Re: [Rd] MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)? (PR#10454)
René,
On Nov 23, 2007, at 6:00 AM, [EMAIL PROTECTED] wrote:
> It seems the recent Mac OS X 10.4.11 update installed a new
> libBLAS.dylib in the Accelerate framework which either contains a
> bug itself or exposes a bug somewhere in R's lapack code on the
> PowerPC G4 and G5.
> My build of R 2.6.0 executed the tests/lapack.R code succesfully
> when I upgraded when 2.6.0 was released. After the OS update, it
> now crashes. This happens both with the version I built using
> Apple's gcc 4.0.1 and gfortran 4.2.2, and with the version built
> completely with gcc 4.2.2 .
>
this is almost certainly a problem with the complex ABI (i.e. the
Fortran compiler and vecLib/ALTAS disagree). Normally R detects
complex ABI mismatch and either enables a work-around (vecLib) or
disables BLAS (others). If the ABI changed between versions, you'll
have to re-compile R. If the problem still persists after a re-
compile, please send me your config.log.
Cheers,
Simon
>> R
>
> R version 2.6.0 (2007-10-03)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> 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.
>
> ##> source("R-2.6.0/tests/lapack.R", echo=TRUE, verbose=TRUE)
> 'envir' chosen:
> encoding = "native.enc" chosen
> --> parsed 40 expressions; now eval(.)ing them:
>
> eval(expression_nr. 1 )
> =
>
> ##> ## tests of R functions based on the lapack module
> ##>
> ##> options(digits=4)
> curr.fun: symbol options
> .. after 'expression(options(digits=4))'
>
>
>
> ##> sm[] <- as.complex(sm)
> curr.fun: symbol <-
> .. after 'expression(sm[] <- as.complex(sm))'
>
> eval(expression_nr. 35 )
> =
>
> ##> Ceigenok(sm, eigen(sm))
>
> *** caught bus error ***
> address 0x1, cause 'invalid alignment'
>
> Traceback:
> 1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
> 2: eigen(sm)
> 3: apply(A, 2, function(x) x * sign(Re(x[1])))
> 4: fixsign(E$vectors)
> 5: print(fixsign(E$vectors))
> 6: Ceigenok(sm, eigen(sm))
> 7: eval.with.vis(expr, envir, enclos)
> 8: eval.with.vis(ei, envir)
> 9: source("~/cworks/new/R-2.6.0/tests/lapack.R", echo = TRUE,
> verbose = TRUE)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> *** OS X Crash report:
> Date/Time: 2007-11-23 11:19:19.135 +0100
> OS Version: 10.4.11 (Build 8S165)
> Report Version: 4
>
> Command: R
> Path:/Library/Frameworks/R.framework/Resources/bin/exec/R
> Parent: tcsh [2437]
>
> Version: ??? (???)
>
> PID:3167
> Thread: 0
>
> Exception: EXC_BAD_ACCESS (0x0001)
> Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x0001
>
> Thread 0 Crashed:
> 0 libBLAS.dylib 0x920fc374 atl_f77wrap_zdotc__ + 80
> 1 libBLAS.dylib 0x920f7864 zdotc_ + 60
> 2 libRlapack.dylib 0x013701a0 zhetd2_ + 960
> 3 libRlapack.dylib 0x0136fcdc zhetrd_ + 1900
> 4 libRlapack.dylib 0x01370ad8 zheev_ + 1016
> 5 lapack.so 0x010a4038 modLa_rs_cmplx + 392
> 6 libR.dylib0x003c99e8 La_rs_cmplx + 72
> 7 libR.dylib0x00372380 do_dotcall + 16864
> 8 libR.dylib0x003a170c Rf_eval + 1804
> 9 libR.dylib0x003a14dc Rf_eval + 1244
> 10 libR.dylib0x003a45f4 do_set + 980
> 11 libR.dylib0x003a14dc Rf_eval + 1244
> 12 libR.dylib0x003a2b08 do_begin + 104
> 13 libR.dylib0x003a14dc Rf_eval + 1244
> 14 libR.dylib0x003a14dc Rf_eval + 1244
> 15 libR.dylib0x003a2b08 do_begin + 104
> 16 libR.dylib0x003a14dc Rf_eval + 1244
> 17 libR.dylib0x003a14dc Rf_eval + 1244
> 18 libR.dylib0x003a2b08 do_begin + 104
> 19 libR.dylib0x003a14dc Rf_eval + 1244
> 20 libR.dylib0x003a4f58 Rf_applyClosure + 728
> 21 libR.dylib0x003a13f0 Rf_eval + 1008
> 22 libR.dylib0x003a62c8 forcePromise + 184
> 23 libR.dylib0x003a12c8 Rf_eval + 712
> 24 libR.dylib0x003a1650 Rf_eval + 1616
> 25 libR.dylib0x003a2714 Rf_DispatchOrEval + 244
> 26 libR.dylib0x0049d190 do_subset3 + 384
> 27 libR.dylib0x003a14dc Rf_eval + 1244
> 28 libR.dylib0x003a62c8 forcePromise + 184
> 29 libR.dylib0x003a12c8 Rf_eval + 712
> 30 libR.dylib0x003a1650 Rf_eval + 1616
> 31 libR.dylib0x003a62c8 forcePromise + 184
> 32 libR.dylib0x003a12c8 Rf_eval + 712
> 33 libR.dylib0x003a1650 Rf_eval + 1616
> 34 libR.dylib
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.
__
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Re: [Rd] package gsl assumes incorrect gcc version during install (PR#10451)
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
[Rd] Bug in pacf -- Proposed patch
Dear all, following the thread http://tolstoy.newcastle.edu.au/R/e2/devel/07/09/4338.html regarding the bug in the partial autocorrelation function for multivariate time series. I have prepared a web page with patches and relevant information. http://www2.stat.unibo.it/giannerini/R/pacf.htm Please do not hesitate to contact me for further clarifications regards Simone -- __ Simone Giannerini Dipartimento di Scienze Statistiche "Paolo Fortunati" Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098262 Fax: +39 051 232153 http://www2.stat.unibo.it/giannerini/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] package gsl assumes incorrect gcc version during install (PR#10451)
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
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.
> 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)
>
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[Rd] bug in getGraphicsEvent (PR#10453)
Full_Name: Seth Roberts
Version: 2.6.0
OS: Windows XP
Submission from: (NULL) (71.139.162.236)
Using getGraphicsEvent produces stack imbalance warnings. This started after I
installed 2.6.0; it did not happen with 2.5.1.
Running the example given in the user manual (retrieved via ?getGraphicsEvent)
produces the following errors:
Key <2>
Key <1>
Buttons 0 at 0.991317 0.9942029
Warning: stack imbalance in 'getGraphicsEvent', 7 then 17
Warning: stack imbalance in '.Internal', 6 then 16
[1] "Done"
I wrote the following program:
function ()
{plot(1:5)
getGraphicsEvent(onKeybd=get.key)
}
get.key
function(key){key}
running the program, switching to the graphics window and typing "4" produced:
Waiting for input
Warning: stack imbalance in 'getGraphicsEvent', 13 then 14
Warning: stack imbalance in '.Internal', 12 then 13
Warning: stack imbalance in '{', 6 then 7
[1] "4"
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[Rd] MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)? (PR#10454)
Hello,
It seems the recent Mac OS X 10.4.11 update installed a new
libBLAS.dylib in the Accelerate framework which either contains a bug
itself or exposes a bug somewhere in R's lapack code on the PowerPC G4
and G5.
My build of R 2.6.0 executed the tests/lapack.R code succesfully when
I upgraded when 2.6.0 was released. After the OS update, it now
crashes. This happens both with the version I built using Apple's gcc
4.0.1 and gfortran 4.2.2, and with the version built completely with
gcc 4.2.2 .
> R
R version 2.6.0 (2007-10-03)
Copyright (C) 2007 The R Foundation for Statistical Computing
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.
##> source("R-2.6.0/tests/lapack.R", echo=TRUE, verbose=TRUE)
'envir' chosen:
encoding = "native.enc" chosen
--> parsed 40 expressions; now eval(.)ing them:
eval(expression_nr. 1 )
=
##> ## tests of R functions based on the lapack module
##>
##> options(digits=4)
curr.fun: symbol options
.. after 'expression(options(digits=4))'
##> sm[] <- as.complex(sm)
curr.fun: symbol <-
.. after 'expression(sm[] <- as.complex(sm))'
eval(expression_nr. 35 )
=
##> Ceigenok(sm, eigen(sm))
*** caught bus error ***
address 0x1, cause 'invalid alignment'
Traceback:
1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
2: eigen(sm)
3: apply(A, 2, function(x) x * sign(Re(x[1])))
4: fixsign(E$vectors)
5: print(fixsign(E$vectors))
6: Ceigenok(sm, eigen(sm))
7: eval.with.vis(expr, envir, enclos)
8: eval.with.vis(ei, envir)
9: source("~/cworks/new/R-2.6.0/tests/lapack.R", echo = TRUE, verbose = TRUE)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
*** OS X Crash report:
Date/Time: 2007-11-23 11:19:19.135 +0100
OS Version: 10.4.11 (Build 8S165)
Report Version: 4
Command: R
Path:/Library/Frameworks/R.framework/Resources/bin/exec/R
Parent: tcsh [2437]
Version: ??? (???)
PID:3167
Thread: 0
Exception: EXC_BAD_ACCESS (0x0001)
Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x0001
Thread 0 Crashed:
0 libBLAS.dylib 0x920fc374 atl_f77wrap_zdotc__ + 80
1 libBLAS.dylib 0x920f7864 zdotc_ + 60
2 libRlapack.dylib0x013701a0 zhetd2_ + 960
3 libRlapack.dylib0x0136fcdc zhetrd_ + 1900
4 libRlapack.dylib0x01370ad8 zheev_ + 1016
5 lapack.so 0x010a4038 modLa_rs_cmplx + 392
6 libR.dylib 0x003c99e8 La_rs_cmplx + 72
7 libR.dylib 0x00372380 do_dotcall + 16864
8 libR.dylib 0x003a170c Rf_eval + 1804
9 libR.dylib 0x003a14dc Rf_eval + 1244
10 libR.dylib 0x003a45f4 do_set + 980
11 libR.dylib 0x003a14dc Rf_eval + 1244
12 libR.dylib 0x003a2b08 do_begin + 104
13 libR.dylib 0x003a14dc Rf_eval + 1244
14 libR.dylib 0x003a14dc Rf_eval + 1244
15 libR.dylib 0x003a2b08 do_begin + 104
16 libR.dylib 0x003a14dc Rf_eval + 1244
17 libR.dylib 0x003a14dc Rf_eval + 1244
18 libR.dylib 0x003a2b08 do_begin + 104
19 libR.dylib 0x003a14dc Rf_eval + 1244
20 libR.dylib 0x003a4f58 Rf_applyClosure + 728
21 libR.dylib 0x003a13f0 Rf_eval + 1008
22 libR.dylib 0x003a62c8 forcePromise + 184
23 libR.dylib 0x003a12c8 Rf_eval + 712
24 libR.dylib 0x003a1650 Rf_eval + 1616
25 libR.dylib 0x003a2714 Rf_DispatchOrEval + 244
26 libR.dylib 0x0049d190 do_subset3 + 384
27 libR.dylib 0x003a14dc Rf_eval + 1244
28 libR.dylib 0x003a62c8 forcePromise + 184
29 libR.dylib 0x003a12c8 Rf_eval + 712
30 libR.dylib 0x003a1650 Rf_eval + 1616
31 libR.dylib 0x003a62c8 forcePromise + 184
32 libR.dylib 0x003a12c8 Rf_eval + 712
33 libR.dylib 0x003a1650 Rf_eval + 1616
34 libR.dylib 0x003a2488 Rf_evalList + 168
35 libR.dylib 0x003a15a8 Rf_eval + 1448
36 libR.dylib 0x003a45f4 do_set + 980
37 libR.dylib 0x003a14dc Rf_eval + 1244
38 libR.dylib 0x003a2b08 do_begin + 104
39 libR.dylib 0x003a14dc Rf_eval + 1244
40 libR.dylib 0x003a4f58 Rf_applyClosure + 728
41 libR.dylib 0x003a13f0 Rf_eval + 1008
42 libR.dylib 0x003a3cdc applydefine + 60
43 libR.dylib 0x003a14dc Rf_eval + 1244
44 libR.dylib 0x003a2b08 do_begin + 104
45 libR.dylib 0x003a14dc Rf_eval + 1244
46 libR.dylib 0x003a4f5
[Rd] Bug in pacf -- Proposed patch (PR#10455)
Dear all, following the thread http://tolstoy.newcastle.edu.au/R/e2/devel/07/09/4338.html regarding the bug in the partial autocorrelation function for multivariate time series. I have prepared a web page with patches and relevant information. http://www2.stat.unibo.it/giannerini/R/pacf.htm Please do not hesitate to contact me for further clarifications regards Simone -- __ Simone Giannerini Dipartimento di Scienze Statistiche "Paolo Fortunati" Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098262 Fax: +39 051 232153 http://www2.stat.unibo.it/giannerini/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Bug in package stats function ar() (PR#10459)
Full_Name: Steven McKinney Version: 2.6.0 OS: OS X Submission from: (NULL) (142.103.207.10) Function ar() in package "stats" is showing a quirky bug. Some calls to ar() run to completion, others throw an error. The bug is reproducible by several people on different machines, however, the ar() function itself ends up throwing the error sporadically. Several calls to ar() may be necessary to trip the error condition. Code to reproduce: x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1980,3)) # ar function res.ar<-ar(x,aic=TRUE,demean=F) # call "ar" again and res.ar<-ar(x,aic=TRUE,demean=F) Example output: (Note that on this attempt the first call to ar() tripped the error.) > x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,- + 1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1980,3)) > > # ar function > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In log(var.pred) : NaNs produced 2: In if (order > 0) coefs[order, 1:order] else numeric(0) : the condition has length > 1 and only the first element will be used > > # call "ar" again and > res.ar<-ar(x,aic=TRUE,demean=F) > x Qtr1 Qtr2 Qtr3 Qtr4 1978 -0.2052083 -0.3764986 1979 -0.3762448 0.3740089 0.2737568 2.8235722 1980 -1.7783313 0.2728676 -0.3273164 > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar$resid Qtr1 Qtr2 Qtr3 Qtr4 1978 -0.2052083 -0.3764986 1979 -0.3762448 0.3740089 0.2737568 2.8235722 1980 -1.7783313 0.2728676 -0.3273164 > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar$resid Qtr1 Qtr2 Qtr3 Qtr4 1978 -0.2052083 -0.3764986 1979 -0.3762448 0.3740089 0.2737568 2.8235722 1980 -1.7783313 0.2728676 -0.3273164 > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning message: In if (order > 0) coefs[order, 1:order] else numeric(0) : the condition has length > 1 and only the first element will be used > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In log(var.pred) : NaNs produced 2: In if (order > 0) coefs[order, 1:order] else numeric(0) : the condition has length > 1 and only the first element will be used > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > sessionInfo() R version 2.6.0 (2007-10-03) powerpc-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base > ###- Also seen in R 2.5.0: > x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1980,3)) > # ar function > res.ar<-ar(x,aic=TRUE,demean=F) > # call "ar" again and > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) > res.ar<-ar(x,aic=TRUE,demean=F) Error in if (order > 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning message: the condition has length > 1 and only the first element will be used in: if (order > 0) coefs[order, 1:order] else numeric(0) > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_P APER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" > ###- However, if I lengthen the input vector x<-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164, -0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313,0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1982,3)) I can not trip the error, so perhaps it is due to the short length of the user's input data. ###- Nov 23, 2007 original email from R-help [R] help please Dears Sirs During my computational work
