("%*s%s%*s", w - 2, "",
+ EncodeRaw(x[k], ""), R_print.gap,""))
attribute_hidden
void printNamedVector(SEXP x, SEXP names, int quote, const char *title)
diff --git a/src/main/raw.c b/src/main/raw.c
index 4ef5a1f..c97c598 100644
--- a/src/main/raw.c
+++ b/src/main/raw.c
@@ -1,6 +1,6 @@
/*
* R : A Computer Language for Statistical Data Analysis
- * Copyright (C) 2001--2015 The R Core Team
+ * Copyright (C) 2001--2017 The R Core Team
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Pulic License as published by
@@ -217,7 +217,8 @@ static int mbrtoint(int *w, const char *s)
| ((s[1] & 0x3F) << 6) | (s[2] & 0x3F));
byte = *w;
if (byte >= 0xD800 && byte <= 0xDFFF) return -1; /* surrogate */
- if (byte == 0xFFFE || byte == 0xFFFF) return -1;
+ // Following Corrigendum 9, these are valid in UTF-8
+// if (byte == 0xFFFE || byte == 0xFFFF) return -1;
return 3;
} else return -1;
} else if (byte < 0xF8) {
@@ -294,7 +295,7 @@ SEXP attribute_hidden do_utf8ToInt(SEXP call, SEXP op, SEXP args, SEXP env)
return ans;
}
-/* based on pcre.c */
+/* based on PCRE */
static const int utf8_table1[] =
{ 0x7f, 0x7ff, 0xffff, 0x1fffff, 0x3ffffff, 0x7fffffff};
static const int utf8_table2[] = { 0, 0xc0, 0xe0, 0xf0, 0xf8, 0xfc};
@@ -334,14 +335,21 @@ SEXP attribute_hidden do_intToUtf8(SEXP call, SEXP op, SEXP args, SEXP env)
multiple = asLogical(CADR(args));
if (multiple == NA_LOGICAL)
error(_("argument 'multiple' must be TRUE or FALSE"));
+ /*
+ Could handle surrogate pairs here,
+ but they should not occur in UTF-32.
+ */
if (multiple) {
R_xlen_t i, nc = XLENGTH(x);
PROTECT(ans = allocVector(STRSXP, nc));
for (i = 0; i < nc; i++) {
- if (INTEGER(x)[i] == NA_INTEGER)
+ int this = INTEGER(x)[i];
+ if (this == NA_INTEGER
+ || (this >= 0xD800 && this <= 0xDFFF)
+ || this > 0x10FFFF)
SET_STRING_ELT(ans, i, NA_STRING);
else {
- used = inttomb(buf, INTEGER(x)[i]);
+ used = inttomb(buf, this);
buf[used] = '\0';
SET_STRING_ELT(ans, i, mkCharCE(buf, CE_UTF8));
}
@@ -352,8 +360,14 @@ SEXP attribute_hidden do_intToUtf8(SEXP call, SEXP op, SEXP args, SEXP env)
Rboolean haveNA = FALSE;
/* Note that this gives zero length for input '0', so it is omitted */
for (i = 0, len = 0; i < nc; i++) {
- if (INTEGER(x)[i] == NA_INTEGER) { haveNA = TRUE; break; }
- len += inttomb(NULL, INTEGER(x)[i]);
+ int this = INTEGER(x)[i];
+ if (this == NA_INTEGER
+ || (this >= 0xD800 && this <= 0xDFFF)
+ || this > 0x10FFFF) {
+ haveNA = TRUE;
+ break;
+ }
+ len += inttomb(NULL, this);
}
if (haveNA) {
PROTECT(ans = allocVector(STRSXP, 1));
diff --git a/src/main/seq.c b/src/main/seq.c
index 716ef3f..4abd298 100644
--- a/src/main/seq.c
+++ b/src/main/seq.c
@@ -924,11 +924,11 @@ SEXP attribute_hidden do_seq(SEXP call, SEXP op, SEXP args, SEXP rho)
if(!R_FINITE(rfrom)) errorcall(call, _("'%s' must be a finite number"), "from");
if(!R_FINITE(rto)) errorcall(call, _("'%s' must be a finite number"), "to");
if(lout > 2) rby = (rto - rfrom)/(double)(lout - 1);
- if(rfrom == (int)rfrom &&
+ if(rfrom <= INT_MAX && rfrom >= INT_MIN &&
+ rto <= INT_MAX && rto >= INT_MIN &&
+ rfrom == (int)rfrom &&
(lout <= 1 || rto == (int)rto) &&
- (lout <= 2 || rby == (int)rby) &&
- rfrom <= INT_MAX && rfrom >= INT_MIN &&
- rto <= INT_MAX && rto >= INT_MIN) {
+ (lout <= 2 || rby == (int)rby)) {
ans = allocVector(INTSXP, lout);
if(lout > 0) INTEGER(ans)[0] = (int)rfrom;
if(lout > 1) INTEGER(ans)[lout - 1] = (int)rto;
diff --git a/src/main/subassign.c b/src/main/subassign.c
index 7aa8460..9523d3e 100644
--- a/src/main/subassign.c
+++ b/src/main/subassign.c
@@ -1571,6 +1571,18 @@ SEXP attribute_hidden do_subassign_dflt(SEXP call, SEXP op, SEXP args, SEXP rho)
nsubs = SubAssignArgs(args, &x, &subs, &y);
+ /* make sure the LHS is duplicated if it matches one of the indices */
+ /* otherwise this gets the wrong answer:
+ permute <- structure(c(3L, 1L, 2L), dim = c(3, 1))
+ permute[permute, 1] <- 1:3
+ as.vector(permute)
+ */
+ for (SEXP s = subs; s != R_NilValue; s = CDR(s)) {
+ SEXP idx = CAR(s);
+ if (x == idx)
+ MARK_NOT_MUTABLE(x);
+ }
+
/* If there are multiple references to an object we must */
/* duplicate it so that only the local version is mutated. */
/* This will duplicate more often than necessary, but saves */
diff --git a/src/main/subscript.c b/src/main/subscript.c
index 4d46e77..f1a3166 100644
--- a/src/main/subscript.c
+++ b/src/main/subscript.c
@@ -144,7 +144,7 @@ OneIndex(SEXP x, SEXP s, R_xlen_t len, int partial, SEXP *newname,
}
if (indx == -1)
indx = nx;
- *newname = STRING_ELT(s, pos);
+ *newname = PRINTNAME(s);
vmaxset(vmax);
break;
default:
diff --git a/src/main/util.c b/src/main/util.c
index 08a9afe..c697238 100644
--- a/src/main/util.c
+++ b/src/main/util.c
@@ -1032,10 +1032,37 @@ const char *getTZinfo(void)
if(p) return p;
#ifdef HAVE_REALPATH
// This works on Linux, macOS and *BSD: other known OSes set TZ.
- static char abspath[PATH_MAX+1] = "";
- if(abspath[0]) return abspath + 20;
- if(realpath("/etc/localtime", abspath))
- return abspath + 20; // strip prefix of /usr/share/zoneinfo/
+ static char def_tz[PATH_MAX+1] = "";
+ if(def_tz[0]) return def_tz;
+
+ char abspath[PATH_MAX + 1];
+ const char* lt = realpath("/etc/localtime", abspath);
+# ifdef __APPLE__
+ // macOS <= 10.12 expands to /usr/share/zoneinfo/<zone name>
+ // macOS 10.13 expands to /usr/share/zoneinfo.default/<zone name>
+ // but 10.13.1 expands to /private/var/db/timezone/tz/2017c.1.0/zoneinfo/<zone name>
+ if(lt) {
+ if(strstr(abspath, ".default/"))
+ strncpy(def_tz, abspath + 28, PATH_MAX);
+ else {
+ // So guess is of the form .../zoneinfo/<real tz>
+ p = strstr(abspath, "/zoneinfo/");
+ if(p) {
+ strncpy(def_tz, p + 10, PATH_MAX);
+ } else {
+ warning("system timezone name is unknown: set environment variable TZ");
+ return "unknown";
+ }
+ }
+// printf("abspath = %s\n", abspath); printf("def_tz = %s\n", def_tz);
+ return def_tz;
+ }
+# else
+ if(lt) {
+ strncpy(def_tz, abspath + 20, PATH_MAX); // strip "/usr/share/zoneinfo/"
+ return def_tz;
+ }
+# endif
#endif
warning("system timezone name is unknown: set environment variable TZ");
return "unknown";
diff --git a/src/modules/internet/Rsock.c b/src/modules/internet/Rsock.c
index 56eaa24..c186470 100644
--- a/src/modules/internet/Rsock.c
+++ b/src/modules/internet/Rsock.c
@@ -47,6 +47,7 @@ extern void R_ProcessEvents(void);
#include "sock.h"
#include <R_ext/Print.h> // for REprintf
+#include <Rmath.h> /* for ceil */
static int sock_inited = 0;
@@ -299,12 +300,12 @@ int R_SocketWaitMultiple(int nsock, int *insockfd, int *ready, int *write,
if (mytimeout < 0 || R_wait_usec / 1e-6 < mytimeout - used)
delta = R_wait_usec;
else
- delta = (int)(1e6 * (mytimeout - used));
+ delta = (int)ceil(1e6 * (mytimeout - used));
tv.tv_sec = 0;
tv.tv_usec = delta;
} else if (mytimeout >= 0) {
tv.tv_sec = (int)(mytimeout - used);
- tv.tv_usec = (int)(1e6 * (mytimeout - used - tv.tv_sec));
+ tv.tv_usec = (int)ceil(1e6 * (mytimeout - used - tv.tv_sec));
} else { /* always poll occationally--not really necessary */
tv.tv_sec = 60;
tv.tv_usec = 0;
@@ -315,7 +316,7 @@ int R_SocketWaitMultiple(int nsock, int *insockfd, int *ready, int *write,
#else
if (mytimeout >= 0) {
tv.tv_sec = mytimeout - used;
- tv.tv_usec = 1e6 * (mytimeout - used - tv.tv_sec);
+ tv.tv_usec = ceil(1e6 * (mytimeout - used - tv.tv_sec));
} else { /* always poll occasionally--not really necessary */
tv.tv_sec = timeout;
tv.tv_usec = 0;
diff --git a/src/scripts/javareconf.in b/src/scripts/javareconf.in
index b5b5aff..1a4d0b2 100644
--- a/src/scripts/javareconf.in
+++ b/src/scripts/javareconf.in
@@ -9,7 +9,7 @@ fi
DYLIB_EXT=`${R_HOME}/bin/R CMD config DYLIB_EXT`
tools_classpath=${R_SHARE_DIR}/java
-revision='$Rev: 71736 $'
+revision='$Rev: 73535 $'
version=`set - ${revision}; echo ${2}`
version="R Java configurator: ${R_VERSION} (r${version})
@@ -197,7 +197,9 @@ custom_JAVA_LD_LIBRARY_PATH="${JAVA_LD_LIBRARY_PATH}"
# sys-dependent tweaks to JNI flags
hostos=`uname 2>/dev/null`
if test "${hostos}" = "Darwin"; then
- pref=`echo "${JAVA_HOME}" | grep "/Home$"`
+ ## This changed for Java 9.
+ ## pref=`echo "${JAVA_HOME}" | grep "/Home$"`
+ pref=`echo "${JAVA_HOME}" | grep "^/System/Library"`
if test "${pref}" = "${JAVA_HOME}"; then
echo "System Java on macOS"
JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers"
diff --git a/src/unix/sys-std.c b/src/unix/sys-std.c
index 3129470..89deaf6 100644
--- a/src/unix/sys-std.c
+++ b/src/unix/sys-std.c
@@ -563,7 +563,11 @@ pushReadline(const char *prompt, rl_vcpfunc_t f)
rl_callback_handler_install(prompt, f);
#ifdef NEED_INT_HANDLER
- signal(SIGWINCH, R_readline_sigwinch_handler);
+ struct sigaction sa;
+ sigemptyset(&sa.sa_mask);
+ sa.sa_handler = &R_readline_sigwinch_handler;
+ sa.sa_flags = SA_RESTART;
+ sigaction(SIGWINCH, &sa, NULL);
#endif
/* flush stdout in case readline wrote the prompt, but didn't flush
diff --git a/src/unix/system.c b/src/unix/system.c
index 7aed630..87a0425 100644
--- a/src/unix/system.c
+++ b/src/unix/system.c
@@ -279,6 +279,8 @@ int Rf_initialize_R(int ac, char **av)
If run from the shell script, only Tk|tk|X11|x11 are allowed.
*/
for(i = 0, avv = av; i < ac; i++, avv++) {
+ if (!strcmp(*avv, "--args"))
+ break;
if(!strncmp(*avv, "--gui", 5) || !strncmp(*avv, "-g", 2)) {
if(!strncmp(*avv, "--gui", 5) && strlen(*avv) >= 7)
p = &(*avv)[6];
diff --git a/tests/Examples/datasets-Ex.Rout.save b/tests/Examples/datasets-Ex.Rout.save
index 2def56c..6d1a55b 100644
--- a/tests/Examples/datasets-Ex.Rout.save
+++ b/tests/Examples/datasets-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -3488,7 +3488,7 @@ c0 -5.14
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 1.413 0.025 1.443 0 0
+Time elapsed: 2.07 0.04 2.121 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/grDevices-Ex.Rout.save b/tests/Examples/grDevices-Ex.Rout.save
index fc31fd8..29a0323 100644
--- a/tests/Examples/grDevices-Ex.Rout.save
+++ b/tests/Examples/grDevices-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -3791,7 +3791,7 @@ $zlab
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 7.755 0.125 7.899 0 0
+Time elapsed: 11.701 0.26 12.013 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/graphics-Ex.Rout.save b/tests/Examples/graphics-Ex.Rout.save
index dec2d2e..4197ed8 100644
--- a/tests/Examples/graphics-Ex.Rout.save
+++ b/tests/Examples/graphics-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -2074,7 +2074,7 @@ N
> points.default # to see how it calls "plot.xy(xy.coords(x, y), ...)"
function (x, y = NULL, type = "p", ...)
plot.xy(xy.coords(x, y), type = type, ...)
-<bytecode: 0x2c4d808>
+<bytecode: 0x38cb148>
<environment: namespace:graphics>
>
>
@@ -2944,7 +2944,7 @@ function (xy = 1, warn.log = TRUE)
u <- par("usr")
xy * c(u[2L] - u[1L], u[4L] - u[3L])/par("pin")
}
-<bytecode: 0x301d5a0>
+<bytecode: 0x453b198>
<environment: namespace:graphics>
>
> ## plot labels offset 0.12 inches to the right
@@ -3024,7 +3024,7 @@ function (xy = 1, warn.log = TRUE)
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 1.994 0.028 2.027 0 0
+Time elapsed: 2.929 0.069 3.014 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/grid-Ex.Rout.save b/tests/Examples/grid-Ex.Rout.save
index dca1d89..ffcbcd8 100644
--- a/tests/Examples/grid-Ex.Rout.save
+++ b/tests/Examples/grid-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -2069,7 +2069,7 @@ vp1::vp2
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 1.181 0.018 1.203 0 0
+Time elapsed: 1.76 0.025 1.793 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/splines-Ex.Rout.save b/tests/Examples/splines-Ex.Rout.save
index 07840b3..0c43bd4 100644
--- a/tests/Examples/splines-Ex.Rout.save
+++ b/tests/Examples/splines-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -582,7 +582,7 @@ attr(,"class")
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 0.154 0.006 0.16 0 0
+Time elapsed: 0.213 0.008 0.222 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/stats-Ex.Rout.save b/tests/Examples/stats-Ex.Rout.save
index fb8ab51..d1bd2aa 100644
--- a/tests/Examples/stats-Ex.Rout.save
+++ b/tests/Examples/stats-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -1473,6 +1473,13 @@ Residual standard error: 0.02684 on 13 degrees of freedom
> ## Don't show:
> require(graphics)
>
+> dwlg1 <- data.frame(Prop = c(rep(0,5), 2, 5, rep(9, 9)), end = 1:16)
+> iPar <- getInitial(Prop ~ SSlogis(end, Asym, xmid, scal), data = dwlg1)
+> ## failed in R <= 3.4.2 (because of the '0's in 'Prop')
+> stopifnot(all.equal(tol = 1e-6,
++ iPar, c(Asym = 9.0678, xmid = 6.79331, scal = 0.499934)))
+>
+> ## Visualize the SSlogis() model parametrization :
> xx <- seq(-0.5, 5, len = 101)
> yy <- 5 / ( 1 + exp((2-xx)))
> par(mar = c(0, 0, 3.5, 0))
@@ -3797,7 +3804,7 @@ sigma^2 estimated as 0.4566: log likelihood = -101.2, aic = 212.4
>
> asOneSidedFormula("age")
~age
-<environment: 0x4944850>
+<environment: 0x42cdd48>
> asOneSidedFormula(~ age)
~age
>
@@ -4782,7 +4789,7 @@ function (V)
r[cbind(1L:p, 1L:p)] <- 1
r
}
-<bytecode: 0x6655678>
+<bytecode: 0x2d97190>
<environment: namespace:stats>
> stopifnot(all.equal(Cl, cov2cor(cov(longley))),
+ all.equal(cor(longley, method = "kendall"),
@@ -7338,7 +7345,7 @@ attr(,".Environment")
> environment(as.formula("y ~ x"))
<environment: R_GlobalEnv>
> environment(as.formula("y ~ x", env = new.env()))
-<environment: 0x63faa68>
+<environment: 0x4d2eda0>
>
>
> ## Create a formula for a model with a large number of variables:
@@ -11948,14 +11955,14 @@ attr(,"class")
$linkfun
function (mu)
mu^lambda
-<bytecode: 0x576af78>
-<environment: 0x57636c0>
+<bytecode: 0x50daff0>
+<environment: 0x50e1b20>
$linkinv
function (eta)
pmax(eta^(1/lambda), .Machine$double.eps)
-<bytecode: 0x576b0c8>
-<environment: 0x57636c0>
+<bytecode: 0x50daea0>
+<environment: 0x50e1b20>
>
>
@@ -16035,8 +16042,8 @@ Step function with continuity 'f'= 0.2 , 3 knots at
> unclass(sfun0)
function (v)
.approxfun(x, y, v, method, yleft, yright, f)
-<bytecode: 0x58f64c0>
-<environment: 0x6bf9798>
+<bytecode: 0x408d7c8>
+<environment: 0x46268b0>
attr(,"call")
stepfun(1:3, y0, f = 0)
> ls(envir = environment(sfun0))
@@ -18360,7 +18367,7 @@ Number of Fisher Scoring iterations: 6
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 5.019 0.085 5.124 0 0
+Time elapsed: 6.89 0.187 7.11 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/stats4-Ex.Rout.save b/tests/Examples/stats4-Ex.Rout.save
index f93385f..460f74a 100644
--- a/tests/Examples/stats4-Ex.Rout.save
+++ b/tests/Examples/stats4-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -184,7 +184,7 @@ Coefficients:
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 0.489 0.004 0.495 0 0
+Time elapsed: 0.609 0.018 0.638 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/Examples/tools-Ex.Rout.save b/tests/Examples/tools-Ex.Rout.save
index 208c528..845ab05 100644
--- a/tests/Examples/tools-Ex.Rout.save
+++ b/tests/Examples/tools-Ex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -202,7 +202,7 @@ Error in assertWarning(ff()) :
> bibstyle("unsorted", sortKeys = function(refs) seq_along(refs),
+ fmtPrefix = function(paper) paste0("[", paper$.index, "]"),
+ .init = TRUE)
-<environment: 0x36b3de8>
+<environment: 0x3744db0>
> print(refs, .bibstyle = "unsorted")
[1] R Core Team (2013). _R: A Language and Environment for Statistical
Computing_. R Foundation for Statistical Computing, Vienna, Austria.
@@ -997,7 +997,7 @@ List of 6
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 0.247 0.01 0.258 0 0
+Time elapsed: 0.39 0.014 0.405 0 0
> grDevices::dev.off()
null device
1
diff --git a/tests/R-intro.Rout.save b/tests/R-intro.Rout.save
index f997f45..95b435f 100644
--- a/tests/R-intro.Rout.save
+++ b/tests/R-intro.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/any-all.Rout.save b/tests/any-all.Rout.save
index 1159533..8c6fbc4 100644
--- a/tests/any-all.Rout.save
+++ b/tests/any-all.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/arith-true.Rout.save b/tests/arith-true.Rout.save
index cbc70a2..62e5ddf 100644
--- a/tests/arith-true.Rout.save
+++ b/tests/arith-true.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -323,5 +323,5 @@ Warning messages:
>
> ## Last Line:
> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
-Time elapsed: 0.278 0.001 0.282 0 0
+Time elapsed: 0.329 0.002 0.332 0 0
>
diff --git a/tests/arith.Rout.save b/tests/arith.Rout.save
index fe7d9a0..14e7413 100644
--- a/tests/arith.Rout.save
+++ b/tests/arith.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/complex.Rout.save b/tests/complex.Rout.save
index a83db17..2194c71 100644
--- a/tests/complex.Rout.save
+++ b/tests/complex.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/d-p-q-r-tests.Rout.save b/tests/d-p-q-r-tests.Rout.save
index 9e22eb2..798d3f1 100644
--- a/tests/d-p-q-r-tests.Rout.save
+++ b/tests/d-p-q-r-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -1467,5 +1467,5 @@ rweibull (4, ..): 1 2 [Ok]
>
>
> cat("Time elapsed: ", proc.time() - .ptime,"\n")
-Time elapsed: 1.372 0.008 1.384 0 0
+Time elapsed: 1.676 0.012 1.695 0 0
>
diff --git a/tests/datasets.Rout.save b/tests/datasets.Rout.save
index 94cacbc..cbc4e08 100644
--- a/tests/datasets.Rout.save
+++ b/tests/datasets.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/datetime.Rout.save b/tests/datetime.Rout.save
index b32b056..9fe3ef0 100644
--- a/tests/datetime.Rout.save
+++ b/tests/datetime.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/datetime2.Rout.save b/tests/datetime2.Rout.save
index b42810a..7298196 100644
--- a/tests/datetime2.Rout.save
+++ b/tests/datetime2.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/demos.Rout.save b/tests/demos.Rout.save
index d807cb8..5efec96 100644
--- a/tests/demos.Rout.save
+++ b/tests/demos.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -1510,5 +1510,5 @@ sm 3 3 3 3 4 4 4 4 2 2 2
> par(op)
>
> cat("Time elapsed: ", proc.time() - .ptime, "\n")
-Time elapsed: 1.089 0.022 1.114 0 0
+Time elapsed: 1.516 0.04 1.561 0 0
>
diff --git a/tests/eval-etc.Rout.save b/tests/eval-etc.Rout.save
index e81ab09..422d0ea 100644
--- a/tests/eval-etc.Rout.save
+++ b/tests/eval-etc.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/iec60559.Rout.save b/tests/iec60559.Rout.save
index 5443889..eb67c5b 100644
--- a/tests/iec60559.Rout.save
+++ b/tests/iec60559.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/internet.Rout.save b/tests/internet.Rout.save
index 2c1bd50..55321ee 100644
--- a/tests/internet.Rout.save
+++ b/tests/internet.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -25,7 +25,7 @@ Type 'q()' to quit R.
> ap <- available.packages(contrib.url("http://cran.r-project.org"))
> ## IGNORE_RDIFF_BEGIN
> nrow(ap)
-[1] 11096
+[1] 11840
> ## IGNORE_RDIFF_END
>
> # test url connections on http
diff --git a/tests/isas-tests.Rout.save b/tests/isas-tests.Rout.save
index 95219c4..5724074 100644
--- a/tests/isas-tests.Rout.save
+++ b/tests/isas-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -2568,6 +2568,6 @@ In as.dist.default(x) : non-square matrix
> f <- try(as.ts( x ), silent = TRUE)
> if(!inherits(f, 'try-error')) report(identical(f, as.ts( f )))
> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
-Time elapsed: 0.169 0.009 0.178 0 0
+Time elapsed: 0.223 0.015 0.239 0 0
>
>
diff --git a/tests/lapack.Rout.save b/tests/lapack.Rout.save
index de932b2..f767c52 100644
--- a/tests/lapack.Rout.save
+++ b/tests/lapack.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/lm-tests.Rout.save b/tests/lm-tests.Rout.save
index a4aa82d..4bb9f87 100644
--- a/tests/lm-tests.Rout.save
+++ b/tests/lm-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/method-dispatch.Rout.save b/tests/method-dispatch.Rout.save
index 71cb7d5..30959c0 100644
--- a/tests/method-dispatch.Rout.save
+++ b/tests/method-dispatch.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/ok-errors.Rout.save b/tests/ok-errors.Rout.save
index 792f99a..d9dc2b5 100644
--- a/tests/ok-errors.Rout.save
+++ b/tests/ok-errors.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/p-r-random-tests.Rout.save b/tests/p-r-random-tests.Rout.save
index 9cad11e..ae03319 100644
--- a/tests/p-r-random-tests.Rout.save
+++ b/tests/p-r-random-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -278,6 +278,6 @@ f(df1 = 10, df2 = 2, ncp = 3) PASSED
>
>
> cat('Time elapsed: ', proc.time() - .proctime00,'\n')
-Time elapsed: 1.286 0 1.289 0 0
+Time elapsed: 1.526 0.006 1.536 0 0
>
>
diff --git a/tests/print-tests.Rout.save b/tests/print-tests.Rout.save
index 50ef9ce..2d15be2 100644
--- a/tests/print-tests.Rout.save
+++ b/tests/print-tests.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/reg-IO.Rout.save b/tests/reg-IO.Rout.save
index 1e764de..f754f14 100644
--- a/tests/reg-IO.Rout.save
+++ b/tests/reg-IO.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/reg-IO2.Rout.save b/tests/reg-IO2.Rout.save
index 33e8f06..634acf2 100644
--- a/tests/reg-IO2.Rout.save
+++ b/tests/reg-IO2.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/reg-S4.R b/tests/reg-S4.R
index 512ab7f..a73f49c 100644
--- a/tests/reg-S4.R
+++ b/tests/reg-S4.R
@@ -912,3 +912,7 @@ setGeneric("f")
setMethod("f", "character", function(...){ callNextMethod() })
stopifnot(identical(f(1, 2, 3), 3L))
stopifnot(identical(f("a", "b", "c"), 3L))
+
+## ensure forwarding works correctly for dots dispatch
+f2 <- function(...) f(...)
+stopifnot(identical(f2(a=1L), 1L))
diff --git a/tests/reg-S4.Rout.save b/tests/reg-S4.Rout.save
index 3e4d743..453e82f 100644
--- a/tests/reg-S4.Rout.save
+++ b/tests/reg-S4.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -665,9 +665,6 @@ An object of class "foo"
+ TRUE)
+ }
Loading required package: Matrix
-Note: method with signature 'numeric#dMatrix' chosen for function '>',
- target signature 'numeric#ddiMatrix'.
- "ANY#ddiMatrix" would also be valid
<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
>
>
@@ -1280,3 +1277,7 @@ Also defined by 'package2'
> stopifnot(identical(f(1, 2, 3), 3L))
> stopifnot(identical(f("a", "b", "c"), 3L))
>
+> ## ensure forwarding works correctly for dots dispatch
+> f2 <- function(...) f(...)
+> stopifnot(identical(f2(a=1L), 1L))
+>
diff --git a/tests/reg-examples3.Rout.save b/tests/reg-examples3.Rout.save
index 2565e0e..10779b2 100644
--- a/tests/reg-examples3.Rout.save
+++ b/tests/reg-examples3.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/reg-packages.R b/tests/reg-packages.R
index 73f65c6..c537842 100644
--- a/tests/reg-packages.R
+++ b/tests/reg-packages.R
@@ -38,7 +38,7 @@ build.pkg <- function(dir) {
stopifnot(dir.exists(dir))
patt <- paste(basename(dir), ".*tar\\.gz$", sep="_")
unlink(dir('.', pattern = patt))
- Rcmd <- paste(file.path(R.home("bin"), "R"), "CMD")
+ Rcmd <- paste(shQuote(file.path(R.home("bin"), "R")), "CMD")
r <- tail(system(paste(Rcmd, "build --keep-empty-dirs", shQuote(dir)),
intern = TRUE), 3)
## return name of tar file built
diff --git a/tests/reg-tests-2.Rout.save b/tests/reg-tests-2.Rout.save
index 9106e5a..7efe5eb 100644
--- a/tests/reg-tests-2.Rout.save
+++ b/tests/reg-tests-2.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -6371,7 +6371,7 @@ function(given = NULL) {
if (is.null(given)) callObj$default <- TRUE
callObj
}
-<bytecode: 0x5407a80>
+<bytecode: 0x582d438>
> print(foo, useSource = FALSE)
function (given = NULL)
{
@@ -6382,7 +6382,7 @@ function (given = NULL)
callObj$default <- TRUE
callObj
}
-<bytecode: 0x5407a80>
+<bytecode: 0x582d438>
> attr(foo, "srcref") <- NULL
> foo
function (given = NULL)
@@ -6394,7 +6394,7 @@ function (given = NULL)
callObj$default <- TRUE
callObj
}
-<bytecode: 0x5407a80>
+<bytecode: 0x582d438>
> (f <- structure(function(){}, note = "just a note",
+ yada = function() "not the same"))
function(){}
@@ -6416,15 +6416,15 @@ function ()
> print.function
function (x, ...)
- attr(*, "srcref")=Class 'srcref' atomic [1:8] 1 19 1 63 19 63 1 1
- .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x545ade0>
+ .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x5875e28>
> f
function ()
- attr(*, "srcref")=Class 'srcref' atomic [1:8] 1 17 1 28 17 28 1 1
- .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x5450730>
+ .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x586d660>
- attr(*, "note")= chr "just a note"
- attr(*, "yada")=function ()
..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 2 24 2 48 24 48 2 2
- .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x5450730>
+ .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x586d660>
> rm(print.function)
> ## auto-printing and printing differed up to R 2.9.x
>
diff --git a/tests/reg-tests-3.Rout.save b/tests/reg-tests-3.Rout.save
index 3e4df53..eebd48e 100644
--- a/tests/reg-tests-3.Rout.save
+++ b/tests/reg-tests-3.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/tests/simple-true.Rout.save b/tests/simple-true.Rout.save
index f8ee6fe..424b59f 100644
--- a/tests/simple-true.Rout.save
+++ b/tests/simple-true.Rout.save
@@ -1,5 +1,5 @@
-R version 3.4.1 Patched (2017-07-19 r72930) -- "Single Candle"
+R version 3.4.2 Patched (2017-11-17 r73741) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)