Commit b68dfcd0 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Debian changes 2.4.1-1

r-base (2.4.1-1) unstable; urgency=low

  * New upstream version released this morning
  
  * Debian package for 'unstable' as Debian 4.0 ('etch') is frozen

r-base (2.4.1~20061205-1) unstable; urgency=low

  * First beta package of the upcoming R 2.4.1 scheduled for December 18

r-base (2.4.0.20061125-1) unstable; urgency=low

  * New upstream version patch version dated 2006-11-03
    -- a new R 2.4.1 release should arrive in just a few weeks
  * debian/r-base-core.postinst: Rewrote paperconf handling one 
    more, with thanks to Marc Glisse for another good suggestion

r-base (2.4.0.20061103-1) unstable; urgency=low

  * New upstream version patch version dated 2006-11-03
    -- a new R 2.4.1 release may arrive in a few weeks

r-base (2.4.0.20061029-2) unstable; urgency=low

  * debian/r-cran.mk: Another brown paperbag fix, this time for the logic

r-base (2.4.0.20061029-1) unstable; urgency=low

  * New upstream version patch version taken from svn as of 2006-10-29 
    -- a new R 2.4.1 release may arrive in a few weeks
  
  * debian/r-cran.mk: Brown paperbag fix replacing space with tabs

r-base (2.4.0.20061027-1) unstable; urgency=low

  * New upstream version patch version dated 2006-10-27
    -- a proper R 2.4.1 is not expected until December 2006
  
  * debian/r-base-core.postinst: Rewrote paperconf handling (Closes: #394114)
  * debian/R.bash_completion: use updated version from Deepayan Sarkar
  * debian/r-cran.mk: If present, also install lintian overrides file
parents 05b86c71 e5673aca
......@@ -30,7 +30,7 @@ Makeconf: $(srcdir)/Makeconf.in $(top_builddir)/config.status
ACLOCAL_M4 = aclocal.m4
ACINCLUDE_DEPENDENCIES = \
m4/R.m4 \
m4/clibs.m4 \
m4/clibs.m4 m4/c99.m4 \
m4/codeset.m4 \
m4/gettext.m4 m4/gettext-lib.m4 \
m4/java.m4 \
......@@ -81,9 +81,6 @@ install: installdirs svnonly
@for f in $(INSTFILES); do \
$(INSTALL_DATA) $(srcdir)/$${f} "$(rhome)"; \
done
@for f in $(INSTFILES); do \
$(INSTALL_DATA) $(srcdir)/$${f} "$(rdocdir)"; \
done
@for f in $(NON_SVN_INSTFILES); do \
$(INSTALL_DATA) $${f} "$(rhome)"; \
done
......@@ -104,15 +101,7 @@ svnonly:
touch non-tarball ; \
(cd $(srcdir); LC_ALL=C TZ=GMT svn info || echo "Revision: unknown") 2> /dev/null \
| sed -n -e '/^Revision/p' -e '/^Last Changed Date/'p \
| cut -d' ' -f1,2,3,4 > SVN-REVISION-tmp ; \
if grep unknown SVN-REVISION-tmp > /dev/null ; then \
echo "Last Changed Date: Today" >> SVN-REVISION-tmp ; \
if test -f "$(srcdir)/.svn/entries" ; then \
rev=`grep committed-rev "$(srcdir)/.svn/entries" | head -1 | sed -e 's/^ *committed-rev=\"//' -e 's/\"//'`; \
cdate=`grep committed-date "$(srcdir)/.svn/entries" | head -1 | sed -e 's/^ *committed-date=\"//' -e 's/T.*//'`; \
sed -e "s/unknown/$${rev}/" -e "s/Today/$${cdate}/" SVN-REVISION-tmp > SVN-REVISION-tmp2; mv SVN-REVISION-tmp2 SVN-REVISION-tmp ; \
fi ; \
fi ; \
| cut -d' ' -f1,2,3,4 > SVN-REVISION-tmp ; \
$(top_srcdir)/tools/move-if-change SVN-REVISION-tmp SVN-REVISION ; \
rm -f SVN-REVISION-tmp ; \
else \
......
......@@ -6,6 +6,222 @@
**************************************************
CHANGES IN R VERSION 2.4.1
INSTALLATION
o The extraction of info from Subversion for an SVN checkout now
also works for svn >= 1.4.0. However, on Windows the 'Last
Changed Date' will be in the local timezone, and not in GMT as
previously.
o configure uses code borrowed from autoconf 2.60 to try harder to
ensure that a C99-compliant compiler is used. (It does so by
appending to CC.) This avoids problems with systems such as FC5
which override CFLAGS and thereby lose flags such as -std=gnu99.
NEW FEATURES
o rainbow(), heat.colors(), terrain.colors(), topo.colors() and
cm.colors() all gain an 'alpha' argument to be passed to hsv().
o dput() will give an incorrect representation of the row names
of a data frame with integer row names. This is now corrected
when the object is recreated.
C-LEVEL FACILITIES
o Using STRICT_R_HEADERS applies to more reported clashes with
Windows headers, including Calloc and Realloc. These and
Free need to be prefixed by R_ when STRICT_R_HEADERS is defined.
DEPRECATED & DEFUNCT
o The previously undocumented behaviour of structure() in adding a
class when specifying "tsp" or "levels" attributes is now
deprecated (with a warning).
BUG FIXES
o Fixed warning() to use .dfltWarn intead of .dfltStop for default
handling (PR#9274).
o R would slow down when the product of the length of a vector and
the length of a character vector used to subset it exceeded 2^31.
(PR#9280)
o merge() now allows zero-row data frames.
o add1.lm() had been broken by other changes for weighted fits.
o axis.POSIXct() would sometimes give the wrong labels.
o Help for a method call would fail. (PR#9291)
o gzfile() returned an object of class "file" not "gzfile". (PR#9271)
o load()ing from a connection had a logic bug in when it closed
the connection. (PR#9271)
o The lowess() algorithm is unstable if the MAD of the residuals
becomes (effectively) zero: R now terminates the iterations at
that point. (This may result in quite different answers.)
The 'delta' argument was incorrectly documented. (PR#9264)
o abbreviate() would only work for strings of up to 8191 bytes,
but this was not checked. Now longer strings are errors.
o Drawing X11 rotated text was buggy for VERY small (negative)
angle of rotation. Reported by Ben Bolker. (PR#9301)
o The X11 data editor would crash in an MBCS locale if R was
compiled with FC's CFLAGS that add buffer overflow and
stack-smashing detection.
o rect() was not accepting border=NA in some cases involving
cross-hatching.
o Fixes to S4 group generics to ensure that the correct number of
active arguments are in the signature of the group and all
members. Also a fix to keep the 'groupMembers' slot up to date.
o S4 group generic "Logic" (with '&', '|', but not '!') has been
created, following the green book (apart from '!').
o removeClass() now takes care to remove any subclass references
to the deleted class.
o mle() (in stats4) might not have worked as intended when the
order of parameters in 'start' differed from that in the
log-likelihood. (PR#9313)
o dotchart() now properly restores par() settings after itself.
o system() on Mac OS X was blocking arbitrary signals during the
call although only SIGPROF was meant to be blocked.
o methods cached via callNextMethod() and (sometimes) as() were
being cached as directly specified although in fact they were
inherited. Caused problems in later search for inherited methods.
o str() works properly for method definitions and other S4-classed
function objects.
o JAVA_LIBS are now set correctly on MacOS X.
o Fix null-termination issue suspected of causing crash with Fedora
Extra RPMS (PR#9339, Justin Harrington, analysis and fix from Bill
Dunlap).
o Namespaces restored via a saved session silently failed to cache
their methods because the methods package was not yet
attached. Fixed by attaching methods before restoring data.
o rbind()ing a list to a data frame generated invalid row names,
which were an error in 2.4.0. (PR#9346)
o boxplot.stats(x) now returns the correct minimum instead of an
error for x <- c(1,Inf,Inf,Inf), and hence boxplot(x) "works".
o promptClass() now uses \linkS4class{<ClassName>} instead of
of \link{<ClassName>-class}.
o gc() no longer reports nonsense values for the number of used
Vcells if the true value exceeds 2^31 (and hence over 16Gb of
heap is in use): it now reports NA. (PR#9345)
o rapply() now detects more user errors in supplying arguments. (PR#9349)
o boxplot() was ignoring argument 'boxfill'. (PR#9352)
o plot.lm(which = 6, id.n = 0) did not work. (PR#9333)
o .deparseOpts("delayPromises") was not matching the C code,
returning 64 rather than 32.
o bxp() could use partial matching on 'pars' when finding
defaults for some of its parameters, e.g. a setting of 'cex.axis'
in 'pars' or inline was used to set a default for 'outcex'.
o acf() now allows lag.max = 0 except when type="partial", and
forces the lag 0 autocorrelation to 1. (PR#9360)
o hist(*, include.lowest=., right=., plot=FALSE) does not warn
anymore, (PR#9356) and more.
o Some bugs in caching superclass/subclass relations and in
removing those relations on detach and on removeClass() have
been fixed.
o readBin() could return one too many strings if 'n' was an
over-estimate. (PR#9361)
o A request for an opaque colour in the pdf() device after a
translucent one did not set the transparency back to opaque in
2.4.0.
Semi-transparent background colours were not being plotted on
the pdf() device.
o plot.lm(which=5) in the case of constant leverage re-ordered
the factor levels but not the residuals, so the labelling by
factor level was often incorrect.
o packBits() was not accepting a logical argument. (PR#9374)
o make install was omitting doc/FAQ and doc/RESOURCES.
o A two-sample t.test(x, y, var.equal=TRUE) did not allow one of the
groups to be of size one.
o The "ts" method for print() failed on some corrupted objects
of class "ts", e.g. those without a "tsp" attribute.
o structure() reordered the "class" value given if there was a
"tsp" value specified.
o pairs() now does pass appropriate parts of '...' to the
'diag.panel' argument. (PR#9384)
o plot.lm() was using an incorrect estimate of dispersion for
some GLMs (including family=binomial and family=poisson).
(PR#9316)
o Subsetting operators were setting R_Visible too early, so
assignments in arguments could make the result invisible.
(PR#9263)
o The tk-GUI was displaying a warning due to an extra comma in
the list of manuals (PR#9396)
o packageDescription() now gives an explicit error on a corrupt
DESCRIPTION file.
o There was a scoping issue with tcltk callbacks given as
unevaluated expressions. This has only been partially fixed, a
complete fix probably requires redesign.
o trace() had its return value documented incorrectly and was
sometimes visible when it should not have been.
o pchisq() would sometimes use the wrong tail when calculating
non-central probabilities with lower.tail = FALSE. (PR#9406)
o rm() could remove the wrong objects when passed an expression.
(PR#9399) Now only names are allowed in the '...' argument,
and the incorrect documentation of what happened with
character objects is corrected.
o url() was not supporting 'encoding' except on file:// URLs.
CHANGES IN R VERSION 2.4.0
......
Revision: 39566
Last Changed Date: 2006-10-03
Revision: 40228
Last Changed Date: 2006-12-18
......@@ -43,12 +43,16 @@
## If unspecified, a search is made for gcc and cc (in that order).
## To override this choice, specify the name of the command which runs
## the compiler here, for example 'c89'.
## It is also convenient to set the architecture here, e.g. 'gcc -m32'.
## NB, as from R 2.5.0 configure will append flags for C99 compliance,
## e.g. CC=gcc -std=gnu99
## To avoid this, set contradictory flags (such as -ansi) as part of CFLAGS.
## CC=
## Debugging and optimization options for the C compiler.
## Use this to specify CFLAGS for the version of the C compiler
## specified above.
## If unspecified, defaults to '-g -O2 -std=gnu99' for gcc,
## If unspecified, defaults to '-g -O2' for gcc,
## and '-g' in all other cases except icc (for which see R-admin.html).
## CFLAGS=
......
This diff is collapsed.
......@@ -534,6 +534,8 @@ R_PROG_BROWSER
R_PROG_PDFVIEWER
AC_PROG_CC
## next is a macro borrowed from autoconf 2.60
AC_PROG_CC_C99
AC_PROG_GCC_TRADITIONAL
AC_PROG_CPP
......@@ -752,12 +754,6 @@ AC_CHECK_SIZEOF(long, 4)
AC_CHECK_SIZEOF(long long, 0)
AC_CHECK_SIZEOF(long double, 0)
if test "$ac_test_CFLAGS" != set; then
if test "$GCC" = yes; then
R_PROG_CC_FLAG([-std=gnu99], R_SH_VAR_ADD(CFLAGS, [-std=gnu99]))
fi
fi
R_PROG_CC_MAKEFRAG
R_PROG_CC_LO_MAKEFRAG
......@@ -890,7 +886,7 @@ case "${host_os}" in
linux*)
case "${CC}" in
## Intel compiler
*icc)
*icc*)
## icc declares __GNUC__, so it picks up CFLAGS intended for gcc.
if test "$ac_test_CFLAGS" != set; then
if test $ac_cv_prog_cc_g = yes; then
......@@ -1077,7 +1073,8 @@ if test -n "${XMKMF}"; then
cc=`echo ${cc} | sed "s/ .*//"`
## Paul Gilbert reported on R-devel 2006-04-13 a system with cc=""
if test -n "${cc}" ; then
if test "`which ${cc}`" = "`which ${CC}`"; then
r_cc_cmd=`echo ${CC} | sed "s/ .*//"`
if test "`which ${cc}`" = "`which ${r_cc_cmd}`"; then
shlib_ldflags=`${srcdir}/tools/GETMAKEVAL SHLIBLDFLAGS`
cpicflags=`${srcdir}/tools/GETMAKEVAL PICFLAGS`
fi
......@@ -1085,7 +1082,8 @@ if test -n "${XMKMF}"; then
cxx=`${srcdir}/tools/GETMAKEVAL CXX`
cxx=`echo ${cxx} | sed "s/ .*//"`
if test -n "${cxx}" ; then
if test "`which ${cxx}`" = "`which ${CXX}`"; then
r_cxx_cmd=`echo ${CXX} | sed "s/ .*//"`
if test "`which ${cxx}`" = "`which ${r_cxx_cmd}`"; then
cxxpicflags=`${srcdir}/tools/GETMAKEVAL CXXPICFLAGS`
fi
fi
......@@ -1289,12 +1287,12 @@ rm -f libconftest${DYLIB_EXT} conftest.c
;;
linux*) # GNU Linux/ELF
case "${CC}" in
## Intel compiler
*icc)
## Intel compiler: note that -c99 may have been appended
*icc*)
cpicflags="-fpic"
;;
## Portland Group
*pgcc)
*pgcc*)
cpicflags="-fpic"
;;
esac
......
### Copyright (C) 2005 Deepayan Sarkar <Deepayan.Sarkar@R-project.org>
### Copyright (C) 2005-2006 Deepayan Sarkar <Deepayan.Sarkar@R-project.org>
###
### This file provides programmable completion for R under the bash
### shell. It is made available under the terms of the GNU General
......@@ -10,13 +8,8 @@
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE. See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
### PURPOSE. See the GNU General Public License, available at
### http://www.gnu.org/licenses/gpl.txt, for more details.
### NOTE: This does NOT provide completion for commands within R, only
......@@ -28,6 +21,7 @@
### potentially useful (for the most part) to package developers, not
### regular users.
### NEWS: Updated for R 2.4.0 (October 2006)
### BUGS: As it stands, this is far from perfect. Known bugs include:
###
......@@ -87,11 +81,21 @@ _R()
--no-restore --vanilla --no-readline -q --quiet --silent --slave \
--verbose -d -g --args'
## these should end with a '=' and not be followed by a space.
## Unfortunately, I haven't figured out how to make that work.
## -nospace doesn't suppress the space, and if I add = at the end,
## they get completed as "--debugger\= " etc. Anyway, they are
## kept separate in anticipation of some future fix...
argOpts='--min-vsize --max-vsize --min-nsize --max-nsize \
--encoding --max-ppsize --debugger --debugger-args --gui'
--encoding --max-ppsize --debugger --debugger-args \
--gui --arch'
cmds='BATCH COMPILE SHLIB INSTALL REMOVE build check LINK Rprof \
Rdconv Rd2dvi Rd2txt Sd2Rd config'
Rdconv Rd2dvi Rd2txt Sd2Rd Sweave Stangle config'
fileNames='' # possible to have files in certain commands (e.g. BATCH)
dirNames=''
......@@ -285,6 +289,44 @@ _R()
dirNames=$( compgen -d -- "$cur" )
;;
Sweave)
## if last word is a filename (not starting with
## -) then nothing more is allowed
if [[ $COMP_CWORD -gt 3 ]] && \
[[ $lastToken != -* ]] ; then
return 0
else
furtherOpts=""
fileNames=$( compgen -f -X '!*.@(Rnw|rnw|Snw|snw)' -- "$cur" )
dirNames=$( compgen -d -- "$cur" )
fi
;;
Stangle)
## if last word is a filename (not starting with
## -) then nothing more is allowed
if [[ $COMP_CWORD -gt 3 ]] && \
[[ $lastToken != -* ]] ; then
return 0
else
furtherOpts=""
fileNames=$( compgen -f -X '!*.@(Rnw|rnw|Snw|snw)' -- "$cur" )
dirNames=$( compgen -d -- "$cur" )
fi
;;
config)
if [[ $COMP_CWORD -gt 3 ]] ; then
......@@ -447,7 +489,7 @@ complete -F _R -o filenames R
## Add more aliases here, e.g.
complete -F _R -o filenames R-2.2
#complete -F _R -o filenames R-2.4
......
r-base (2.4.1-1) unstable; urgency=low
* New upstream version released this morning
* Debian package for 'unstable' as Debian 4.0 ('etch') is frozen
-- Dirk Eddelbuettel <edd@debian.org> Mon, 18 Dec 2006 08:53:09 -0600
r-base (2.4.1~20061205-1) unstable; urgency=low
* First beta package of the upcoming R 2.4.1 scheduled for December 18
-- Dirk Eddelbuettel <edd@debian.org> Wed, 6 Dec 2006 22:51:18 -0600
r-base (2.4.0.20061125-1) unstable; urgency=low
* New upstream version patch version dated 2006-11-03
-- a new R 2.4.1 release should arrive in just a few weeks
* debian/r-base-core.postinst: Rewrote paperconf handling one
more, with thanks to Marc Glisse for another good suggestion
-- Dirk Eddelbuettel <edd@debian.org> Sun, 26 Nov 2006 18:21:16 -0600
r-base (2.4.0.20061103-1) unstable; urgency=low
* New upstream version patch version dated 2006-11-03
-- a new R 2.4.1 release may arrive in a few weeks
-- Dirk Eddelbuettel <edd@debian.org> Thu, 2 Nov 2006 21:50:13 -0600
r-base (2.4.0.20061029-2) unstable; urgency=low
* debian/r-cran.mk: Another brown paperbag fix, this time for the logic
-- Dirk Eddelbuettel <edd@debian.org> Sun, 29 Oct 2006 17:36:36 -0600
r-base (2.4.0.20061029-1) unstable; urgency=low
* New upstream version patch version taken from svn as of 2006-10-29
-- a new R 2.4.1 release may arrive in a few weeks
* debian/r-cran.mk: Brown paperbag fix replacing space with tabs
-- Dirk Eddelbuettel <edd@debian.org> Sun, 29 Oct 2006 11:35:16 -0600
r-base (2.4.0.20061027-1) unstable; urgency=low
* New upstream version patch version dated 2006-10-27
-- a proper R 2.4.1 is not expected until December 2006
* debian/r-base-core.postinst: Rewrote paperconf handling (Closes: #394114)
* debian/R.bash_completion: use updated version from Deepayan Sarkar
* debian/r-cran.mk: If present, also install lintian overrides file
-- Dirk Eddelbuettel <edd@debian.org> Sat, 28 Oct 2006 20:11:10 -0500
r-base (2.4.0-1) unstable; urgency=low
* New upstream version released this morning
......
......@@ -2,6 +2,7 @@
#
# postinst script for the Debian GNU/Linux r-base-core package
# This version originally written by Douglas Bates <bates@stat.wisc.edu>
# and now written and maintained by Dirk Eddelbuettel <edd@debian.org>
set -e
......@@ -9,62 +10,51 @@ set -e
case "$1" in
configure)
#if [ -x /usr/bin/paperconf ]
#then
# perl -pi -e \
# '$P=`/usr/bin/paperconf`,chop $P,s:a4:$P: if /{R_PAPERSIZE/' /usr/bin/R
#fi
# edd 19 June 2004 deal with papersize
# edd 22 June 2004 make that conditional on paperconf
if [ -x /usr/bin/paperconf ]
then
#Sysfile=`/etc/papersize`
#syspaper=`cat $Sysfile`
syspaper=`/usr/bin/paperconf`
#echo "Papersize in /etc is $syspaper"
Rfile=/etc/R/Renviron
rpaper=`grep ^R_PAPERSIZE $Rfile | cut -d"'" -f2`
#echo "Papersize in Renviron is $rpaper"
if [ "$syspaper" != "$rpaper" ]
then
echo "Changing R_PAPERSIZE from $rpaper to $syspaper"
perl -p -i -e "s|\'$rpaper\'|\'$syspaper\'|" "$Rfile"
fi
fi
if [ -x /usr/bin/update-menus ]
then
update-menus