[Rd] (Debian Bug 344248): R segfaults when pressing Delete (PR#8420)
--CE+1k2dSO48ffgeK Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Resend after type in mailheader. I have the bug on my system with yesterday's R 2.2.1. A library mismatch is still a likely cause. Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison --CE+1k2dSO48ffgeK Content-Type: message/rfc822 Content-Disposition: inline Return-path: <> X-Spam-Checker-Version: SpamAssassin 3.1.0 (2005-09-13) on basebud.nulle.part X-Spam-Level: X-Spam-Status: No, score=-2.5 required=4.9 tests=BAYES_00,FORGED_RCVD_HELO autolearn=ham version=3.1.0 Received: from sccrmhc11.comcast.net ([63.240.77.81]) by master.debian.org with esmtp (Exim 4.50) id 1Ep3A7-0001sJ-Py for [EMAIL PROTECTED]; Wed, 21 Dec 2005 06:33:43 -0600 Received: from basebud.nulle.part (c-67-174-11-185.hsd1.il.comcast.net[67.174.11.185]) by comcast.net (sccrmhc11) with ESMTP id <20051221123308011005fbjme>; Wed, 21 Dec 2005 12:33:13 + Received: from Debian-exim by basebud.nulle.part with local (Exim 4.60) id 1Ep39X-0005dm-5V for [EMAIL PROTECTED]; Wed, 21 Dec 2005 06:33:07 -0600 Auto-Submitted: auto-replied From: Mail Delivery System <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Subject: Mail failure - malformed recipient address Message-Id: <[EMAIL PROTECTED]> Date: Wed, 21 Dec 2005 06:33:07 -0600 Delivered-To: [EMAIL PROTECTED] A message that you sent contained one or more recipient addresses that were incorrectly constructed: [EMAIL PROTECTED]@ku.dk: malformed address: @ku.dk may not follow [EMAIL PROTECTED] This address has been ignored. The other addresses in the message were syntactically valid and have been passed on for an attempt at delivery. -- This is a copy of your message, including all the headers. -- MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <[EMAIL PROTECTED]> Date: Wed, 21 Dec 2005 06:33:07 -0600 To: [EMAIL PROTECTED]@ku.dk CC: Ethan Glasser-Camp <[EMAIL PROTECTED]>, [EMAIL PROTECTED], Subject: Re: Bug#344248: R crashes when I press "Delete" In-Reply-To: <[EMAIL PROTECTED]> References: <[EMAIL PROTECTED]> X-Mailer: VM 7.19 under Emacs 21.4.1 From: Dirk Eddelbuettel <[EMAIL PROTECTED]> X-rewrote-sender: [EMAIL PROTECTED] On 21 December 2005 at 01:50, Ethan Glasser-Camp wrote: | Package: r-base-core | Version: 2.2.1-1 | | When I run R, I can cause a crash by simply pressing Delete. Backspace works | fine, and I can use ESS without problems. Uh-oh. | [EMAIL PROTECTED]:~$ R | | R : Copyright 2005, The R Foundation for Statistical Computing | Version 2.2.1 (2005-12-20 r36812) | ISBN 3-900051-07-0 | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | R is a collaborative project with many contributors. | Type 'contributors()' for more information and | 'citation()' on how to cite R or R packages in publications. | | Type 'demo()' for some demos, 'help()' for on-line help, or | 'help.start()' for an HTML browser interface to help. | Type 'q()' to quit R. | | [Previously saved workspace restored] Could you (temporarily) remove that file? | > Segmentation fault | [EMAIL PROTECTED]:~$ That said, I just tried this where I seemed to have no ~/.RData file. Pressing leads to a SegFault. I will pass this on R Core. Thanks for the bug report. Dirk | | | Here is a list of packages I thought might be relevant: | | $ dpkg -l r-* libreadline* | Desired=Unknown/Install/Remove/Purge/Hold | | Status=Not/Installed/Config-files/Unpacked/Failed-config/Half-installed | |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad) | ||/ Name VersionDescription | +++-==-==- | un libreadline-co (no description available) | un libreadline-de (no description available) | ii libreadline-ru 1.8.3+1.8.4pre Readline interface for Ruby 1.8 | ii libreadline4 4.3-18 GNU readline and history libraries, run-time | un libreadline4-d (no description available) | ii libreadline5 5.1-1 GNU readline and history libraries, run-time | ii libreadline5-d 5.1-1 GNU readline and history libraries, developm | ii r-base 2.2.1-1GNU R statistical computing language and env | ii r-base-core2.2.1-1GNU R core of statistical computing language | un r-base-dev (no description available) | ii r-base-html2.2.1-1GNU R html docs for statistical computing sy | ii r-base-latex 2.2.1-1GNU R LaTeX docs for statistical computing s | ii r-cran-boot1.2.24-1 GNU R package for bootstrapping functions fr | ii r-cran-cluster 1.10.2-1 GNU
Re: [Rd] rJava downloads but cannot load, (PR#13997)
On 10 October 2009 at 05:40, lmra...@gmail.com wrote:
| > library(rJava)
| Error in library(rJava) : there is no package called 'rJava'
| > install.packages("rJava")
| Warning in install.packages("rJava") :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| trying URL 'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz'
| Content type 'application/x-gzip' length 249486 bytes (243 Kb)
| opened URL
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
| downloaded 243 Kb
|
| * Installing *source* package =91rJava=92 ...
| checking for gcc... gcc -std=3Dgnu99
| checking for C compiler default output file name... a.out
[...]
| configure: checking whether gcc -std=3Dgnu99 supports static inline...
| yes
| checking Java support in R... present:
| interpreter : '/usr/bin/java'
| archiver: '/usr/bin/jar'
| compiler: '/usr/bin/javac'
| header prep.: '/usr/bin/javah'
| cpp flags : ''
| java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server
| -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
| -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L
| -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
| configure: error: One or more Java configuration variables are not set.
| Make sure R is configured with full Java support (including JDK). Run
| R CMD javareconf
| as root to add Java support to R.
R tells you your Java setup is not right. This *is* difficult, which is why I
have offered to maintain and provide the rJava in Debian / Ubuntu as
r-cran-rjava.
As demonstrated to you two emails ago, it also works. I would use that.
Otherwise, fix your Java setup first as R told you to here.
|
| If you don't have root privileges, run
| R CMD javareconf -e
| to set all Java-related variables and then install rJava.
|
| ERROR: configuration failed for package =91rJava=92
| * Removing =91/usr/local/lib/R/site-library/rJava=92
|
| The downloaded packages are in
| =91/tmp/RtmpOjM9hY/downloaded_packages=92
| Warning message:
| In install.packages("rJava") :
| installation of package 'rJava' had non-zero exit status
| >
|
|
| I went ahead and did this:
|
| r...@lmramba-laptop:/home/lmramba# R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_0
| Java home path : /usr/lib/jvm/java-6-openjdk/jre
| Java compiler: /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
| Java library path:
| $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386=
| ::/usr/java/packages/lib/i386:/lib:/usr/lib
| JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
| -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib
| -L/usr/lib -ljvm
| JNI cpp flags:
| Updating Java configuration in /etc/R
| Done.
|
|
| But still installing rJava fails
As before: not a bug in R and you just created extra work for R Core to
maintain the bug database.
Dirk
| Plz help
|
| Regards,
| Lazarus
|
| [[alternative HTML version deleted]]
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
Three out of two people have difficulties with fractions.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] installing any package fails using 'install.packages()' (PR#13996)
On 10 October 2009 at 05:25, lmra...@gmail.com wrote:
| Dear all,
| I installed my R-2.9.2 on my ubuntu version 9.04 successfully using=
the
| command
|=20
|sudo apt-get install r-base-dev
|=20
| The problem is that I cannot install any package.
Huh? This has _nothing_ to do with the error below.
=20
| See my details below:
|=20
|=20
|=20
| > install.packages("epicalc")
| Warning in install.packages("epicalc") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
This is suspicuous.=20
If you used the Ubuntu package, it would use /usr/local/lib/R/site-libr=
ary by
default. So if you have a locally built version *you* need to figure o=
ut
what you broke there.
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| Error in read.dcf(file =3D tmpf) : Line starting ' ...' is malf=
ormed!
| >
| > install.packages("lattice")
| Warning in install.packages("lattice") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| Error in read.dcf(file =3D tmpf) : Line starting ' ...' is malf=
ormed!
No idea but you busted there. But it looks suspiciously like a local er=
ror on
your end.
Set an explicit argument for the repos, e.g. via ~/.Rprofile
options("repos"=3D"http://cran.us.r-project.org";)## US mirror
(as I am in the US, adapt accordingly for a close mirror for you) to av=
oid
the tcl/tk query. =20
That, again, works like a charm here on Ubuntu 9.10:
R> install.packages("epicalc")
Warning in install.packages("epicalc") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
trying URL 'http://cran.us.r-project.org/src/contrib/epicalc_2.9.2.5.ta=
r.gz'
Content type 'application/x-gzip' length 201849 bytes (197 Kb) =
=20
opened URL =
=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D =20
downloaded 197 Kb =
=20
* Installing *source* package =E2=80=98epicalc=E2=80=99 ...
** R =20
** data =20
** demo =20
** preparing package for lazy loading =20
Loading required package: splines =20
** help =20
*** installing help indices =20
>>> Building/Updating help pages for package 'epicalc'
Formats: text html latex example =20
ANCdata texthtmllatex
[...]
use texthtmllatex example
zap texthtmllatex example
** building package indices ...
* DONE (epicalc)
The downloaded packages are in
=E2=80=98/tmp/RtmpydkfiZ/downloaded_packages=E2=80=99
R>
If you install into /usr/local/lib/R/site-library, I recommend making t=
hat
directory's group mode one of the ones you have and set it to group-wri=
te. I
typically make myself member of group 'staff' (or 'admin').
Again, in sum: not a bug in R and you just created extra work for R Cor=
e to
maintain the bug database.
Dirk
| > sessionInfo()
| R version 2.9.2 (2009-08-24)
| i486-pc-linux-gnu
|=20
| locale:
| LC_CTYPE=3Den_GB.UTF-8;LC_NUMERIC=3DC;LC_TIME=3Den_GB.UTF-8;LC_COLLAT=
E=3Den_GB.UTF-8;LC_MONETARY=3DC;LC_MESSAGES=3Den_GB.UTF-8;LC_PAPER=3Den=
_GB.UTF-8;LC_NAME=3DC;LC_ADDRESS=3DC;LC_TELEPHONE=3DC;LC_MEASUREMENT=3D=
en_GB.UTF-8;LC_IDENTIFICATION=3DC
|=20
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|=20
| loaded via a namespace (and not attached):
| [1] tcltk_2.9.2 tools_2.9.2
| >
|=20
| =09[[alternative HTML version deleted]]
|=20
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--=20
Three out of two people have difficulties with fractions.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Bug#424696: R CMD INSTALL -l does not create path (PR#9691)
Soeren,
On 16 May 2007 at 23:00, Soeren Sonnenburg wrote:
| Package: r-base-core
| Version: 2.5.1~20070513-1[ aka R-patched as of 20070513 ]
| Severity: important
|
| R CMD INSTALL -l /path/to/lib
|
| no longer creates /path/to/lib but assumes it does already exist. This
| is a change in behaviour as it has worked with R 2.4.X
Let me pass that on to R Bugs then as it is in no way related to any Debian
changes.
Thanks, Dirk
| looking at /usr/lib/R/bin/INSTALL, the problem seems to be in the block
starting at line 298:
|
|
|
| lib=`tilde_expand "${lib}"`
| if test -z "${lib}"; then
| lib=`echo "cat('\n~~~', .libPaths()[1], '\n', sep = '')" | \
| R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave | \
| grep '^~~~' | sed 's/.*~~~//'`
| message "Installing to library '$lib'"
| else
| lib0=${lib}
| cd ${lib}<-- PROBLEM directory must not exist (call
MKDIR_P before ?)
| lib=`${GETWD}`
| cd ${startdir}
| fi
|
|
| -- System Information:
| Debian Release: lenny/sid
| APT prefers stable
| APT policy: (700, 'stable'), (650, 'testing'), (600, 'unstable'), (1,
'experimental')
| Architecture: i386 (i686)
|
| Kernel: Linux 2.6.21.1-sonne (SMP w/2 CPU cores; PREEMPT)
| Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
| Shell: /bin/sh linked to /bin/dash
|
| Versions of packages r-base-core depends on:
| ii atlas3-base [libblas.so.3 3.6.0-20.6 Automatically Tuned Linear
Algebra
| ii atlas3-sse2 [libblas.so.3 3.6.0-20.6 Automatically Tuned Linear
Algebra
| ii libbz2-1.01.0.3-6high-quality block-sorting file
co
| ii libc6 2.5-7 GNU C Library: Shared libraries
| ii libgfortran1 4.1.2-7Runtime library for GNU Fortran
ap
| ii libice6 1:1.0.3-2 X11 Inter-Client Exchange library
| ii libjpeg62 6b-13 The Independent JPEG Group's
JPEG
| ii libpaper-utils1.1.21 Library for handling paper
charact
| ii libpcre3 6.7-1 Perl 5 Compatible Regular
Expressi
| ii libpng12-01.2.15~beta5-1 PNG library - runtime
| ii libreadline5 5.2-2 GNU readline and history
libraries
| ii libsm62:1.0.3-1 X11 Session Management library
| ii libx11-6 2:1.0.3-7 X11 client-side library
| ii libxt61:1.0.5-2 X11 toolkit intrinsics library
| ii perl 5.8.8-7Larry Wall's Practical
Extraction
| ii refblas3 [libblas.so.3] 1.2-8 Basic Linear Algebra Subroutines
3
| ii tcl8.48.4.12-1.1 Tcl (the Tool Command Language)
v8
| ii tk8.4 8.4.12-1 Tk toolkit for Tcl and X11, v8.4
-
| ii unzip 5.52-9 De-archiver for .zip files
| ii zip 2.32-1 Archiver for .zip files
| ii zlib1g1:1.2.3-14 compression library - runtime
|
| Versions of packages r-base-core recommends:
| ii r-base-dev 2.5.1~20070513-1 GNU R installation of auxiliary
GN
| ii r-recommended 2.5.1~20070513-1 GNU R collection of recommended
pa
|
| -- no debconf information
|
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] package gsl assumes incorrect gcc version during install (PR#10456)
On 22 November 2007 at 20:00, [EMAIL PROTECTED] wrote:
| Full_Name: Levi Waldron
| Version: 2.5.1
| OS: Ubuntu Gutsy
| Submission from: (NULL) (206.248.157.88)
|
|
| I installed libgsl0-dev then tried to install the gsl cran package,
| unsuccessfully (see output below). As a workaround I created a symbolic link
to
| /usr/bin/gcc-4.2, ie:
|
| sudo ln -s /usr/bin/gcc-4.1 /usr/bin/gcc-4.2
I would strongly advise not to do that.
| The correct behavior of the gsl package should be to use the executable
| '/usr/bin/gcc' which is already linked to the current gcc version.
No. You misunderstand. It has nothing to do with the package.
When R is built, it 'stores' its compiler version etc in the file
Makeconf. The Debian (and hence Ubuntu) packages store that file for you as
/etc/R/Makeconf via a link; the file is as always in $RHOME/etc/Makeconf.
This file defines a variable CC for the compiler. All you need to do is to
set it back to 'gcc' from its value 'gcc-4.2'.
This really is a local admin issue (ie you need to fix it) and not a problem
with R, or gsl.
If you got R from Ubuntu, file a bug report _with Ubuntu_ as they seem to
have forgotten to switch from gcc-4.2 (which we use in Debian as default) to
gcc-4.1 (which is Ubuntu's default).
| > install.packages("gsl",dependencies=T)
| Warning in install.packages("gsl", dependencies = T) :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| trying URL 'http://probability.ca/cran/src/contrib/gsl_1.8-8.tar.gz'
| Content type 'application/x-tar' length 59084 bytes
| opened URL
| ==
| downloaded 57Kb
|
| * Installing *source* package 'gsl' ...
| checking for gcc... gcc
| checking for C compiler default output... a.out
| checking whether the C compiler works... yes
| checking whether we are cross compiling... no
| checking for suffix of executables...
| checking for suffix of object files... o
| checking whether we are using the GNU C compiler... yes
| checking whether gcc accepts -g... yes
| checking for gcc option to accept ANSI C... none needed
| checking for gsl_sf_airy_Ai_e in -lgsl... yes
| checking how to run the C preprocessor... gcc -E
| checking for egrep... grep -E
| checking for ANSI C header files... yes
| checking for sys/types.h... yes
| checking for sys/stat.h... yes
| checking for stdlib.h... yes
| checking for string.h... yes
| checking for memory.h... yes
| checking for strings.h... yes
| checking for inttypes.h... yes
| checking for stdint.h... yes
| checking for unistd.h... yes
| checking gsl/gsl_version.h usability... yes
| checking gsl/gsl_version.h presence... yes
| checking for gsl/gsl_version.h... yes
| checking if GSL version >= 1.8... yes
| configure: creating ./config.status
| ** libs
| gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic
-g
| -O2 -c airy.c -o airy.o
| /bin/bash: gcc-4.2: command not found
| make: *** [airy.o] Error 127
| chmod: cannot access `/usr/local/lib/R/site-library/gsl/libs/*': No such file
or
| directory
| ERROR: compilation failed for package 'gsl'
| ** Removing '/usr/local/lib/R/site-library/gsl'
|
| The downloaded packages are in
| /tmp/RtmpW60zFl/downloaded_packages
| Warning message:
| installation of package 'gsl' had non-zero exit status in:
| install.packages("gsl", dependencies = T)
|
| > version
|_
| platform i486-pc-linux-gnu
| arch i486
| os linux-gnu
| system i486, linux-gnu
| status
| major 2
| minor 5.1
| year 2007
| month 06
| day27
| svn rev42083
| language R
| version.string R version 2.5.1 (2007-06-27)
Also note that CRAN has prebuilt versions of the current R release, ie 2.6.0,
for Ubuntu Gutsy, see $CRAN/bin/linux/ubuntu
The CRAN version of R for Ubuntu is quite possibly of better quality than the
distro's version.
Dirk
| >
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
Three out of two people have difficulties with fractions.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Bug#454678: r-base-core: Crash when calling edit.matrix with edit.row.names = TRUE when there are no rownames (PR#10500)
Ben,
Thanks for the bug report. I am off two minds about it as discussed below.
But as it does indeed create a crash / segfault, I am passing this on to the
R bug tracker. A suggested two-line patch is below; I tested the patch
against a 'vanilla' 2.6.1 source tree.
On 6 December 2007 at 19:32, Ben Goodrich wrote:
| -BEGIN PGP SIGNED MESSAGE-
| Hash: SHA1
|
| Package: r-base-core
| Version: 2.6.1-1
| Severity: important
|
| Hi Dirk,
|
| My strong hunch is that this bug should just be forwarded upstream but
| it might have something to do with libc6 on Debian. To reproduce it, do
|
| args(utils:::edit.matrix)
| mat <- matrix(rnorm(30), nrow = 10, ncol = 3)
| edit(mat, edit.row.names = TRUE) #crash
I can confirm that it crashes 2.6.0 and 2.6.1. I also spent the last little
while building a (non-stripped) debug version that reveals:
(gdb) where
#0 0xb7b2ef2c in __gconv_transform_utf8_internal () from
/lib/i686/cmov/libc.so.6
#1 0xb7b89f75 in mbrtowc () from /lib/i686/cmov/libc.so.6
#2 0xb7db05e3 in Rstrwid (str=0x8052010 "\020!\005\b\002", slen=134595712,
quote=0) at printutils.c:284
#3 0xb7db0888 in Rstrlen (s=0x8051ff8, quote=0) at printutils.c:377
#4 0xb7d2de24 in Rf_formatString (x=0x873bbb8, n=1, fieldwidth=0xbfd0fc04,
quote=0) at format.c:62
#5 0xb7db12b5 in Rf_EncodeElement (x=0x873ba10, indx=100, quote=0, dec=46 '.')
at printutils.c:576
#6 0xb754ae0d in get_col_width (DE=0xbfd100b0, col=1) at dataentry.c:804
#7 0xb754edb4 in initwin (DE=0xbfd100b0, title=0xb755eed9 "R Data Editor")
at dataentry.c:1986
#8 0xb7549319 in RX11_dataentry (call=0x89b3fe8, op=0x806c970, args=0x8ba40c8,
rho=0x89b4bd0) at dataentry.c:382
#9 0xb7e52771 in do_dataentry (call=0x89b3fe8, op=0x806c970, args=0x8ba40c8,
rho=0x89b4bd0) at X11.c:91
#10 0xb7d6045e in do_internal (call=0x89b4020, op=0x8061fa4, args=0x8ba40c8,
env=0x89b4bd0) at names.c:1120
#11 0xb7d1f352 in Rf_eval (e=0x89b4020, rho=0x89b4bd0) at eval.c:463
#12 0xb7d21d5d in do_set (call=0x89b4074, op=0x8060df0, args=0x89b4058,
rho=0x89b4bd0) at eval.c:1407
#13 0xb7d1f352 in Rf_eval (e=0x89b4074, rho=0x89b4bd0) at eval.c:463
#14 0xb7d212b4 in do_begin (call=0x89b2798, op=0x8062458, args=0x89b4090,
rho=0x89b4bd0) at eval.c:1159
#15 0xb7d1f352 in Rf_eval (e=0x89b2798, rho=0x89b4bd0) at eval.c:463
#16 0xb7d1fb67 in Rf_applyClosure (call=0x89b1c9c, op=0x89b1ba0,
arglist=0x89b1e24, rho=0x89b1d7c, suppliedenv=0x89b1cd4) at eval.c:669
#17 0xb7d60a32 in applyMethod (call=0x89b1c9c, op=0x89b1ba0, args=0x89b1e24,
rho=0x89b1d7c, newrho=0x89b1cd4) at objects.c:126
#18 0xb7d61223 in Rf_usemethod (generic=0x8069af8 "edit", obj=0x8a87868,
call=0x89b1e94, args=0x8052110, rho=0x89b1d7c, callrho=0x8073f9c,
defrho=0x828f2fc, ans=0xbfd10d00) at objects.c:291
#19 0xb7d61776 in do_usemethod (call=0x89b1e94, op=0x80711b8, args=0x89b1e78,
env=0x89b1d7c) at objects.c:399
#20 0xb7d1f352 in Rf_eval (e=0x89b1e94, rho=0x89b1d7c) at eval.c:463
#21 0xb7d1fb67 in Rf_applyClosure (call=0x89b2230, op=0x89b2150,
arglist=0x89b1e24, rho=0x8073f9c, suppliedenv=0x8073fb8) at eval.c:669
#22 0xb7d1f601 in Rf_eval (e=0x89b2230, rho=0x8073f9c) at eval.c:507
#23 0xb7d4a879 in Rf_ReplIteration (rho=0x8073f9c, savestack=0, browselevel=0,
state=0xbfd1116c) at main.c:263
#24 0xb7d4aa61 in R_ReplConsole (rho=0x8073f9c, savestack=0, browselevel=0)
at main.c:312
#25 0xb7d4bec7 in run_Rmainloop () at main.c:975
#26 0xb7d4beee in Rf_mainloop () at main.c:982
#27 0x08048733 in main (ac=0, av=0x0) at Rmain.c:35
#28 0xb7b27450 in __libc_start_main () from /lib/i686/cmov/libc.so.6
#29 0x08048691 in _start ()
(gdb) up
Now, two comments.
Firstly, we all prefer if R would not crash. So this may need some fixing.
Secondly, I think you are rather close to bordering on user error. As your
snippet shows, you need to invoke args on the non-exported edit.matrix to
learn about the edit.row.names argument. Moreover, you also know full well
from looking at this that this will only be true when there actually are
names set --- and you then proceed to call it when there are none. Guess
what: it blows up.
So we could fix this in a number of places. Here is one which I tested; R
Core may opt to apply this, or a better version, or to drop the issue:
[EMAIL PROTECTED]:~/src/debian/R> diff -u
R-2.6.1/src/library/utils/R/edit.R{.orig,}
--- R-2.6.1/src/library/utils/R/edit.R.orig 2007-09-04 17:12:32.0
-0500
+++ R-2.6.1/src/library/utils/R/edit.R 2007-12-06 21:12:32.0 -0600
@@ -166,6 +166,8 @@
else names(datalist) <- paste("col", 1:ncol(name), sep = "")
modes <- as.list(rep.int(mode(name), ncol(name)))
if (edit.row.names) {
+if (is.null(dn[[1]])) ## true if forced edit.row.names as TRUE on null
+dn[[1]] <- paste("row", 1:dim(name)[1], sep="")
datalist <- c(list(row.names = dn[[1]]), datalist)
modes <- c(list(row.names = "character"), modes)
}
This results in
Re: [Rd] r won't start: "r: symbol lookup error: r: undefined symbol: (PR#11274)
On 24 April 2008 at 20:20, [EMAIL PROTECTED] wrote:
| Full_Name: Jakob Stoeger
| Version: 2.7.0
| OS: ubuntu 7.10
| Submission from: (NULL) (137.248.74.38)
|
|
| Hi!
|
| I hope, it is justified to write this email...
| I'm relatively new to linux, and haven't worked with r, yet, so please pardon
| any things I do not know...
|
| I tried installing r on my computer, and didn't manage to get the program
| running.
| After having installed littler, typing r into the bash results in following
| message:
|
| r: symbol lookup error: r: undefined symbol: R_Visible
You need to rebuild littler ('r') against the new version of R ('R').
I did that for Debian, looks like Ubuntu could do with it too. Your R
version was provided by volunteers outside of Ubuntu.
Vincent: In a perfect world, could you rebuild littler and provide it?
Jakob: Barring a new littler you can apt-get, the easiest may be to just
uninstall littler and rebuild it locally so that thew R 2.7.0 is used.
Ping me, or better still, the r-sig-debian list, with questions if you have
any. You need to subscribe to r-sig-debian before you can post there.
Lastly, if you only want or use R, use R :) 'r' is for scripting and short
command-line uses.
Dirk
PS It is the same with RPy.
| I found a bugreport here:
| http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=418686
| I'm not sure, if this has anything to do with it, as it concerns rkward...
|
| Anyway, this information might come handy:
| my system:
| ubuntu 7.10
| Kernel 2.6.22-14-generic
| GNOME 2.20.1
|
| installed packages:
| r-base 2.7.0-1gutsy0
| r-base-core 2.7.1gutsy0
| r-cran-cluster 1.11.10-1gutsy0
| r-cran-boot 1.2.32-1gutsy0
| r-cran-cluster 1.11.10-1gutsy0
| r-cran-codetools 0.2-0-1gutsy0
| r-cran-foreign 0.8.24-1gutsy0
| r-cran-kernsmooth 2.22.22-1gutsy0
| r-cran-lattice 0.17-6-1gutsy0
| r-cran-mgcv 1.3-30-1gutsy0
| r-cran-nlme 3.1.88-1gutsy0
| r-cran-rpart 3.1.41-1gutsy0
| r-cran-survival 2.34-1gutsy0
| r-cran-vr 7.2.41-1gutsy0
|
| rkward 0.4.7a-1ubuntu1
|
| r-recommended 2.7.0-1gutsy0
|
|
| I can't guarantee, that this list is complete, as I don't know (yet), how to
| check for it...
|
| Not really relevant, but I feel that I should tell you:
|
| The university at which I study used to use SPSS. Until this term, from which
on
| we will officially use r. Yeah!
|
| So, I hope you can help me getting r working. If I can help by doing anything,
| please tell me how...
| Also, I hope, this is a problem with r and not with my ubuntu, in which case I
| probably wouldn't have contacted you, if I would have known...
|
| Thank you very much!
|
| All the best,
| Jakob
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
Three out of two people have difficulties with fractions.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] (PR#11281) Bug in R 2.7 for over long lines
On 13 May 2008 at 09:46, Soeren Sonnenburg wrote:
| On Tue, 2008-05-13 at 09:01 +0200, Martin Maechler wrote:
| > > "BDR" == Prof Brian Ripley <[EMAIL PROTECTED]>
| > > on Tue, 13 May 2008 07:32:43 +0100 (BST) writes:
| >
| > BDR> This example does not crash in R 2.7.0, R-patched nor
| > BDR> R-devel (r45677) for me (x86_64 F8 Linux.) It also
| > BDR> does not crash with the CRAN build of R 2.7.0 on
| > BDR> Windows XP.
| >
| > Neither does it for me in R 2.7.0
| > on two x86_64 Linux platforms:
| >Ubuntu 8.04 and Redhat Enterprise 5.1
|
| ?source("http://nn7.de/debugging/Features.R";)
|
| crashes here on debian-sid (32bit x86 architecture).
|
| @dirk: could you give it a go on some debian x86 and amd64 machine?
I don't have easy access to amd64. I could test on x86 for Debian testing,
and in the unstable chroot, but aren't those cases already covered?
Dirk
--
Three out of two people have difficulties with fractions.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R-sig-Debian] problem with update.packages (PR#13161)
On 14 October 2008 at 09:39, Simon Blomberg wrote: | Hi, is anyone else getting this error? Could this be a bug?: | | > update.packages(ask=FALSE) | Error in read.dcf(pkgpath, fields = fields) : | Line starting 'unix; ...' is malformed! | | > sessionInfo() | R version 2.8.0 RC (2008-10-12 r46696) | x86_64-pc-linux-gnu Confirmed in plain R using the same package built this morning from last night's tarball from Denmark: Running update.packages() yields: > update.packages() --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done Error in read.dcf(pkgpath, fields = fields) : Line starting 'unix; ...' is malformed! OTOH I don't have a problem running my 'update.r' script (included in littler as /usr/share/doc/littler/examples/update.r) which just downloaded / upgraded ten packages. It is equivalent to calling > repos <- "http://cran.r-project.org"; > lib.loc <- "/usr/local/lib/R/site-library" > update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc) and that sequence also works in plain R. Could someone please dig into update.packages() ? Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Bug#505698: r-base-core: dev2bitmap fails with gsexe related error (PR#13288)
Stefano,
Thanks for the bug report.
On 14 November 2008 at 14:35, Stefano Costa wrote:
| Package: r-base-core
| Version: 2.8.0-1
| Severity: normal
|
| As in subject. The bug is reproducible on my machine with these
| commands:
|
| > x <- rnorm(100)
| > plot(density(x))
| > dev2bitmap("density.png")
| Error in paste(shQuote(gsexe), " -dNOPAUSE -dBATCH -q -sDEVICE=", type,
| :
| object "extra" not found
| >
Confirmed. The code in looks a little off inasmuch as in
if (!is.na(taa))
extra <- paste(" -dTextAlphaBits=", taa, sep = "")
if (!is.na(gaa))
extra <- paste(extra, " -dGraphicsAlphaBits=", gaa, sep = "")
cmd <- paste(shQuote(gsexe), " -dNOPAUSE -dBATCH -q -sDEVICE=",
type, " -r", res, "-dAutoRotatePages=/None", " -g", ceiling(res *
width), "x", ceiling(res * height), extra, " -sOutputFile=",
shQuote(file), " ", tmp, sep = "")
system(cmd)
'extra' does get set if and only if taa or gaa are given. Adding a simple
extra <- ""
before the quoted code block fixes the trivial bug. I am CC'ing upstream.
All that said, you may also want to consider the somewhat better usage of
x <- rnorm(100)
png("density.png") ## also see additional png arguments
plot(density(x))
dev.off()
to create density.png.
Thanks, Dirk
|
|
| Best,
| Steko
|
|
|
| -- System Information:
| Debian Release: lenny/sid
| APT prefers unstable
| APT policy: (500, 'unstable'), (101, 'experimental')
| Architecture: amd64 (x86_64)
|
| Kernel: Linux 2.6.26-1-amd64 (SMP w/2 CPU cores)
| Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8)
| Shell: /bin/sh linked to /bin/dash
|
| Versions of packages r-base-core depends on:
| ii libatlas3gf-base [libl 3.6.0-22 Automatically Tuned Linear
Algebra
| ii libblas3gf [libblas.so 1.2-2 Basic Linear Algebra Subroutines
3
| ii libc6 2.7-16GNU C Library: Shared libraries
| ii libcairo2 1.6.4-6.1 The Cairo 2D vector graphics
libra
| ii libgfortran3 4.3.2-1 Runtime library for GNU Fortran
ap
| ii libglib2.0-0 2.16.6-1 The GLib library of C routines
| ii libice62:1.0.4-1 X11 Inter-Client Exchange library
| ii libjpeg62 6b-14 The Independent JPEG Group's
JPEG
| ii liblapack3gf [liblapac 3.1.1-6 library of linear algebra
routines
| ii libpango1.0-0 1.20.5-3 Layout and rendering of
internatio
| ii libpaper-utils 1.1.23+nmu1 library for handling paper
charact
| ii libpcre3 7.8-2 Perl 5 Compatible Regular
Expressi
| ii libpng12-0 1.2.27-2 PNG library - runtime
| ii libreadline5 5.2-3 GNU readline and history
libraries
| ii libsm6 2:1.0.3-2 X11 Session Management library
| ii libtiff4 3.8.2-11 Tag Image File Format (TIFF)
libra
| ii libx11-6 2:1.1.5-2 X11 client-side library
| ii libxext6 2:1.0.4-1 X11 miscellaneous extension
librar
| ii libxss11:1.1.3-1 X11 Screen Saver extension
library
| ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library
| ii perl 5.10.0-17 Larry Wall's Practical
Extraction
| ii tcl8.5 8.5.3-2 Tcl (the Tool Command Language)
v8
| ii tk8.5 8.5.3-4 Tk toolkit for Tcl and X11, v8.5
-
| ii ucf3.0010Update Configuration File:
preserv
| ii unzip 5.52-12 De-archiver for .zip files
| ii zip2.32-1Archiver for .zip files
| ii zlib1g 1:1.2.3.3.dfsg-12 compression library - runtime
|
| Versions of packages r-base-core recommends:
| ii r-base-dev2.8.0-1GNU R installation of auxiliary
GN
| ii r-recommended 2.8.0-1GNU R collection of recommended
pa
|
| Versions of packages r-base-core suggests:
| pn ess(no description available)
| ii r-base-html 2.8.0-1GNU R html docs for statistical
co
| ii r-base-latex 2.8.0-1GNU R LaTeX docs for statistical
c
| pn r-doc-info | r-doc-pdf | r-do (no description available)
| pn r-mathlib (no description available)
|
| -- no debconf information
|
|
--
Three out of two people have difficulties with fractions.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
